Dissertation article Essay Example | Topics and Well Written Essays - 750 words

Dissertation article - Essay Example Quality: The topic chosen in the paper is quite interesting. Studying security threats has always interested to the masses especially after the internet boom in the early 1990s. Protection of personal valuable data is one of the majors reasons for the developing interest in cyber security. Regarding research into earlier work the paper hasn’t identified a lot of previous works by different researchers especially considering the fact that there is so much literature present regarding computer security, vulnerability and cyber threats (Lowe & Byres, 2004). However the lack of literature can be explained due to the fact that VoIP has only recently gained popularity. In order to obtain maximum information regarding the threats the authors of the paper have conducted vast researches using various books and secondary sources. The paper also uses various case studies of companies that provide security to organizations and personal users using VoIP. The facts stated in the paper are c orrect and provide an excellent detail of all the threats that is faced by every organization and user making use of VoIP technology. The authors have also been able to identify and discussed all measures that can be taken against these threats. For future studies the authors of the paper have summarized required efforts into two categories. The first factor that the authors recommend is focusing on the improving the security structure of VoIP services. The second factor that the author points out is the need to set proper standards regarding the security of VoIP systems. Structure of the paper: The paper was very well structured in terms of headings. The paper started with the abstract where the author explains briefly the purpose of the paper and an overview of what VoIP is. The next section covers the introduction of VoIP technology in detail and provides details of its working. The main body of the article has been divided into two sections. The first section provides a brief in troduction of what security is and why is it important to VoIP. After introduction to security the first section then deals with discussing what the potential threats there are to the VoIP system. The second section then deals with recommendations made by the authors on how to prevent these attacks. The third section of the paper states the conclusion drawn by the authors from their research paper. Conclusion is one of the most vital parts of the research paper. The conclusion sums up all the work of the paper and sheds a light on whether or not the research question was answered (Wallwork, 2011). The last part of the paper covers the reference list and works cited by authors. The paper was written in simple English and could easily be understood by various readers who have slight knowledge regarding the field of computer science. The flow of the paper was also quite nice different parts of the paper were related to each other. As for the length of the paper the paper was of ten pag es which is regarded by many as the average length of research papers (Bing, 1988). Conclusion: The analysis of the paper brought three main factors about the paper into light. For the first factor is that is compared to the literature available on the subject, the authors have not provided enough support to their claims in the paper. Adding more references in a paper increases the credibility of

My Life had stood - a Loaded Gun Essay Example for Free

My Life had stood a Loaded Gun Essay Emily Dickinson’s â€Å"My Life had stood a Loaded Gun† is a powerful poem that takes into account various thematic expressions. Its comprehensiveness in brevity is another essential feature of this poem. It symbolizes power and unconventional feminist urges on the art of the poetess. In this poem, Emily Dickinson finds an instrument adequate enough to render her need for fulfillment through absolute commitment to love’s service. The poem begins with a brilliant conceit. Fused from the ambiguous abstraction of life and the explicit concretion of loaded gun, it expresses the charged potential of the human being who remains dormant until â€Å"identified† into a conscious vitality. And after hat identification, we observe the start of a new poem i. e. the start of a new life. Historically, it was written in age when American society was torn with civil war. The symbol that Emily Dickenson has used is an essence of an experience. It is quite obvious that a universal insight that the poet tries to express in not obtained merely by imaginative wandering, it is based on concrete experiences. Emily Dickinson presents the same insight into the historical experiences of her time. The very first stanza symbolizes the paradox of finding oneself through losing oneself. It is rendered in the poem by one word: identity is claimed when someone claimed the gun as her own. The American civil war was also the process of finding ones own identity by losing ones own identity. The internal rivalries and petty identities were to be removed to achieve a national reconciliation. This national reconciliation ultimately brought the national identity. Although this process was on halt and stayed â€Å"in corners† for many decades till a day came. Now they â€Å"roam in Sovereign Woods†. So Emily Dickinson has epitomized a national experience. Now this â€Å"gun† is â€Å"foe of His Im deadly foe†. â€Å"His can be described in various connotations. â€Å"His† is emblem of nation state that is fully sovereign. â€Å"His† is an integrated society or the one who longs to be integrated after the pathos and miseries of Civil war. Poetess further emphasize that â€Å"None stir the second time -/ whom I lay a Yellow Eye -/ an emphatic Thumb†. All these gestures are for those who are internal or external antagonists to the new national experience. This poem has also captivated the feminist attention who has given it a new evaluative dimension. Some critics are of the view that thorough this poem, Emily has tried to present a woman that she was not primarily in the second half of the 19th century whereas other feminist critics holds the view that poem totally negates the feminine qualities and the main metaphor considers â€Å"everything [that]woman is not: cruel not pleasant, hard not soft, emphatic not weak, one who kills not one who nurtures. † (Bennet, 1986) But Emily Dickinson has provided a framework of power i. e. feminine power and established certain pattern on which women power can grow and has shown certain direction where women power can direct itself. It must be kept in mind that all the action verbs in the poem are not destructive or of insidious nature. It expresses powers to hunt speak† smile guard and kill. So this power has paradoxical nature and a balance mix of these powers is necessary as shown and done by Emily Dickinson. Furthermore, Miss Dickinson does show a longing for deadliness but in actuality it is only for safeguarding. Wrath is a part of her being but she does not let it go if not invoked or incited. So her aggression and anger and the consequences as a result of it (killing and deaths) are not unwomanly but are an extension of her very personality. These feelings are not uncommon but are surely unpredictable. In the second half of the poem, she is only providing guard to one who has helped her to get rid of her alienation and had blessed her with intimacy. Here Emily Dickinson seems conventional in her feminist approach that a woman can do everything unwomanly for the one who is her companion in true sense of the word. Christine Miller (1987) says in this regard that â€Å"In the second instance, the speaker prefers guarding the master to having shared his pillow, that is, to having shared intimacy with himprimarily sexual, one would guess from the general structure of the poem. † On the other hand, this poem expresses the agonies of a female poet that was restricted by her family and society to a narrow life devoid of any intellectual and/or literary independence. These social and familial compulsion produced rashness in Emily’s attitude. She was forced to produce art in seclusion and to it keep to herself only. So language becomes her only mean and tool to bear the torments of her intellectual beings. She embodies language as gun and is of the view that this loaded gun accompanied with her literary beings is fatal for socio-cultural compulsion against women. It provided her a sense of power and control. She further eulogizes language and considers it a safeguard to her literary being. And her language is enemy to al those traditions, norms, people and things who are against her poetical endeavors. This poem can further illustrate the conflicts between two classes with their interest. Although this conflict is not materialistic or monetary but it exists in the socio-cultural domain. One class adheres to the conventions and does not allow female members to express their view on any issue especially in the form of poetry whereas other lass are comprised of the intellectual beings who consider it their right to create and disseminate their thoughts and ideas in the literary form. This poem symbolizes the struggle of the latter class and demonstrates that they are more powerful than the convention-ridden society. The poem starts with an individual quest for his/her identity but it changed into a capitalized â€Å"We†. Now the concern of the poetess is no more individualistic and sentimental, rather it has been transformed into something collective, societal and concrete. The identities have been mingled up with each other. Both owner and the â€Å"owned† perform the same masculine activities. They are no more individual but become a part of the larger whole i. e. society. Overall the poem captures a variety of themes through various thematic expressions. Although the conclusion is disturbing but it has relevance to the thematic expressions as it tries to resolve the problem initiated in the first half. Powerlessness or even fear of that is death to the poetess has no other option but â€Å"to die† without powerlessness. Last stanza is not a moralistic commentary but is identification of a wider truth. Bennett, Paula. My Life a Loaded Gun: Dickinson, Plath, Rich, and Female Creativity. Boston: Beacon Press. 1986. Gilbert, Sandra M Gubar, Susan. The madwoman in the attic: the woman writer and the nineteenth-century literary imagination. New Haven: Yale University Press. 1979. Miller, Christanne. Emily Dickinson, a poets grammar. Cambridge, Mass. : Harvard University Press. 1987. Smith, Martha Nell Loeffelholz, Mary. A companion to Emily Dickinson. Malden, MA: Blackwell Pubishers. 2008.

Diabetes Essay -- essays research papers

There are two types of diabetes: diabetes insipidus and diabetes mellitus. Diabetes insipidus is a rare metabolic disorder caused by a deficiency of the pituitary hormone, which is usually the result of damage to the pituitary gland. Diabetes insipidus is characterized by enormous amounts of urine that are produced by the body regardless of how much liquid is consumed. Diabetes mellitus results from the production of insufficient amounts of insulin by the pancreas. Without insulin the body cannot utilize glucose, thus creating a high level of glucose in the blood and a low level of glucose absorption by the tissues. Diabetes mellitus is generally divided into two categories: type I called insulin-dependent or juvenile diabetes and type II in which the onset of the diabetes occurs during adulthood. The symptoms of the type I diabetic include irritability, frequent urination, abnormal thirst, nausea or vomiting, weakness, fatigue, and unusual hunger. This type of diabetes occurs mostly in children or young adults. The type I diabetic may have an insulin reaction in an instant, seeming perfectly normal one second and becoming unconscious the next. The early warning signs of this type of reaction are hunger, dizziness, sweating, confusion, palpitation, and numbness or tingling of the lips. If left untreated, the insulin-dependent diabetic may also experience double vision, trembling, and disorientation, may perform strange actions, and may eventually lose consciousness. While experiencing any one of these symptoms, quick consumption of a piece of candy, some soda pop, or anything else that contains sugar will bring blood sugar levels back to normal.Recovery is more difficult for the diabetic whose insulin reaction is left untreated for a long period of time. An insulin reaction producing low blood sugar can be life threatening. Therefore, it is safer to "spill" small amounts of urine sugar when taking insulin.The second type of diabetes, often referred to as maturity-onset diabetes, is likely to occur in those with a family history of diabetes and is characterized by blurred vision, itching, unusual thirst, drowsiness, obesity, fatigue, skin infections, slow healing, and tingling or numbness in the feet. Onset of symptoms is usually later in life.Diet often controls this type and insulin is not usually required. Obesity is a major factor in type I... ...esults in an elevation of blood sugar. It is important to get protein from a vegetable source. CONSIDERATIONSDo not take large doses of cysteine. It has the ability to break down the bonds of the hormone insulin. Be careful not to take extremely large doses of vitamins B1 and C. Excessive amounts may inactivate insulin. They may, however, be taken in normal amounts. Type II diabetics should avoid large amounts of niacin, but niacinamide for type I diabetics slows down destruction of beta cells in the pancreas and enhances their regeneration, extending the remission time. The statements and products in this article have not been evaluated by the Food and Drug Administration, and are not intended to diagnose, treat, cure or prevent disease.ADDITIONAL SOURCES OF INFORMATIONFor more information on diabetes, contact the following organizations:<font size="1">American Diabetes Association1660 Duke StreetAlexandria, VA 22314(703) 549-1500International Diabetes Center5000 W. 39th StreetMinneapolis, MI 55416(612) 927-3393Joslin Diabetes FoundationOne Joslin PlaceBoston, MA 02215617) 732-2415Juvenile Diabetes Foundation60 Madison AvenueNew York, NY 10010-1550(212) 889-7575

Older Than America Essay

1. Film Information: The title of film we watched this week is Older than America. The lead actors and actresses are Adam Beach, Tantoo Cardinal, Bradley Cooper Georgina Lightning, Bradley Cooper, and Tantoo Cardinal. movie was released Oct 12, 2010 by the IFC Films studio. The length of the film is about one hundred minutes. The film genre is trying to expose the history with horror atmosphere. The director of the film is Georgina Lightning . 2. Brief summary: A woman’s haunting visions reveal a Catholic priest’s sinister plot to silence Rain’s mother from speaking the truth about the atrocities that took place at her Native American boarding school. The story along with her daughter, Rain haunted by visions that led to her own mother’s forced institutionalization. The film mixes the true story of the US’s forced boarding of Native American children, subjecting them to a wide variety of abuses. The film is not that easy to follow up because it started with some suspension and wired dreams at the beginning. As the story goes along, more and more clues reveal. It is hard to believe what the boarding school did to Native American kids based on my perception to boarding school. The film has enough twists and turns to keep my attentions while watching it. 3. Identify the main problem(s) or issue(s) addressed in the film: The problem is mainly addressed in boarding school. They remove children from the influence of their families and culture and assimilate them into the dominant Canadian culture. Father Bartoli paralyzed Rain’s mother in order to hide the truth about atrocities in boarding school. The Native American kids were beaten, whipped, raped and killed in the school. Later on, Father Bartoli also tried to convince Auntie Apple to keep Rain in captivity in order to stop memorizing the truth from the past. Rain was somehow rescued from tying up her hands by a spiritual guy who is her classmate in boarding school. She intellectually escaped from the room when the cleaner opened the door. Rain and Jonny decided to discover the truth in the mysterious cellar. After Father Bartoli knew Rain had escaped, he decided to go to cellar to kill her. Finally, Rain collected all the clues and memorized all the things happened in boarding school. Father Batoli was tangled up with all the lost soul who were abused and died under his hands. He got punished. 4. Main characters review: The main characters are Jonny, Rain, Luke, and Father Batoli. Director and co-writer Lightning also plays Rain, the lead role in Older Than America. Rain lives with her police officer boyfriend Johnny (Adam Beach) in snowy, rural Minnesota. Adom Beach plays her boyfriend. Luke (Bradley Cooper) is a government geologist investigating reports of a recent earthquake on his own time; Steve Klamath (Glen Gould) has returned home to run for mayor on an anti-development platform, opposing the incumbent, developer Paul Gunderson (Chris Mulkey). I think the actors are good in these roles especially Johnny because I can feel his love to Rain. They play believable roles, but I was confused about those spiritual figures. They are not quite believable, though. Those children in the board school make me sympathetic. There is no â€Å"Hollywood stereotypes†. 5. Portrayal of authority: Father Bartoli is a typical guy who has authority in religious figures. He is a priest minister who controls all the regulations in boarding school. Auntie Apple (Tantoo Cardinal), who raised Rain, leans heavily upon local Catholic priest Father Bartoli (Steve Yoakum). The two of them shake their heads disapprovingly when Rain and Johnny do not immediately agree to having a Catholic marriage ceremony. The boarding school is a nightmare to Native American children. Priests tried to remove their identity and assimilated them into American culture. I dislike Father Bartoli. He did not only a lot of bad things to the Native American children but also silenced Rain and her mother to erase the past crimes. 6. Discuss the role of gender in the film: The major players are not predominantly of one sex. Johnny has the subordinate role. I think Women and men are not drawn as variations of stereotypes. Rain plays a kindergarten teacher. She is portrayed as a perceptual and strong Native American woman. She cares about her mother very much. The matriarchal female roles are not recognized in the film. Jonny is her husband. He loves Rain very much, too. He cares about everything regarding Rain including family. He behaved anxious and crazy when Rain is disappeared. 7. Discuss the role of class and nation: I did not see any characters do anything for living. Jonny works in police office and Rain works in kindergarten. They seem pretty knowledgeable about their work, and they valued for what they do. There is no very obvious class hierarchy in the film. They are all kind of middle class people in modern society. The film did not spend a lot of attention to portray the poor. 8. Discuss the identity of the Native/tribal/ethnic groups portrayed in the film: I did not really often hear the Native American characters mention something about their identity, but I can feel the sense of strong ethnic tie between real physical characters and those spiritual characters. The souls are the things make this film so special to us. Those souls imply some sort of spiritual culture to Native American. Although they are already died, they still got together and help their companions or ethic group to get through the obstacles. They are likely to be seen in Native Americans’ perspective. The relationship between them is really subtle but meaningful. The live characters try to expose the truth hidden in the boarding school whereas the spiritual characters keep helping them get through the crises. They somehow interact with each other and make the whole story looks reasonable. It is pretty interesting and makes audience want to watch it. The movie really empathizes with the identity issues although the ethnic characters are not actually from the portrayed ethnic group because basically the film tells the repulsive atrocities and assimilation behind the boarding school back 1900s. It wants to remind Native American audiences to recognize the history and do not lose the cultural identity no matter what. 9. How are social and familial relationships portrayed: Throughout the film, Native Americans always have a strong family tie and hold together. In the film, I can feel Rain really loves his mother. She takes care of her a lot even she has got some mental issues. She is also really respecting her mother because she comes to her mother and tells her mother every decision she is going to make. In modern days, she still inherits a lot of traditional Native American woman’s traits. Those spiritual figures also give us a strong background of ethnic sense. They have a connection with Rain to keep reminding her past, and they help her to find the clues of the truth and get her through crisis. Jonny is a good and reliable boyfriend, too. He also really loves Rain. He is sharing of confidences with her and giving care to her when Rain faced up difficulties. I am able to relate to the familial roles and experiences in the film because film makes it really touch my heart. 10. Language: There are few scenes that other language other than English spoken in the film. It is used effectively. The boy spoke Native American language when the teacher forced them to declare to be Americans in the classroom. He did not want to lose his own culture identity. The use of another language bears a lot value to the film. It exposed the atrocities in boarding school. You would be beaten to death even if you say an Indian word. It set off the inhuman behaviors they did to every Native American child in boarding school. It is ironic that person who actually behaves a savage wants to civilize Native Americans, they called â€Å"savage†. 11. Personal likes and dislikes: This movie really is not a view of life in boarding schools, per se. I don’t believe it was intended to be. It is a metaphor for the effects still felt today by nearly all Native Americans here in the U. S. The movie â€Å"is† a period place. All of the issues that the story touches base on are those that Natives all over Indian Country are dealing with today. It is not the direct reflection of one single reason why Natives today face the afflictions of poverty, alcoholism, abuse, unemployment, illiteracy, and loss of identity as a culture, but the culmination of many. Forced attendance into an institution specifically designed to strip away everything it means to be â€Å"Indian† just so happens to be the primary area of focus in this film. The sub-plots add depth to the characters as well as much needed comic relief. Even though this film is classified as a drama, it should be shown in every history class across the United States. 12. Research connection: The story of American Indian boarding schools needs to be told. In the past Indian children were taken from their parents, often forcibly, and put into highly- regimented schools designed to eradicate all signs of their â€Å"savagery. † Use of Indian languages in these schools was forbidden and harshly punished. This movie probably should have been a â€Å"period place† showing the experiences of an Indian child thrust into the soul-killing world of the boarding school. Perhaps it was feared this approach would limit the size of the audience. In any case we get a modern-day story, set in northern Minnesota, in which a boarding school is glimpsed only occasionally in brief flashbacks. Surrounding these flashbacks lie a plot cluttered with a bewildering number of elements: the arrogance of the Catholic Church, shock treatments, commercial development of sacred Indian lands, an election for mayor pitting a white man against a red man, gambling casinos, a love story, hallucinations and visions, family secrets leading to tensions.

Phylogenetic

Molecular Phylogenetics An introduction to computational methods and tools for analyzing evolutionary relationships Karen Dowell Math 500 Fall 2008 Molecular Phylogenetics Karen Dowell 1 Abstract Molecular phylogenetics applies a combination of molecular and statistical techniques to infer evolutionary relationships among organisms or genes.This review paper provides a general introduction to phylogenetics and phylogenetic trees, describes some of the most common computational methods used to infer phylogenetic information from molecular data, and provides an overview of some of the many different online tools available for phylogenetic analysis. In addition, several phylogenetic case studies are summarized to illustrate how researchers in different biological disciplines are applying molecular phylogenetics in their work. Introduction to Molecular PhylogeneticsThe similarity of biological functions and molecular mechanisms in living organisms strongly suggests that species descended from a common ancestor. Molecular phylogenetics uses the structure and function of molecules and how they change over time to infer these evolutionary relationships. This branch of study emerged in the early 20th century but didn’t begin in earnest until the 1960s, with the advent of protein sequencing, PCR, electrophoresis, and other molecular biology techniques.Over the past 30 years, as computers have become more powerful and more generally accessible, and computer algorithms more sophisticated, researchers have been able to tackle the immensely complicated stochastic and probabilistic problems that define evolution at the molecular level more effectively. Within past decade, this field has been further reenergized and redefined as whole genome sequencing for complex organisms has become faster and less expensive. As mounds of genomic data becomes publically available, molecular phylogenetics is continuing to grow and find new applications. 4, 10, 17, 20, 22] The primary objective of molecular phylogenetic studies is to recover the order of evolutionary events and represent them in evolutionary trees that graphically depict relationships among species or genes over time. This is an extremely complex process, further complicated by the fact that there is no one right way to approach all phylogenetic problems. Phylogenetic data sets can consist of hundreds of different species, each of which may have varying mutation rates and patterns that influence evolutionary change.Consequently, there are numerous different evolutionary models and stochastic methods available. The optimal methods for a phylogenetic analysis depend on the nature of the study and data used. [5, 19, 20] Molecular Evolution: Beyond Darwin Evolution is a process by which the traits of a population change from one generation to another. In On the Origin of Species by Means of Natural Selection, Darwin proposed that, given overwhelming evidence from his extensive comparative analysis of living specimens and fossils, all living organisms descended from a common ancestor.The book’s only illustration (see Figure 1) is a tree-like structure that suggests how slow and successive modifications could lead to the extreme variations seen in species today. [11, 27] Molecular Phylogenetics Karen Dowell 2 Figure 1. Evolution Defined Graphically. The sole illustration in Darwin’s Origin of the Species uses a tree-like structure to describe evolution. This drawing shows ancestors at the limbs and branches of the tree, more recent ancestors at its twigs, and contemporary organisms at its buds. [34] Darwin’s theory of evolution is based on three underlying principles: ariation in traits exist among individuals within a population, these variations can be passed from one generation to the next via inheritance, and that some forms of inherited traits provide individuals a higher chance of survival and reproduction than others. [11] Although Darwin developed his theory of evolution without any knowledge of the molecular basis of life, it has since been determined that evolution is actually a molecular process based on genetic information, encoded in DNA, RNA, and proteins. At a molecular level, evolution is driven by the same types of mechanisms Darwin observed at the species level.One molecule undergoes diversification into many variations. One or more of those variants can be selected to be reproduced or amplified throughout a population over many generations. Such variations at the molecular level can be caused by mutations, such as deletions, insertions, inversions, or substitutions at the nucleotide level, which in turn affect protein structure and biological function. [11, 22] What is a Phylogeny? According to modern evolutionary theory, all organisms on earth have descended from a common ancestor, which means that any set of species, extant or extinct, is related.This relationship is called a phylogeny, and is represented by phyloge netic trees, which graphically represent the evolutionary history related to the species of interest (see Figure 2). Phylogenetics infers trees from observations about existing organisms using morphological, physiological, and molecular characteristics. Figure 2. Phylogeny of Mammalia. This phylogenetic tree shows the evolutionary relationships among six orders of Mammalian species (taxa). Taxa listed in grey are extinct. The â€Å"tree of life† represents a phylogeny of all organisms, living and extinct.Other, more specialized species and molecular phylogenies are used to support comparative studies, test biogeographic hypotheses, evaluate mode and timing of speciation, infer amino acid sequence of extinct proteins, track the evolution of diseases, and even provide evidence in criminal cases. [19] Molecular Phylogenetics Karen Dowell 3 Understanding Phylogenetic Trees Before exploring statistical and bioinformatic methods for estimating phylogenetic trees from molecular data , it’s important to have a basic familiarity of the terms and elements common to these types of trees. See Figure 3. ) Figure 3. Basic elements of a phylogenetic tree. Phylogenetic trees are composed of branches, also known as edges, that connect and terminate at nodes. Branches and nodes can be internal or external (terminal). The terminal nodes at the tips of trees represent operational taxonomic units (OTUs). OTUs correspond to the molecular sequences or taxa (species) from which the tree was inferred. Internal nodes represent the last common ancestor (LCA) to all nodes that arise from that point.Trees can be made of a single gene from many taxa (a species tree) or multi-gene families (gene trees). [1, 10] A tree is considered to be â€Å"rooted† if there is a particular node or outgroup (an external point of reference) from which all OTUs in the tree arises. The root is the oldest point in the tree and the common ancestor of all taxa in the analysis. In the absence of a known outgroup, the root can be placed in the middle of the tree or a rootless tree may be generated. Branches of a tree can be grouped together in different ways. (See Figure 4. ) Figure 4.Groups and associations of taxonomical units in trees. A monophyletic group consists of an internal LCA node and all OTUs arising from it. All members within the group are derived from a common ancestor and have inherited a set of unique common traits. A paraphyletic group excludes some of its descendents (for examples all mammals, except the marsupialia Molecular Phylogenetics Karen Dowell 4 taxa). And a polyphyletic group can be a collection of distantly related OTUs that are associated by a similar characteristic or phenotype, but are not directly descended from a common ancestor. 1, 17] Trees and Homology Evolution is shaped by homology, which refers to any similarity due to common ancestry. Similarly, phylogenetic trees are defined by homologous relationships. Paralogs are homologous s equences separated by a gene duplication event. Orthologs are homologous sequences separated by a speciation event (when one species diverges into two). Homologs can be either paralogs or orthologs. [1, 11, 22] Molecular phylogenetic trees are drawn so that branch length corresponds to amount of evolution (the percent difference in molecular sequences) between nodes. 1, 19] Figure 5. Understanding paralogs and orthologs. Paralogs are created by gene duplication events. (See Figure 5. ) Once a gene has been duplicated, all subsequent species in the phylogeny will inherit both copies of the gene, creating orthologs. Interestingly, evolutionary divergence of different species may result in many variations of a protein, all with similar structures and functions, but with very different amino acid sequences. Phylogenetic studies can trace the origin of such proteins to an ancestral protein family or gene. [1, 22] Figure 6. Mirror Phylogenies.Gene A and Gene A1 are paralogs, whereas all i nstances of Gene A are orthologs of each other in different Canid species. One way to ensure that paralogs and orthologs are appropriately referenced in a phylogenetic tree, and guard against misrepresentation due to missing or incomplete taxonomic information is to generate mirror phylogenies (see Figure 6) in which paralogs serve as each other’s outgroup. [1, 4, 19, 22] Estimating Molecular Phylogenetic Trees Molecular phylogenetic trees are generated from character datasets that provides evolutionary content and context.Character data may consist of biomolecular sequence alignments of DNA, RNA, or amino acids, molecular markers, such as single nucleotide polymorphisms (SNPs) or restriction fragment length polymorphisms (RFLPs), morphology data, or information on gene order and content. Evolution is modeled as a process that changes the state of a character, such as the type of nucleotide (AGTC) at a Molecular Phylogenetics Karen Dowell 5 specific location in a DNA sequence ; each character is a function that maps a set of taxa to distinct states. 1, 19] Note that most of the examples in this paper use DNA sequences as character data, but trees can be accurately estimated from many different types of molecular data. Figure 7. Evolution of a DNA Sequence Figure 7 illustrates how a molecular sequence might evolve over time as a result of multiple mutations that results small, but evolutionarily important changes in a nucleotide sequence. At the protein level, these changes may not initially affect protein structure or function, but over time, they may eventually shape a new purpose for a protein within divergent species. 10, 19, 22] OTUs can be used to build an unrooted phylogenetic tree that clearly depicts a path of evolutionary change. Steps in Phylogenetic Analysis Although the nature and scope of phylogenetic studies may vary significantly and require different datasets and computational methods, the basic steps in any phylogenetic analysis remain t he same: assemble and align a dataset, build (estimate) phylogenetic trees from sequences using computational methods and stochastic models, and statistically test and assess the estimated trees. 4, 19, 20] Assemble and Align Datasets The first step is to identify a protein or DNA sequence of interest and assemble a dataset consisting of other related sequences. For example, to explore relationships among different members of the Notch family of proteins, one might select DNA sequences for Notch1 through Notch4, in different species, such as human, dog, rat, and mouse, then perform a multiple sequence alignment to identify homologies. [1, 10, 13, 19, 20] There are a number of free, online tools available to simplify and streamline this process. DNA sequences of interest can be retrieved using NCBI BLAST or similar search tools.When evaluating a set of related sequences retrieved in a BLAST search, pay close attention to the score and E-value. A high score indicates the subject seque nce retrieved with closely related to the sequence used to initiate the query. The smaller the E-value, the higher the probability that the homology reflects a true evolutionary relationship, as opposed to sequence similarity due to chance. As a general rule, sequences with E-values less than 10-5 are homologs of a query sequence. [10] Once sequences are selected and retrieved, multiple sequence alignment is created.This involves arranging a set of sequences in a matrix to identify regions of homology. Typically, gaps (one or more spaces in the alignment) are introduced in one or more sequences to represent insertions or deletions in the molecular code that may have occurred over time. Effective multiple sequence alignment hinged on gap analysis—determining where to insert gaps and how large to make them. There are many websites and software programs, such as ClustalW, MSA, MAFFT, and T-Coffee, designed to perform multiple sequence on a given set of molecular data. ClustalW i s currently the most mature and most widely used. 1, 10. 19] Molecular Phylogenetics Karen Dowell 6 Building Phylogenetic Trees To build phylogenetic trees, statistical methods are applied to determine the tree topology and calculate the branch lengths that best describe the phylogenetic relationships of the aligned sequences in a dataset. Many different methods for building trees exist and no single method performs well for all types of trees and datasets. The most common computational methods applied include distance-matrix methods, and discrete data methods, such as maximum parsimony and maximum likelihood. 4, 17, 20] There are several software packages, such as Paup*, PAML, PHYLIP, that apply most popular methods. [4] Paup* is a commercially available program that implements a wide variety of methods for phylogenetic inference, including maximum likelihood analysis for DNA data using different models. Paup* also includes a set of exact and heuristic methods for searching optimal trees. PAML (Phylogenetic Analysis by Maximum Likelihood) is open-access set of programs for phylogenetic analysis and evolutionary model comparison.PAML includes many advanced models—DNA- and AAbased models as well as codon-based models that can be used to detect positive selection. Many of the programs in PAML can model heterogeneity of evolutionary rates among sequence sites using ? distributions, and evolutionary dynamics of different sequence regions (concatenated gene sequences). PHYLIP is another large suite of open-access programs for phylogenetic inference that estimates trees using numerous methods, including pairwise distance, maximum parsimony, and maximum likelihood.The maximum likelihood programs can handle a few simple stochastic models and have good tree searching capabilities. PHYLIP is generally considered good educational software for novice phylogeneticists. Distance-Matrix Methods Distance matrix methods compute a matrix of pairwise â€Å"distances† between sequences that approximate evolutionary distance. Distance-based methods tend to be in polynomial time and are quite fast in practice. These methods use clustering techniques to compute evolutionary distances, such as the number of nucleotide or amino acid substitutions between sequences, for all pairs of taxa.They then construct phylogenetic trees using algorithms based on functional relationships among distance values. There are several different distance-matrix methods, including the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA), which uses a sequential clustering algorithm; the Transformed Distance Method, which uses an outgroup as a reference, then applies UPGMA; the Neighbor-Relations Method, which applies 4point condition to adjust the distance matrix, then applies UPGMA; and the Neighbor-Joining Method, which arranges OTUs in a star, the finds neighbors sequentially to minimize total length of tree. 4, 17] The following section on the UPGMA method prov ides a more detailed example of how distance-matrix methods work. UPGMA Method UPGMA produces rooted trees for which the edge lengths can be viewed as times measured by a molecular clock with a constant rate. This method uses a sequential clustering algorithm to identify two OTUs that are most similar (meaning they have the shortest evolutionary distance and are most similar in sequence) and treat them as a single new composite OTU. This process is repeated iteratively until only two OTUs remain.The algorithm defines the distance (d) between two clusters Ci and Cj as the average distance between pairs of sequences from each cluster: Molecular Phylogenetics Karen Dowell 7 Where |Ci| and |Cj| are the number of sequences in clusters i and j. This sequential clustering process is visually described in Figure 8. In this example, the two most homologous sequences are 1 and 2. They are clustered into a new composite parent node (6), and the branch lengths (t1 and t2) are defined as 1/2d1,2 . The next step is to search for the closest pair among remaining sequences and node 6.Pair 4 and 5 are identified and clustered into a new parent node (7), and the branch length for t4 and t5 is calculated. [4, 17] Figure 8. Sequential clustering of sequences using the UPGMA method. [17] In this interactive process, parent node 8 is created from pairs 7 and 3, and parent node 9 is created by clustering nodes 6 and 8. [4, 17] Thus, all sequences are clustered into a single evolutionary tree. The total time (t9) can be calculated as: D6,8 = 1/6 (d1,3 + d1,4 + d1,5 + d2,3 + d2,4 +d2,5)Discrete Data Methods Discrete data methods examine each column of a multiple sequence alignment dataset separately and search for the tree that best represents all this information. Although distance-based methods tend to be much faster than discrete data methods, they typically yield little information beyond the basic tree structure. Discrete data analyses, on the other hand, are information rich. The se methods produce a separate tree for each column in the alignment, so it is possible to trace the evolution for specific elements within a given sequence, such as catalytic sites or regulatory regions. 10, 17, 19, 20) Commonly used discrete data methods include maximum parsimony, which searches for the most parsimonious tree that requires the least number of evolutionary changes to explain differences observed, maximum likelihood, which requires a probabilistic model for the process of nucleotide substitution, and Bayesian MCMC, which also requires a stochastic model of evolution, but creates a probability distribution on a set of trees or aspects of evolutionary history. [17, 19, 20] Discrete data methods are generally considered to produce the best estimates of evolutionary history.However, these methods can be computationally expensive, and it can take weeks or months to obtain a reasonable level of accuracy for moderate to large datasets with 100 or more OTUs. [19] Molecular P hylogenetics Maximum Parsimony Karen Dowell 8 Among the most widely used tree-estimation techniques, maximum parsimony applies a set of algorithms to search for the tree that requires the minimum number of evolutionary changes observed among the OTUs in the study. For example, Figure 9 lists four sample sequences from which phylogenetic trees could be inferred using maximum parsimony.Site Seq 1 2 3 4 1 A A A A 2 A G G G 3 G C A A 4 A C T G 5 G G A A 6 T T T T 7 G G C C 8 C C C C 9 A G A G Figure 9. Sample sequences for a maximum parsimony study [17] Maximum parsimony algorithms identify phylogenetically informative sites, meaning the site favors some trees over others. Consider the sequences in Figure 9: Site 1 is not informative, because all sequences at that site (in column 1) are A (Adenine), and no change in state is required to match any one sequence (1-4) to another.Similarly, Site 2 is not informative because all three trees require one change and there is no reason to favor one tree over another. Site 3 is not informative because all three trees require two changes. (See Figure 10). Figure 10. Site 3 trees all require one evolutionary change. [17] Site 4 is not informative because all three trees require three changes. No one tree can be identified as parsimonious. (See Figure 10 Figure 11. Site 4 trees all require three evolutionary changes. [17] Site 5 is informative because one tree requires only one nucleotide change, whereas the other two trees require 2 changes.In Figure 12, the first tree on the left, which requires only one nucleotide change, is identified as the maximum parsimony tree. Figure 12. Site 5 trees vary in the number of evolutionary changes required. [17] Molecular Phylogenetics Maximum Likelihood Karen Dowell 9 The maximum likelihood method requires a probabalistic model of evolution for estimating nucleotide substitution. This method evaluates competing hypotheses (trees and parameters) by selecting those with the highest likeliho od, meaning those that render the observed data most plausible. The ikelihood of a hypothesis is defined as the probability of the data given that hypothesis. In phylogeny reconstruction, the hypotheses are the evolutionary tree (its topology and branch lengths) and any other parameters of the evolutionary model. [17, 20] The likelihood calculations required for evolutionary trees are far from straightforward and usually require complex computations that must allow for all possible unobserved sequences at the LCA nodes of hypothesized trees. This method specifies the transition probability from one nucleotide state to another in a time interval in each branch.For example, for a one-parameter model with rate of substitution ? per site per unit time, the probability that the nucleotide at time t is i is: The probability that the nucleotide at time t is j is: To set up a likelihood function, given x as the ancestral node and y and z as internal nodes, the probability of observing nucle otides i, j, k, l at the tips of the tree is computed as: Pxl(t1+t2+t3)Pxy(t1)Pyk(t2+t3)Pyz(t2)Pzi(t3)Pzj(t3) For the ancestral node (root) x, the probability of having nucleotide l in sequence 4 is calculated as: Pxl(t1+t2+t3)Because x, y, and z can be any one of four nucleotides (ACGT), it is necessary to sum over all possibilities to obtain the probability of observing the configuration of nucleotides i, j, k, l, in sequences 1, 2, 3, 4, for a given hypothetical tree (see Figure 13. ). This likelihood probability is calculated as: h(I,j,k,l)= [? gxPxl(t1+t2+t3)] [? Pxy(t1)Pyk(t2+t3)] [? Pyz(t2)Pzi(t3) Pzj(t3)] The appropriate likelihood function depends on the hypothetical tree and the evolutionary model used. (See Figure 13. ) [17] Figure 13. Different types of model trees for the derivation of the maximum likelihood function. 17] Molecular Phylogenetics Stochastic Models of Evolution Karen Dowell 10 Evolutionary changes in molecular sequences result from mutations, some of whic h occur by chance, others by natural selection. Rates of change can also differ among OTUs, depending on several factors ranging from GC content to genome size. To accurately estimate phylogenetic trees, assumptions must be made about the substitution process and those assumptions must be stated in the form of a stochastic evolutionary model. These probabilistic models are used to rank trees according to likelihood: P(data|tree).From a Bayesian perspective, they rank trees according to a posterior probability: P(tree|data). [17, 20] The objective of probabilistic models is to find likelihood or posterior probability of a particular taxonomic feature, then define and compute: P(x? |T,t ? ) Where x ? is xj for j=1†¦n, T is a tree with n leaves with sequence j at leaf j, and t ? are tree edge lengths. [17] A few popular stochastic models of evolution include the single parameter Jukes-Cantor (JC) method, Kimura 2-parameter (K2P), Hasegawa-Kishino-Yano (HKY), and Equal-Input.Some s oftware programs, such as Paup*, will automatically use a default model for the tree estimation method chosen. The JC method is the easiest one to comprehend, because it assumes that if a site changes its state, it changes with equal probability to the other states. This is not very realistic, however, as some sites are known to evolve more rapidly than others, and some sites may be invariable and not allowed to change at all. Determining how best to select the appropriate model is a topic of another paper (or papers) as there is no one model that incorporates all mutation rules and patterns across different species and macromolecules. 4, 17, 20] Hidden Markov Models Profile hidden Markov models (HMMs) are a form of Bayesian network that provides statistical models of the consensus structure of a sequence family. Gary Churchill at The Jackson Lab was the first evolutionary geneticist to propose using profile HMMs to model rates of evolution. Many software packages and web services n ow apply HMMs to estimate phylogenetic relationships. [8] In the HMM format, each position in the model corresponds to a site in the sequence alignment. For each position, there are a number of possible states, each of which corresponds to a different rate of evolution.In addition, transitions between all possible rate-states at adjacent positions. Transition probabilities capture any tendency for patterns of rates to occur in successive sites. [2, 4] Assessing Trees Tree estimating algorithms generate one or more optimal trees. This set of possible trees is subjected to a series of statistical tests to evaluate whether one tree is better than another – and if the proposed phylogeny is reasonable. Common methods for assessing trees include the Bootstrap and Jackknife Resampling methods, and analytical methods, such as parsimony, distance, and likelihood.To illustrate how these methods are used, consider the steps involved in a bootstrap analysis. Bootstrap Analysis A bootstra p is a statistical method for assessing trees that takes its name from the fact that it can â€Å"pull itself up by its bootstraps† and generate meaningful statistical distributions from almost nothing. Using bootstrap analysis, distributions that would otherwise be difficult to calculate exactly are estimated by repeated creation and analysis of artificial datasets. In a Non-parametric bootstrap, artificial datasets Molecular Phylogenetics Karen Dowell 11 generated by resampling from original data.In a parametric bootstrap, data is simulated according to hypothesis tested. The objective of any bootstrap analysis is to test whether the whole dataset supports the tree. [1, 4, 17] Figure 14 illustrates the basic steps in any bootstrap analysis. Sample datasets are automatically generated from an original dataset. Trees are then estimated from each sample dataset. The results are compiled and compared to determine a bootstrap consensus tree. Figure 14. Steps in a phylogenetic tr ee bootstrap analysis. [1] Phylogenetic Analysis Tools There are several good online tools and databases that can be used for phylogenetic analysis.These include PANTHER, P-Pod, PFam, TreeFam, and the PhyloFacts structural phylogenomic encyclopedia. Each of these databases uses different algorithms and draws on different sources for sequence information, and therefore the trees estimated by PANTHER, for example, may differ significantly from those generated by P-Pod or PFam. As with all bioinformatics tools of this type, it is important to test different methods, compare the results, then determine which database works best (according to consensus results, not researcher bias) for studies involving different types of datasets.In addition, to the phylogenetic programs already mentioned in this paper, a comprehensive list of more than 350 software packages, web-services, and other resources can be found here: http://evolution. genetics. washington. edu/phylip/software. html. PANTHER ( pantherdb. org) Protein ANalysis Through Evolutionary Relationships, known by its acronym PANTHER, is a library of protein families and subfamilies indexed by function. Panther version 6. 1 contains 5547 protein families. Molecular Phylogenetics Karen Dowell 12It categorizes proteins by evolutionary related proteins (families) and related proteins with same function (subfamilies). [8, 21, 26] PANTHER is composed of both a library and index. The library is a collection of â€Å"books† that represent a protein family as a collection of multiple sequence alignments, HMMs, and a family phylogenetic tree. Functional divergence within the tree is represented by dividing the parent tree into child trees and HMMs based on shared functions. These subfamilies enable database curators to more accurately capture functional divergence of protein sequences as inferred from genomic DNA. 25, 26] PANTHER database entries are annotated to molecular function, biological process and pathway with a proprietary PANTHER/X ontology system, which is supposed to be easier to understand than the more global standard Gene Ontology (GO). Database entries in PANTHER are generated through clustering of UniProt database using a BLAST-based similarity score. Trees are automatically generated based on multiple sequence alignments and parameters of the protein family HMMs using the Tree Inferred from Profile Score (TIPS) clustering algorithm.Scientific curators review all family trees, annotate each tree, and determine how best to divide them into subtrees using a tree-attribute viewer that tabulates annotations for sequences in a tree. In addition, trees and subfamilies are manually cross-checked and validated by curators. [25, 26] P-POD (ortholog. princeton. edu) The Princeton Protein Orthology Database (P-POD) combines results from multiple comparative methods with curated information culled from the literature.Designed to be a resource for experimental biologists seeking evolutionary information on genes on interest, P-POD employs a modular architecture, based on their Generic Model Organism Database (GMOD). P-POD can be accessed from their web service or downloaded to run on local computer systems. [12] P-POD accepts FASTA-formatted protein sequences as input, and performs comparative genomic analyses on those sequences using OrthoMCL and Jaccard clustering methods. The P-POD database contains both phylogenetic information and manually curated experimental results.The site also provides many links to sites rich in human disease and gene information. This tool may be particularly helpful for bioinformaticists and statisticians developing comparative genomic database tools and resources. Pfam (pfam. sanger. ac. uk/) PFam is a collection of protein families represented by multiple sequence alignments and HMMs. It contains models of protein clans, families, domains, and motifs, and uses HMMs representing conserved functional and structural domains. It is a large, widely used, actively curated mature database that has been available online since 1995.Pfam can be used to retrieve the domain architectures for a specific protein by conducting a search using a protein sequence against the Pfam library of HMMs. This database is also helpful for proteomes and protein domain architecture analysis. [6, 8, 24] There are two versions of the Pfam database: Pfam–B is generated automatically from ProDom, using PsiBLAST, an open access bioinformatics tool available through NCBI for identifying weak, but biologically relevant sequence similarities. Pfam-A is hand-curated from custom multiple sequence alignments. Pfam protein domain families are clustered with Mkdom2, and aligned with ProDomAlign.ProDom is a comprehensive set of protein domain families automatically generated from the SWISSPROT and TrEMBL sequence databases. Mkdom2 is a ProDom program used to make ProDom family clusters. Protein domain families in ProDom were aligned using an improved parallelized program called Molecular Phylogenetics Karen Dowell 13 ProDomAlign, developed in C++ using OpenMP. ProDomAlign is based on MultAlign, a program well suited for aligning very large sequence families with thousands of associated sequences. As of early 2008, Pfam matched 72 percent of known proteins sequences, and 95 percent of proteins for which there is a known structure.Within the Pfam database, 75 percent of sequences will have one match to Pfam-A, 19 percent to Pfam-B. There are also two versions of Pfam-A and Pfam-B. Pfam-ls handles global alignments, and Pfam-fs is optimized for local alignments. Interestingly, Pfam entries can be classified as â€Å"unknown,† but that doesn’t mean the protein is undocumented. Unknown entries can be proteins for which some information is known, but it has not been fully researched or cannot be adequately annotated. For example, Pfam entry PFO1816 is a LeucineRich Repeat Variant (LRV), which has a known structure (1LRV ) available in the Protein Databank (pdb. rg). LRV repeat regions, which are found in many different proteins, are often involved in cell adhesion, DNA repair, and hormone reception—but identification of an LRV within a sequence encoding a protein doesn’t specifically reveal the protein’s function. For studies involving a large number of protein searches, it may be more convenient to run Pfam locally on a client machine. The standalone Pfam system requires the HMMER2 software, the Pfam HMM libraries and a couple of additional files from the Pfam website to be installed on the client machine. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. ) Once the initial search is complete, researchers can go to the Pfam website to further analyze select number of sequences using additional features on website. [6, 8, 24] TreeFam (TreeFam. org) TreeFam is a curated database of phylogenetic trees and orthology predictions f or all animal gene families that focuses on gene sets from animals with completely sequenced genomes. Orthologs and paralogs are inferred from phylogenetic tree of gene family.Release 4 contains curated trees for 1314 families and automatically generated trees for another 14351 families. [16, 23] Like Pfam, TreeFam is a two-part database: TreeFam-B contains automatically generated trees, and TreeFam-A consists of manually curated trees. To automatically generate trees, an algorithm selects clusters of genes to create TreeFam-B â€Å"seeds† from core species with high-quality reference genome sequences, first using BLAST to rapidly assemble an initial list of possible matches, then HMMER to expand and filter probable sequence matches for each TreeFam B seed family.The filtered alignment is fed into a neighbor-joining algorithm and a tree is constructed based on amino acid mismatch distances. For TreeFam version 4, the most current release, five â€Å"clean† family trees were built for each TreeFam B seed, two using a maximum likelihood tree generated using PHYML (one based on the protein alignment, the other on codon alignment), three using a neighbor joining tree, using different distance measurements based on codon alignments. 16, 23] Scientific curators then manually any correct errors (based on information in the literature) in automatically generated TreeFam-B trees. Curated TreeFam-B trees then become seeds for TreeFam-A trees. Clean TreeFam-A trees are build using three merging algorithms and bootstrapping to find the consensus tree of seven trees: two constrained maximum likelihood trees based on protein and codon alignment, and five unconstrained neighbor-joining trees generated using different distance measurements based on codon alignments.For both TreeFam-B and TreeFam-A families, orthologs and paralogs are inferred only from clean trees using Duplication/Loss Inference (DLI) algorithm that requires a species tree (NCBI taxonomy tree). [16, 23] Molecular Phylogenetics PhyloFacts (phylogenomics. berkeley. edu/phylofacts) Karen Dowell 14 PhyloFacts is an online phylogenomic encyclopedia for protein functional and structural classification. It contains more than 57,000 â€Å"books† for protein superfamilies and structural domains.Each book contains heterogenous data for protein families, including multiple sequence alignments, one or more phylogenetic trees, predicted 3-D protein structures, predicted functional subfamilies, taxonomic distributions, GO annotations, and PFAM domains. HMMs constructed for each family and subfamily permit novel sequences to be classified to different functional classes. [14] Unlike other databases mentioned in this paper, PhyloFacts seeks to correct and clarify annotation errors associated with computational methods for predicting protein function based on sequence homology.It uses a consensus approach that integrates many different prediction methods and sources of experimental data over an evolutionary tree. By applying evolutionary and structural clustering of proteins, PhyloFacts is able to analyze disparate datasets using multiple methods, identify potential errors in database annotations, and provide a mechanism for improving the accuracy of functional annotation in general. [14] PhyloFacts can be used to search for protein structure prediction or functional classification for a particular protein sequence.Researchers may also browse through protein family books and multiple sequence alignments, phylogenetic trees, HMMs and other pertinent information for proteins of interest. This webservice also provides many links to literature and other information sources. [14] Applied Molecular Phylogenetics Molecular phylogenetic studies have many diverse applications. As the amount of publically available molecular sequence data grows and methods for modeling evolution become more sophisticated and accessible, more and more biologists are incorporating phylog enetic analyses into their research trategy. Here’s a sampling of how molecular phylogenetics might be applied. Tracing the evolution of man In one case study, molecular phylogenetic techniques were used to compare and analyze variation in DNA sequences using modern human and Neanderthal mitochondrial DNA (mtDNA). For this study, 206 modern human mtDNAs and parts of two Neanderthal mtDNAs sequences derived from skeletal remains were used to generate an initial dataset. Genetic distance was first estimated using the Jukes-Cantor single parameter model.Then the Kimura 2-Parameter model was used to distinguish between transition (replacement of one purine with another purine or one pyrimidine with another pyrimidine) and transversion (replacement of one purine with a pyrimidine or vice versa) probabilities with Kimura 2parameter model. A phylogenetic tree representing primate evolution was generated using pairwise genetic distances between primate Hypervariable regions I and II of mtDNA. [3] Chasing an epidemic: SARS Using publically available genomic data, it is possible to reconstruct the progression of the SARS epidemic over time and geographically.To conduct this phylogenetic analysis, researchers used the neighborjoining method to construct a phylogenetic tree of spike proteins in various coronaviruses and identify the viral host (a Himalyan palm civet). They then obtained 13 SARs genome sequences with documented information on the date and location of the sample. The neighbor-joining method and a distance matrix based on Jukes-Cantor model, were used to generate an epidemic tree, from which it was possible to identify the origin (date and location) of the virus by observing progression of mutations over time. 3] Molecular Phylogenetics Barking up the right tree Karen Dowell 15 Phylogenetics is increasingly incorporated into biological and biomedical research papers. When the canine genome was published, researchers used sequence data to estimate a co mprehensive phylogeny of the canid family. Figure 15. Phylogenetic Tree of the Canid family This canid family phylogenetic tree is based on 15 kb of exon and intron sequence. It was constructed using the maximum parsimony method and represents the single most parsimonious tree.A good example of how phylogenies are referenced in the literature, this tree includes bootstrap values and Bayesian posterior probability values listed above and below internodes, respectively. Dashes indicate bootstrap values below 50%. In addition, divergence time in millions of years (Myr) is indicated for three nodes. [18] Seeing the Forest from the Trees Molecular phylogenetics is a broad, diverse field with many applications, supported by multiple computational and statistical methods. The sheer volumes of genomic data currently available (and rapidly growing) render molecular phylogenetics a key component of much biological research.Genome-scale studies on gene content, conserved gene order, gene expre ssion, regulatory networks, metabolic pathways, functional genome annotation can all be enriched by evolutionary studies based on phylogenetic statistical analyses. [19, 25 27] Molecular phylogenies have fast become an integral part of biological research, pharmaceutical drug design, and bioinformatics techniques for protein structure prediction and multiple sequence alignment. Although not all molecular biologists and bioinformaticians may be familiar with the techniques describedMolecular Phylogenetics Karen Dowell 16 in this paper, this is a rapidly growing and expanding field and there is ongoing need for novel algorithms to solve complex phylogeny reconstruction problems. References 1. Baldauf, SL (2003) â€Å"Phylogeny for the faint of heart: a tutorial. † Trends in Genetics, 19(6):345-351. 2. Brown, D, K Sjolander (2006) â€Å"Functional Classification Using Phylogenomic Inference. † PLos Computational Biology, 2(6):0479-0483. 3. Cristianini, N, and M Hahn (2007 ) Introduction to Computational Genomics: A Case Studies Approach.Cambridge University Press: Cambridge. 4. Durbin, R, S Eddy, A Krogh, G Mitchison (1998) Biological Sequence Analysis. Cambridge University Press: Cambridge. 5. Ewens, WJ, R Grant (2005) Statistical Methods in Bioinformatics. Springer Science and Business Media: New York. 6. Finn, RD, J Tate, J Mistry, PC Coggill, SJ Sammut, HR Hotz, G Ceric, K Forslund, SR Eddy, ELL Sonnhammer, A Bateman (2008) â€Å"The Pfam protein families database. † Nucleic Acids Research, 36:D281288. 7. Gabaldon, T (2008) â€Å"Large-scale assignment of orthology: back to phylogenetics? Genome Biology, 9:235. 1-235. 6. 8. Gollery, M. (2008) Handbook of Hidden Markov Models in Bioinformatics. CRC Press, Taylor & Francis Group: London. 9. Goodstadt, L, CP Ponting (2006) â€Å"Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human. † PLoS Computational Biology, 2(9):1134-1150. 10. Hall, BG. (2004 ) Phylogenetic Trees Made Easy: A How-To Manual, 2nd ed. Sinauer Associates, Inc. : Sunderland, MA. 11. Hartwell, LH, L Hood, ML Goldberg, AE Reynolds, LM Silver, RC Veres (2008) Genetics: From Genes to Genomes, 3rd Ed.McGraw-Hill: New York. 12. Heinicke, S, MS Livstone, C Lu, R Oughtred, F Kang, SV Angiuoli, O White, D Botstein, K Dolinski (2007) â€Å"The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists. † PLoS ONE, 8:e766. 1-15. 13. Kortschak, RD, R Tamme (2001) â€Å"Evolutionary analysis of vertebrate Notch genes. † Dev Genes Evol, 211:350-354. 14. Krishnamurthy, N, DP Brown, D Kirshner, K Sjolander (2006) â€Å"PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. † Genome Biology, 7:R83. -13. 15. Kuzniar, A, RCHJ van Ham, S Pongor, JAM Leunissen (2008) â€Å"The quest for orthologs: finding the corresponding gene across genomes. † Trends in G enetics, 24(11):539-551. Molecular Phylogenetics Karen Dowell 17 16. Li, H, A Coghlan, J Ruan, LJ Coin, JK Heriche, L Osmotherly, R Li, T Liu, Z Zhang, L Bolund, GKS Wong, W Zheng, P Dehal, J Wang, R Durbin (2006) â€Å"TreeFam: a curated database of phylgenetic trees of animal gene families. † Nucleic Acids Research, 34:D573-580. 17. Li, WH (1997) Molecular Evolution. Sinauer Associates: Sunderland, MA. 18.Lindblad-Toh, K, CM Wade, TS Mikkelsen, EK Karlsson, DB Jaffe, M Kamal, M Clamp, JL Chang, EJ Kulbokas III, MC Zody, E Mauceli, X Xie, M Breen, RK Wayne, EA Ostrander, CP Ponting, F Galibert, DR Smith, PJ deJong, E Kirkness, P Alvarez, T Biagi, W Brockman, J Butler, C Chin, A Cook, J Cuff, MJ Daly, D DeCaprio, S Gnerre, M Grabherr, M Kellis, M Kleber, C Bardeleben, L Goodstadt, A Heger, C Hitte, L Kim, KP Koepfli, HG Parker, JP Pollinger, SMJ Searle, NB Sutter, R Thomas, C Webber, ES Lander (2005) â€Å"Genome Sequence, Comparative Analysis and Haplotype Structure of the Domestic Dog.Nature, 438:803-819. 19. Linder, CR, T Warnow (2005) â€Å"An overview of phylogeny reconstruction. † In the Handbook of Computational Molecular Biology, Chapman and Hall/CRC Computer & Information Science. 20. Lio, P, N Goldman (1998) â€Å"Models of Molecular Evolution and Phylogeny. † Genome Research, 8:12331244. 21. Mi, H, N Guo, A Kejariwal, PD Thomas (2007) â€Å"PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Research, 35:D247-252. 22. Patthy, Laszlo. (1999) Protein Evolution. Blackwell Science, Ltd: Malden, MA. 23. Ruan, J, H Li Z Chen, A Coghlan, LJM Coin, Y Guo, JK Heriche, Y Hu, K Kristiansen, R Li, T Liu, A Mose, J Qin, S Vang, AJ Vilella, A Ureta-Vidal, L Bolund, J Wang, R Durbin (2008) â€Å"TreeFam: 2008 Update. † Nucleic Acids Research, 36:D735-740. 24. Sammut, SJ, RD Finn, A Bateman (2008) â€Å"Pfam 10 years on: 10000 families and still growing. â €  Briefings in Bioinformatics, 9(3):210-219. 5. Thomas, PD, A Kejariwal, N Guo, H Mi, MJ Campbell, A Muruganujan, B Lazareva-Ulitsky (2006) â€Å"Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. † Nucleic Acids Research, 34:W645-650. 26. Thomas, PD, MJ Campbell, A Kejariwal, H Mi, B Karlak, R Daverman, K Diemer, A Muruganujan, A Narechania. â€Å"PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. † Genome Research, 13:2129-2141. 27.Warnow, T (2004) â€Å"Computational Methods in Phylogenetics† Computational Systems Biology Conference, Stanford, CA 28. Whelan, S, P Lio, N Goldman (2001) â€Å"Molecular phylogenetics: state of the art methods for looking into the past. † Trends in Genetics, 17(5):262-272. Molecular Phylogenetics Karen Dowell 18 Appendix Website Resources Phylogeny Programs. A University of Washington site formerly supported by the National Science Foundation. http://www. evolution. genetics. washington. edu/phylip/software. tml TreeFam Tree Families Database. http://wwww. treefam. org Protein Analysis Through Evolutionary Relationships (PANTHER) Classification System. http://www. pantherdb. org. 29. Pfam Database of Protein Families. http://pfam. sanger. ac. uk 30. Princeton Protein Orthology Database (P-POD). http://ppod. princeton. edu 31. Wikipedia. http://en. wikipedia. org/wiki/Tree_of_life(science) Cover Page The cover image is from a phylogeny of canid species that appeared in Lindblad-Toh et al, 2005. [18]

Managing Solid Wastes in the Philippines Essay Example

Managing Solid Wastes in the Philippines Essay Example Managing Solid Wastes in the Philippines Paper Managing Solid Wastes in the Philippines Paper Waste management is the collection, transport, processing or disposal, managing and monitoring of waste materials. The term usually relates to materials produced by human activity, and the process is generally undertaken to reduce their effect on health, the environment or aesthetics. Waste management is a distinct practice from resource recovery which focuses on delaying the rate of consumption of natural resources. All waste materials, whether they are solid, liquid, gaseous or radioactive fall within the remit of waste management Managing Solid Wastes in the Philippines Solid waste, over the past thirty years, has remained the most visible, and silently dangerous, environmental problem in the country. In September 1999, not one Filipino was left without a trauma out of the tragedy that befell Payatas in Quezon City. Hundreds died, buried alive underneath filth, as mountains of garbage collapsed due to heavy downpour. This is among the worst human-made disasters that have ever hit the Philippines, a disaster we should never allow to happen again. Dirty Living The countrys garbage problem has a lot to do with lifestyle. Every individual must be responsible for the wastes he generates. Considering that we are among the most populated in the world, with the amount of trash each of us produces, it is no surprise that our lands have become the largest dumpsite. Our streets are lined with garbage, our waters flooded, and our creeks clogged with trash, even our mountains are junk all these are reflections of the need to heed to the serious call for waste management it is time for each and every one of us to stop living dirty. And why? The indiscriminate throwing of garbage contaminates our waters, with clogged drains open for insect breeding which brings about diseases like cholera and dengue, targeting most especially, our children. Floods have become a common sight during rainy seasons. Backyard burning, or simply, burning of garbage, releases toxic air pollutants, which leads to respiratory diseases like asthma, bronchitis, lung cancer, even death. To be direct, dirty living equals death. Trash Course The National Solid Waste Management Commission (NSWMC), chaired by the Department of Environment and Natural Resources (DENR), has identified three key trends in the local garbage situation: 1) increase in sheer volume of generated wastes; 2) change in the quality and make-up of waste generated; and 3) waste handling methods. Everyday, the country has a per capita waste generation of 0.3 to 0.7 kilograms of garbage. In 2003*, we have generated 27,397 tons of garbage daily, a step backwards compared to the 19,700 tons of garbage we have generated daily in 2000 (*based on the study conducted by the NSWMC-Secretariat and the Metro Manila Solid Waste Management Project of the Asian Development Bank in 2003). That is tantamount to ten million tons of garbage generated in 2003. Of the ten million tons of generated garbage in 2003, 2.5 million came from Metro Manila. This is a strong evidence of the forecast which indicated that by 2010, in comparison to the 2000 data, waste generation shall have increased by 47%. Ways to Beat Wastes Lucky for us, the Philippine solid waste composition is generally highly-organic (biodegradable) and recyclable, with 50 percent of the wastes made up of yard, wood, and kitchen wastes. The high percentage of biodegradables is an indication of the great potential of composting as a means to recover this type of wastes, especially those coming from agricultural zones. Moreover, potentials for recycling are good considering that the remaining wastes are made up of recyclable materials. The DENR has always been steadfast in its commitment to reduce, and eventually, eradicate the amount of garbage in the country. Projects and programs on solid waste management are consistently being implemented by the Department, through the NSWMC, in coordination with the local government units, non-government organizations, international groups, and other government agencies. To date, the Commission has initiated the closure and rehabilitation of existing open dumpsites, the establishment of sanitary landfills in municipalities, the establishment of an ecological solid waste management system, the categorized compliance for disposal facilities, and the promotion and development of alternative technologies to process residual wastes. The DENR, along with the Department of Interior and Local Government and some civil society groups, has also conducted the Nationwide Search for Model Barangays for Eco-Waste Management System, to assist our local communities to comply with, and reward them on their compliance, to Republic Act No. 9003, or the Ecological Solid Waste Management Act. Waste Recovery Programs are also being instituted by the government. The DENR has forged an agreement with the Recyclean Foundation, Inc (RFI) on a waste paper recovery program. The NSWMC, Tire Importers and Traders Association of the Philippines, Tire Manufacturers of the Philippines, and the Philippine Retreaders Association agreed to facilitate recovery of used tires for the effective management of the waste material which would include their recycling, re-use, and environmentally sound disposal. In terms of plastics and plastic packaging, the Polystyrene Packaging Council of the Philippines coordinated with several malls and industrial parks, to recover polystyrene wastes which resulted to the recovery of about 8,000 cu. m. of said plastics in 2003. An Agreement was made between the council and the Department of Science and Technology to design melting kettles for potential recyclers to convert polystyrene into other form of materials. To spread environmental awareness, particularly on solid waste management concerns, the DENR, together with the Eco-Waste Coalition signed an agreement for the establishment of the Ecological Solid Waste Pavilion. It is a national center for meetings, congregations, trainings, educational purposes particularly for showcasing effective, innovative and creative SWM procedures, techniques and activities. The DENR is vigilant in its quest to manage solid wastes in the Philippines. The government is bent on empowering the municipalities to address their own garbage issues. We are all parts which make up a whole in each municipality. Together, let us put a stop to the thirty years of garbage problem we have stumbled upon. We have more than enough.

Indian removal assignment Essays - Free Essays, Term Papers

Indian removal assignment Essays - Free Essays, Term Papers Yasmine Gist U.S History John Paris 28 November 2018 Indian Removal Jackson says that taking over the native land will help to provide resources for the natives. This is positive because the Natives will have access to resources they did not have before. Jackson also thought that taking over their land would help to civilize the native people. If the Natives where under his power, he believed the natives would advance. Jackson also believed that the Native Americans were falling apart so if they were placed under his rule then it would make them stronger and have a better bond. Jackson thinks the white race is superior because he thinks the Natives should join his race. Jackson saying that taking over their land will help them be more civilized is pro-white because he's basically saying that white people are more civilized people and that the natives are not and because of that we can fix them. Jackson also assumes that his race has more resources making his to assume whites have better advancements. I believe we should condemn these goals these goals as paternalistic arrogance. I believe that humans have a basic understanding of what is right and what is wrong. I don't think Jackson had good intentions. The natives were human beings that were treated awful and Jackson thought he was inferior. Jackson suggest a compromise between the Natives and the Americans. The compromise suggest that the Natives migrate past the Mississippi if they want to continue their Native culture. Jackson proposes this because then the Natives can have their own space but if they do choose to stay, they have to follow Jackson's laws. This is the most beneficial policy for Natives because Jackson is giving them a choice and they are not being forced. Both have a Legislative, Executive, and Judicial branch and also promise to a fair trial. These promises are both in the Cherokee Constitution and the U.S constitution. The Authors would not be happy with Jacksons civilizing goals. I believe they would have been insulted because in a lot of ways they have similarities and could have worked together, but instead Jackson in a way wanted to have control over them. "Chiefs, head-men and warriors! Will you then, by resistance, compel us to resort to arms? God forbid! Or will you, by flight, seek to hid yourselves in mountains and forests, and thus oblige us to hunt you down? Remember that, in pursuit, it may be impossible to avoid conflicts." I don't think it was necessary to to say to the Natives that they would get hunted down if they didn't obey. It Sounds like they would kill them. "The blood of the white man or the blood of the red man may be spilt, and, if spilt, however accidentally, it may be impossible for the discreet and humane among you, or among us, to prevent a general war and carnage. "This was also not necessary to threaten the Natives with a bloody war. One hardship the Natives endured was the cruel treatment they received from the soilders. Natives were whipped and arrested if they did not follow direct orders. Another hardship was the conditions the Natives had to travel. They did not have the resources to survive so a lot of Natives died. Both of these hardships could have been avoided if the Americans let them be and not force them to leave their homes. Since Americans were forcing the Natives out, they could of provided an adequate amount of resources but they didn't. "Murder is murder, and somebody must answer. Somebody must explain the streams of blood that flowed in the Indian country in the summer of 1838. Somebody must explain the 4000 silent graves that mark the trail of the Cherokees to their exile. I wish I could forget it all, but the picture of 645 wagons lumbering over the frozen ground with their cargo of suffering humanity still lingers in my memory." It is clear in this statement he regrets it because he says he wish he could forget it all and that murder is bad. "Truth is, the facts are being concealed from the young people of today. School children of today

Ever and Never

Ever and Never Ever and Never Ever and Never By Mark Nichol Ever and never are adverbs employed in strictly defined ways. Here are the parameters of usage for the two terms. Ever, from the Old English word aefre, is used in these types of constructions: In positively constructed questions: â€Å"Have you ever been to Disneyland?† In negatively constructed questions: â€Å"Haven’t you ever been to Disneyland?† In positively constructed statements referring to a first instance: â€Å"That’s the first time anyone has ever asked me.† In negatively constructed statements expressing that something has not occurred: â€Å"Nobody has ever asked me that before.† To describe a continuous state: â€Å"I have ever wanted to go to Disneyland.† To mean â€Å"at any time†: â€Å"I want to go to Disneyland more than ever before.† To mean â€Å"in any way†: â€Å"How can I ever go to Disneyland?† Note that the word is not essential in any of these questions or statements; it simply intensifies the verb it modifies. For example, â€Å"I want to go to Disneyland more than before† simply states that the desire to go is greater than it used to be, while â€Å"I want to go to Disneyland more than ever before† suggests a strength of feeling about the subject. Never, from the Old English word naefre, consisting of ne (â€Å"not†) attached to aefre, is more limited in usage: In positively constructed questions prompting or confirming a negative response: â€Å"Have you never been to Disneyland?† (Using never with the negative form of a verb, such as haven’t, is redundant but appears occasionally in colloquial usage.) In negatively constructed statements expressing that something has not occurred: â€Å"I have never been asked that before.† (This is merely a passively written version of the equivalent sentence using ever.) Again, the adverb is not required, though in the second example, not would have to replace it; not could replace never in the first example but is not essential. Two related words, already and yet, each from Old English as well, also refer to occurrence. Already, a compound formed from all and ready, refers to something that has occurred before now at an unspecified time: I’ve already been to Disneyland. Have you already been to Disneyland? Ever and never are limited in the ways they can be relocated in a sentence (with varying degrees of acceptance of the syntax; only the last example is proper English): Have you been to Disneyland ever? / Haven’t you been to Disneyland ever? Nobody has asked me that before ever. Never have I been asked that before. Already, however, is more versatile (again, the choices differ in grammatical formality; the third and fifth examples are considered good English): Already, I’ve been to Disneyland. I’ve been already to Disneyland. I’ve been to Disneyland already. Have you been already to Disneyland? Have you been to Disneyland already? Yet appears in sentences indicating that something hasn’t occurred up to the present: I haven’t been to Disneyland yet. It is usually placed at the end of the sentence but for emphasis occasionally appears near the beginning: I haven’t yet been to Disneyland. The implication is that the speaker expects or hopes that the action will occur at some point; without yet, a simple fact is stated with no additional implication. Also, â€Å"Yet, I haven’t been to Disneyland† has a different meaning: As an alternative to however or nevertheless, it points out a contradiction or a rebuttal in response to a statement such as â€Å"You’ve been all over the world.† Yet can also have the sense of â€Å"in addition† or be a synonym for one sense of even, as in â€Å"We’re facing yet another problem† and â€Å"Tomorrow, they have yet more ground to cover† respectively. Want to improve your English in five minutes a day? Get a subscription and start receiving our writing tips and exercises daily! Keep learning! Browse the Vocabulary category, check our popular posts, or choose a related post below:50 Handy Expressions About HandsFlier vs. FlyerStarting a Business Letter with Dear Mr.

Accounts in the Balance Sheet and Income Statement of the Bank of Abu Assignment

Accounts in the Balance Sheet and Income Statement of the Bank of Abu Dhabi - Assignment Example Overall the bank’s statements reflect the quality of the bank's operations. Although there can be a few improvements in the operations of the bank and its customer base, however, the bank has performed remarkably well showing high revenues and net profits. The National Bank of Abu Dhabi was founded in 1968 in the United Arab Emirates. It is the market leader amongst lending banks in the Emirate of Abu Dhabi and the second largest player in the United Arab Emirate lending market. The bank has a presence in various regions including Hong Kong, Shanghai and Kuala Lumpur. The National Bank of Abu Dhabi is a premier bank offering the complete range of financial services in 18 countries. It is ranked in the Worlds 50 Safest Banks and the Safest Bank in emerging banks. This is a testament to the quality of the services and the operations of the bank. This assignment aims to analyze the balance sheet and income statements of the bank for the year 2012 and 2011. All accounts under assets, liabilities, equity, expenses and revenue will be defined and analyzed in this report. An asset on a balance sheet represents what a firm owns. They can be categorized as current assets and fixed assets. Current assets are ones that are consumed in a years’ time and the fixed assets are those that provide benefit over a certain period of time. I will now be defining the assets that are in the financial statements of the National Bank of Abu Dhabi. This account includes all the cash that is currently with the bank, the balances with the central bank and the dues from other banks (maturing within 3 months). Cash is the most liquid of all the current assets. The balance at the central bank is a percentage of the total customer deposits given to the central bank as a measure of avoiding bank runs. These are identified as financial assets which are held for the purpose of trading them in the market. are assets measured at fair value and the gains and losses are recorded in the income statements under the subheading of â€Å"Gains or Losses on Derivative Financial Instrument Transactions†.

Assignment Example | Topics and Well Written Essays - 250 words - 46

Assignment Example Compared to average gross earnings, the cost of Russian labor continues to grow at a very high rate, it has been the strongest at 20% and over, due to which industrial production and exports had declined significantly towards the end of 2008. (Rapid increase of labour costs in Central and Eastern Europe in 2008) According to the Pew Research Center poll, many Russians believe that they were better off in terms of their economic well being under the communism because even though democracy promised them an equal distribution of poverty, that has not been the case. Ordinary citizens believes that democracy has been beneficent for elites, educated and the political leaders and it has had little or adverse affect on ordinary people. Hence, the negative perception that prevails among is that those who belong to the rural, old and the average citizens are behind the privileged, educated elite, which was not the case in a communist regime. (End of Communism Cheered but Now with More Reservations) "End of Communism Cheered but Now with More Reservations." 2 November 2009. Pew Global Attitudes Project. 7 October 2010 . Lazzaro, Joseph. "Russia cuts off all natural gas to Ukraine; Europe shortages may spread." 7 January 2009. Blogging Stocks. 7 October 2010

Multijurisdictional tax final exam (emergency - has limited time) Coursework

Multijurisdictional tax final exam (emergency - has limited time) - Coursework Example Treaty with Country X PERMANENT ESTABLISHMENT 1. For the purposes of this Convention, the term "permanent establishment" means a fixed place of business through which the business of an enterprise is wholly or partly carried on. 2. The term "permanent establishment" includes especially: a) a place of management; b) a branch; c) an office; d) a factory; e) a workshop; and f) a mine, an oil or gas well, a quarry, or any other place of extraction of natural resources. 3. A building site or construction or installation project, or an installation or drilling rig or ship used for the exploration of natural resources, constitutes a permanent establishment only if it lasts, or the exploration activity continues for more than twelve months. 4. Notwithstanding the preceding provisions of this Article, the term "permanent establishment" shall be deemed not to include: a) the use of facilities solely for the purpose of storage, display or delivery of goods or merchandise belonging to the enterp rise; b) the maintenance of a stock of goods or merchandise belonging to the enterprise solely for the purpose of storage, display or delivery; c) the maintenance of a stock of goods or merchandise belonging to the enterprise solely for the purpose of processing by another enterprise; d) the maintenance of a fixed place of business solely for the purpose of purchasing goods or merchandise, or of collecting information, for the enterprise; e) the maintenance of a fixed place of business solely for the purpose of carrying on, for the enterprise, any other activity of a preparatory or auxiliary character; f) the maintenance of a fixed place of business solely for any combination of the activities mentioned in subparagraphs a) through e), provided that the overall activity of the fixed place of business resulting from this combination is of a preparatory or auxiliary character. MASSACHUSETTS LAW Except as otherwise provided in this section, every business corporation, organized under th e laws of the commonwealth, or exercising its charter or other means of legal authority, or qualified to do business or actually doing business in the commonwealth, or owning or using any part or all of its capital, plant or any other property in the commonwealth, shall pay an income measure tax. A business corporation shall not be subject to the income measure of tax under if it is engaged in the business of selling tangible personal property and taxation of that business corporation under this chapter is precluded by the constitution or laws of the United States, or would be so precluded except for the fact that the business corporation stored tangible personal property in a licensed public storage warehouse, but no portion of any warehouse which is owned or leased by a consignor or consignee of the tangible personal property shall be considered a licensed public warehouse. 1. Does the treaty provision protect Corporation A from taxation by the US? Why or why not? The treaty provi sion protects Corporation A from taxation in the US on multiple fronts. Under regular Massachusetts law, any business that has a de minimis physical presence in the form of any assets, employees, contracted obligations, rented property etc. in Massachusetts is subject to taxation. This clause applies equally well to any foreign corporations doing

Theories of Counseling Term Paper Example | Topics and Well Written Essays - 1250 words

Theories of Counseling - Term Paper Example If he gets demotivated and stops working hard his grades may even drop. The bottom line is that an individual endeavors to achieve success through hard work thereby overcoming the weaknesses. This contributes towards a personal drive to completeness. Hence, my view of the nature of people is closest to Alfred Alder’s Individual Psychology according to which people strive towards achieving success and this is referred to as a personal growth towards perfection. Also, according to Alder social interest was affected by social training and was not inborn. Unlike Freud’s theory, Alder believed that the conscious behavior was the backbone of an individual’s personal development. As a result, this theory makes an individual responsible for their perception and adaptations to the different events. An individual’s own lack of properly adjustment explains their lack of growth. If an individual is discouraged or his or her positive gestures do not result in required outcome, misbehavior occurs (University of Nevada Las Vegas, 2010). Individuals act as the components upon which the structure of family is made up of. An individual is affected by the family system very deeply as the family as a whole is a complex and dynamic collection of these individuals playing their roles (Hammond, 2010). The behavior of an individual in their family is shaped by the expectation of the family. This is the same reason why an individual may behave differently with their family members and their friends. This is because an individual is aware of what is expected of him as a brother, sister, daughter, son, parent, or grandparent. The theory which is closest to me view is the Family Systems theory according to which a family is a group of individuals, components and subparts. Similar to any mechanical system, a family can also be diagnosed by researchers and therapists so as to locate the point of repair by investigating its members (Hammond, 2010).

Starkey HR Ltd Essay Example | Topics and Well Written Essays - 1750 words

Starkey HR Ltd - Essay Example Redundancies should be a matter of last resort. Starkey must initially make efforts to identify the employees with special skills and experience and retain them. Reducing working time, pay cut, temporary leaves, less dependence on casual staff are some of the desirable measures. If redundancies are inevitable, a voluntary redundancy scheme should be employed. The offers of the scheme should be clearly outlined and sent to all applicable employees. In case of forced redundancies, the method of selection should be fair and non-discriminatory that takes the expertise and experience into consideration.Redundancy is enhanced in companies where statutory entitlements are low. The redundancy packages in most EU countries are quite high in comparison to the UK with a few exceptions such as the Netherlands and France. The average redundancy pay in the EU is more than twice the amount paid by employers in the UK. Under EU regulation, workers are supposed to be informed and consulted in any cas e of redundancies. Additionally, companies need to determine a threshold level for the redundancy and are determined by the size of the workforce and number of required redundancies.Forecasting allows a business to create and modify the financial and promotional strategy of a company in addition to allowing it to keep track of the performance of all requisite parameters, which play a crucial role in decision making and implementing the required changes to existing strategy.

Theories of Counseling Term Paper Example | Topics and Well Written Essays - 1250 words

Theories of Counseling - Term Paper Example If he gets demotivated and stops working hard his grades may even drop. The bottom line is that an individual endeavors to achieve success through hard work thereby overcoming the weaknesses. This contributes towards a personal drive to completeness. Hence, my view of the nature of people is closest to Alfred Alder’s Individual Psychology according to which people strive towards achieving success and this is referred to as a personal growth towards perfection. Also, according to Alder social interest was affected by social training and was not inborn. Unlike Freud’s theory, Alder believed that the conscious behavior was the backbone of an individual’s personal development. As a result, this theory makes an individual responsible for their perception and adaptations to the different events. An individual’s own lack of properly adjustment explains their lack of growth. If an individual is discouraged or his or her positive gestures do not result in required outcome, misbehavior occurs (University of Nevada Las Vegas, 2010). Individuals act as the components upon which the structure of family is made up of. An individual is affected by the family system very deeply as the family as a whole is a complex and dynamic collection of these individuals playing their roles (Hammond, 2010). The behavior of an individual in their family is shaped by the expectation of the family. This is the same reason why an individual may behave differently with their family members and their friends. This is because an individual is aware of what is expected of him as a brother, sister, daughter, son, parent, or grandparent. The theory which is closest to me view is the Family Systems theory according to which a family is a group of individuals, components and subparts. Similar to any mechanical system, a family can also be diagnosed by researchers and therapists so as to locate the point of repair by investigating its members (Hammond, 2010).