bluuebunny/crossref_metadata_2025_split huggingface dataset:
The WRKY transcription factor family in Brachypodium distachyon
Authors: Tripathi Prateek , Rabara Roel C , Langum Tanner J , Boken Ashley K , Rushton Deena L , Boomsma Darius D , Rinerson Charles I , Rabara Jennifer , Reese R Neil , Chen Xianfeng , Rohila Jai S , Rushton Paul J 
Published: January 2013

Abstract

Background
A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement.

Results
We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors.

Conclusions
The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.
Selecting Optimal Fracture Fluids, Breaker System, and Proppant Type for Successful Hydraulic Fracturing and Enhanced Gas Production – Case Studies
Authors: Rahim Zillur , Al-Anazi Hamoud , Al-Kanaan Adnan 
Published: January 2013

Abstract
Hydraulic fracturing is required to commercially produce low to moderate permeability gas reservoirs. The selection of fracturing fluids, additives, and proppant types are major components when designing and implementing a hydraulic fracturing treatment. A viscous, unbroken fracture fluid that remains after the treatment compounds the effects of fracture face skin and causes severe deterioration to proppant conductivity. With the advancement of technology, many novel fracture fluid systems are available in the industry with reduced polymer concentration to preserve reservoir and proppant integrity. The advantages of these fluids include less formation damage, low cost, and reduced treatment pressure. Subsequent to the fracture operation, an aggressive breaker treatment is often necessary to effectively clean up the fracture and restore proppant conductivity. Proppant conductivity plays a tremendous role in the post-fracture production enhancement and any damage left from the fluids can impair well potential considerably. Similarly, correct choice of proppant based on the rock strength, reservoir fluid properties, expected production rate, pressure, and temperature is important. Proppant type and scheduling determine the ultimate propped fracture geometry that controls the gas flow from the reservoir to the wellbore.
Application of new technologies in combination with better job design to obtain improved results in the deep sandstone reservoirs of Saudi Arabia is ongoing. In the process of optimization, fluids along with its gel type, polymer concentration, and additives have been modified and changed to provide better results. Similarly proppant size, types, and schedule have been optimized. Different types of aqueous-based fracturing fluids used with various polymer loadings as well as the use of hybrid systems and viscoelastic fluids (VES) used in deep and high temperature reservoirs are currently in use. Several case studies provided in this paper demonstrate how the critical fracturing parameters have progressed with time, been customized, and made to fit the reservoir conditions to make a noticeable impact on well productivity and recovery.
Understanding Ceramic Proppants: Are They All Created Equal?
Authors: Saldungaray Pedro , Palisch Terry 
Published: January 2013

Abstract
Introduced in the 1970's, ceramic proppants have provided the industry with higher conductivity alternatives to naturally occurring frac sand, and are used to increase well productivity in a wide range of reservoir conditions. Initially dominated by a handful of ceramic proppant manufacturers, the increased recognition of the need for highly conductive fractures has led to a tremendous growth in the industry, with nearly 100 ceramic proppant plants in operation today [Kim 2012]. The oil and gas industry used more than 65 billion pounds of proppant in 2011, and the rapid growth of the ceramic industry often could not keep pace with the surging global demand. This explosive growth has led to significant variations in ceramic proppant quality and sustained conductivity, which affects production benefits.
Although the industry has historically considered ceramic proppants to be interchangeable, they represent a wide range of different materials whose properties are highly dependent upon their composition and manufacturing technology. This paper will examine the performance of different types of ceramic, including lightweight, intermediate density and high density proppants, and some of the new materials that don't necessarily fit neatly into these categories. It will also describe the major manufacturing techniques used in the industry, and illustrate the differences that key steps in the industrial process have in the quality and conductivity of the final product. Microphotographs and laboratory testing will be supplemented with modeling forecasts to show the productivity expected from specific ceramic proppants at realistic conditions. Finally, field studies will be presented which corroborate the predictions that proppant quality significantly affects well productivity and proppants within the same generic categorization do not provide identical productivity.
This paper will serve as an excellent resource to completion and fracture design engineers as they navigate their way to choosing the optimal proppant for specific well parameters and economic conditions. It will be clear that proppants should not be considered an interchangeable commodity, and that well performance will be dependent on the quality and characteristics of the specific proppants selected.
Existence of nonoscillatory solutions of higher order neutral differential equations with distributed deviating arguments
Authors: Candan T. , Dahiya R. 
Published: January 2013

Abstract
In this work, we consider the existence of nonoscillatory solutions of variable coefficient higher order linear neutral differential equations with distributed deviating arguments. We use the Banach contraction principle to obtain new sufficient conditions, which are weaker than those known, for the existence of nonoscillatory solutions.
Overridingness, Moral
Authors: Gert Joshua 
Published: January 2013

Abstract

Morality is one normative domain among many. That is, not only can we assess actions as morally right or wrong, or as morally good or bad, but we can also assess them as legal or illegal, prudent or imprudent, or as prohibited or required by the rules of etiquette. It is quite obvious that these assessments need not always favor and disfavor precisely the same actions. For example, it might be morally required in some cases to perform an action that is prohibited by law, or – some might suggest – it might be imprudent to do something morally good. The thesis of moral overridingness is the thesis that moral verdicts are always in some sense supreme whenever they come into conflict with the verdicts of a distinct normative domain. This general thesis can be understood in a number of ways. To begin with, we need to offer an interpretation of the claim that one verdict overrides another. One might interpret this claim as entailing that, in conflicts of verdicts, it is
irrational
to go against the moral verdict (
see
Rationality). Or, one might interpret it as the claim that the totality of practical reasons, taken together, always uniquely favors acting in line with a moral verdict, even though it may not always be irrational to act in ways that are not uniquely favored in this way (
see
Reasons; Satisficing). In making the overridingness thesis clear, one also needs to specify
which
verdicts are relevant. Very often, the thesis is understood as restricted to claims about conflicts of
requirements
. This is an important restriction, since morality can yield the verdict that an action would be morally
good
without being morally
required
. For example, in many views, we are not morally required to volunteer our free time doing charitable activity. In such views, morality favors such action, but does not require it (
see
Supererogation). On a common interpretation of the overridingness thesis, the fact that morality favors such action does not imply that there would be anything problematic in deciding against such a morally good action, and performing some other action instead: say, an action that would do a better job of promoting one's own interests.
Sustainability
Authors: Attfield Robin 
Published: January 2013

AbstractThe concept of sustainability, like the related concept of sustainable development, has come to be used in multiple ways. This results from the endorsement of sustainable development, in face of global environmental problems and problems of poverty and underdevelopment, by the World Commission on Environment and Development (WCED) in the “Brundtland Report” (WCED 1987) and its subsequent adoption by more than 180 countries at the Rio Summit in 1992. Governments, corporations, their advisors and think‐tanks then had strong incentives to reinterpret or redefine this policy to which all were by now committed; hence the multiple and divergent uses of “sustainability.” Yet addressing the original problems remains more crucial than ever.
Corporal Punishment
Authors: Benatar David 
Published: January 2013

AbstractAlthough philosophers have written a great deal about whether punishment can ever be justified (seePunishment), that discussion is rightly bracketed when asking whether particular forms of punishment can be justified. This is not because the latter question is theoretically independent of the former question. Obviously, if punishment cannot be justified then neither can corporal punishment. Similarly, if punishment can sometimes be justified, it would help to know how it is justified if we are then to determine whether corporal punishment is acceptable. However, as a practical matter, if we were to await the resolution of the more foundational question before asking whether specific forms of punishment can be justified, we would never consider the acceptability of specific forms of punishment.
Criminal Justice Ethics
Authors: Reiman Jeffrey 
Published: January 2013

AbstractCriminal justice ethics is a subdiscipline of ethics that explores the nature, justification, and practice of criminal justice. It investigates the role of the criminal law within society (seeCriminal Law), the moral limits on what behaviors can be appropriately criminalized, the proper governmental response to criminal activities, and the unique ethical issues facing agents of the criminal justice system: legislators, police, prosecutors, judges, prison wardens and guards, parole and probation officers. These issues are tied together by the fact that they all involve the use of coercion, and thus raise profound questions about individual liberty and social authority (seeAuthority).
Civilian Immunity
Authors: Primoratz Igor 
Published: January 2013

AbstractThe idea that warfare ought to be subject to restraint is probably as old as war itself. The restraints morality and law place on war fall under two heads: those concerning resort to war (jus ad bellum) and those concerning the ways war is fought (jus in bello). One of the rules comprisingjus in bello– on most accounts, its centerpiece – is that of discrimination (or, in legal parlance, distinction). It enjoins us to discriminate between legitimate and illegitimate targets in war and to restrict our attacks to the former. That means, roughly, that our acts of war may be directed only at enemy soldiers or combatants and military facilities, and that we must not attack civilians or noncombatants. Civilians (noncombatants) enjoy immunity against deliberately inflicted harm to life, limb, or property.
War Crimes
Authors: May Larry 
Published: January 2013

AbstractWar crimes are a species of international crimes (seeInternational Criminal Justice) committed during armed conflict. The other major international crimes are crimes against humanity (seeCrimes Against Humanity), genocide (seeGenocide), and the crime of aggression (Statute of the International Criminal Court: Art. 5). While the term “war crime” is sometimes popularly used to cover all international crimes committed during war (seeWar), it is properly restricted in international law to violations of the principle requiring that soldiers act humanely. Soldiers are supposed to act with mercy (seeMercy) and compassion, even as these same soldiers are allowed to kill enemy soldiers. The apparent paradox of this remark illustrates the conceptual problems of normatively grounding the idea of war crimes, and of international prosecutions for such crimes.
Bergson, Henri
Authors: Ansell‐Pearson Keith 
Published: January 2013

AbstractHenri Bergson's (1859–1941) most sustained contribution to ethics is to be found in his final main book,The Two Sources of Morality and Religion(TSMR), which was published in 1932. Prior to the appearance of this work his commentators could only speculate on the “ethical implications” of his philosophy, linking his critique of scientific and psychological determinism and championing of unforeseeable novelty in the world – as espoused in his three previous main books,Time and Free Will(1889),Matter and Memory(1896), andCreative Evolution(1907) – with the concerns of ethics, especially questions of freedom (for one such attempt, see the study by Sait 1914). As one commentator notes, for several years Bergson had expressed doubts whether he would publish a book on ethics or morals simply because he doubted whether he could attain conclusions as demonstrable as those of his other texts. Philosophy proceeds by a definite method and can legitimately claim as much objectivity as the positive sciences, though of a different kind (Lacey 1989: 197). Bergson was, therefore, in search of an approach to ethics that would satisfy the ambition he had set for philosophy: that of achieving precision (Bergson 1965: 11). In what follows I will outline the contribution to ethics Bergson makes in the opening chapter of the TSMR and focus on illuminating the two sources morality has in his account. At the end of the opening chapter of the book Bergson states that all morality is in essence “biological,” though he does say we need to give the word “biology” the wide meaning it should have. Bergson is often construed, along with Nietzsche, as an irrationalist and a philosopher of life (seeNietzsche, Friedrich). However, what Bergson criticizes is the idea of self‐sufficient reason and so he is better seen as being anti‐intellectualist rather than advocating irrationalism (William James [1909] said it was Bergson who liberated him from intellectualism;seeJames, William). This has two main aspects: first, a rejection of the view that we can be moved by ideas or intelligence alone; and, second, criticism of Kant's conception of an ethics of duty (seeKant, Immanuel).
Euthyphro Dilemma
Authors: Miller Christian 
Published: January 2013

AbstractThe Euthyphro dilemma is named after a particular exchange between Socrates and Euthyphro in Plato's dialogueEuthyphro. In a famous passage, Socrates asks, “Is the pious loved by the gods because it is pious, or is it pious because it is loved by the gods?” (Plato 1981: 10a), and proceeds to advance arguments which clearly favor the first of these two options (seePlato). The primary interest in the Euthyphro dilemma over the years, however, has concerned the relationship between God and morality in the monotheistic religious tradition, where God is taken to be omnipotent, omniscient, and omnibenevolent, having created the universe initially and still actively involved in it today. But as we will see at the end of this essay, there has also been a recent surge of interest in a version of the dilemma which applies to so‐called response‐dependent accounts of normative properties in metaethics.
Psychopathy
Authors: Maibom Heidi L. 
Published: January 2013

AbstractPsychopathy is a serious, life‐long, largely untreatable disorder characterized by abnormal emotions, impulsivity, irresponsibility, problems learning from experience, and antisocial behavior. Psychopaths experience little guilt, remorse, or empathy (Hare 2004;seeGuilt; Empathy). They have also been thought to lack the ability to love and to feel shame (Cleckley 1982). Psychopathy is of particular interest to moral philosophers because the deficits that psychopaths suffer from are primarily moral: they are manipulative, exploitative, pathological liars, utterly egocentric, etc. On a conservative measure, one‐third of the deficits characteristic of psychopathy is moral, or morally relevant. And, whereas the prevalence of psychopathy is around 1 percent in the general population, roughly 20 percent of prison inmates are psychopaths (Blair et al. 2005; Hare 1993). Psychopaths in the community, who have never been convicted of any crime, nevertheless report engaging regularly in immoral and illegal activities (Ishikawa et al. 2001). This strongly suggests that psychopaths are immoral or amoral.
Psychiatric Ethics
Authors: McMillan John 
Published: January 2013

AbstractAs is the case for other medical specialties, many ethical issues in psychiatry are generic problems for medicine. Issues such as research on human subjects, consent to treatment, and the basis of professional obligations are generally relevant to medicine and are discussed under other headings (seeBioethics; Consent; Research Ethics). However, there are some other ethical issues that, although common to other areas in medicine, are particularly relevant to psychiatry. The creation of new diseases in order to create a market for pharmaceuticals is a key challenge to psychiatry, but one that is also discussed under other headings (seeDisease Mongering; Psychopharmacology).
Quotidian Ethics
Authors: Benatar David 
Published: January 2013

Abstract
Quotidian ethics, or “everyday ethics,” as it is sometimes known, is a branch of applied ethics devoted to studying the moral questions, problems, and issues that arise in the daily lives of ordinary people. These include such questions as: Which, if any, jokes is it wrong to tell? May I gossip with my friends? Do the environmental effects and other dangers of cars make it wrong to drive? Is it wrong to keep animals as pets? If it is not wrong, how should I treat my companion animals? Is it morally permissible to live a lavish or luxurious lifestyle? When should I forgive those who have wronged me? Is jealousy ever appropriate?
Buck‐Passing Accounts
Authors: Olson Jonas 
Published: January 2013

AbstractIt is a common view that there is an intimate tie betweenevaluativeproperties like goodness, badness, and betterness andappropriate responsesto bearers of such properties. For instance, if an object is good there arereasonsto favor it, or as some say, a favorable response would befitting. Similarly, many people take there to be a close tie betweendeonticproperties like rightness and wrongness and appropriate responses: if an action is wrong, there are reasons to respond disfavorably, e.g., to blame agents for performing actions of that type. According tobuck‐passingaccounts (henceforth BPA), evaluative and deontic properties do not themselves provide reasons for responses. Rather, reasons to respond in various ways are provided by good‐, bad‐, better‐, right‐, and wrong‐makingproperties.
Egoism
Authors: Fumerton Richard 
Published: January 2013

Abstract

There are a number of important and potentially interrelated theses associated with the concept of egoistic action. In particular, it is useful to distinguish the psychological claim that everyone always does act egoistically (sometimes called psychological egoism), claims about the
morality
of acting egoistically, and claims about the
rationality
of acting egoistically. As we shall see, the nature of the connection, if any, between these views is a matter of considerable controversy. At least some philosophers will argue that if it is virtually a law of human nature that people act egoistically, then questions about whether they rationally or morally ought to act that way are moot. Claims about what one rationally ought to do might be distinct from claims about what one morally ought to do, but, again, as we shall see, there may be a serious price to be paid by the philosopher who lets morality and rationality come apart. But before we try to say more about any of these issues we must define more clearly the critical concept of acting egoistically.
Perfectionism
Authors: Kraut Richard 
Published: January 2013

Abstract“Perfectionism” is a term that began to gain currency among Anglo‐American philosophers during the 1970s, due, in large part, to its use by John Rawls (1921–2002) inA Theory of Justiceto designate one of the moral and political theories to which he was opposed (seeRawls, John). Although his principal target in that work is not perfectionism but utilitarianism (seeConsequentialism; Utilitarianism), he takes both to share a single structure: each proposes a theory of what is good, and each defines moral rightness as the maximization of that good (which, in order to avoid circularity, is identified independently of rightness). Utilitarianism, as he defines it, holds that an action is right if and only if it maximizes the satisfaction of rational desires. Perfectionism similarly proposes that right actions maximize something, namely “the realization of human excellence in the various forms of culture” (1999: 22).