bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the viability of unsupervised T-cell receptor sequence clustering for epitope preference
Authors: Meysman Pieter , De Neuter Nicolas , Gielis Sofie , Bui Thi Danh , Ogunjimi Benson , Laukens Kris 
Published: September 2018

Abstract

Motivation
The T-cell receptor (TCR) is responsible for recognizing epitopes presented on cell surfaces. Linking TCR sequences to their ability to target specific epitopes is currently an unsolved problem, yet one of great interest. Indeed, it is currently unknown how dissimilar TCR sequences can be before they no longer bind the same epitope. This question is confounded by the fact that there are many ways to define the similarity between two TCR sequences. Here we investigate both issues in the context of TCR sequence unsupervised clustering.

Results
We provide an overview of the performance of various distance metrics on two large independent datasets with 412 and 2835 TCR sequences respectively. Our results confirm the presence of structural distinct TCR groups that target identical epitopes. In addition, we put forward several recommendations to perform unsupervised T-cell receptor sequence clustering.

Availability and implementation
Source code implemented in Python 3 available at https://github.com/pmeysman/TCRclusteringPaper.

Supplementary information
Supplementary data are available at Bioinformatics online.
iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators
Authors: Feng Chao-Qin , Zhang Zhao-Yue , Zhu Xiao-Juan , Lin Yan , Chen Wei , Tang Hua , Lin Hao 
Published: September 2018

Abstract

Motivation
Transcription termination is an important regulatory step of gene expression. If there is no terminator in gene, transcription could not stop, which will result in abnormal gene expression. Detecting such terminators can determine the operon structure in bacterial organisms and improve genome annotation. Thus, accurate identification of transcriptional terminators is essential and extremely important in the research of transcription regulations.

Results
In this study, we developed a new predictor called ‘iTerm-PseKNC’ based on support vector machine to identify transcription terminators. The binomial distribution approach was used to pick out the optimal feature subset derived from pseudo k-tuple nucleotide composition (PseKNC). The 5-fold cross-validation test results showed that our proposed method achieved an accuracy of 95%. To further evaluate the generalization ability of ‘iTerm-PseKNC’, the model was examined on independent datasets which are experimentally confirmed Rho-independent terminators in Escherichia coli and Bacillus subtilis genomes. As a result, all the terminators in E. coli and 87.5% of the terminators in B. subtilis were correctly identified, suggesting that the proposed model could become a powerful tool for bacterial terminator recognition.

Availability and implementation
For the convenience of most of wet-experimental researchers, the web-server for ‘iTerm-PseKNC’ was established at http://lin-group.cn/server/iTerm-PseKNC/, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
Error Correction by Structural Simplicity: Correcting Samplable Additive Errors
Authors: Yasunaga Kenji 
Published: September 2018

Abstract
This paper explores the possibilities and limitations of error correction by the structural simplicity of error mechanisms. Specifically, we consider channel models, called samplable additive channels, in which (i) errors are efficiently sampled without the knowledge of the coding scheme or the transmitted codeword; (ii) the entropy of the error distribution is bounded; and (iii) the number of errors introduced by the channel is unbounded. For the channels, several negative and positive results are provided. Assuming the existence of one-way functions, there are samplable additive errors of entropy nε for ε∈(0,1) that are pseudorandom, and thus not correctable by efficient coding schemes. It is shown that there is an oracle algorithm that induces a samplable distribution over {0,1}n of entropy m=ω(logn) that is not pseudorandom, but is uncorrectable by efficient schemes of rate less than 1−m/n−o(1). The results indicate that restricting error mechanisms to be efficiently samplable and not pseudorandom is insufficient for error correction. As positive results, some conditions are provided under which efficient error correction is possible.
Stressors and Resources Related to Medication Management: Associations With Spousal Caregivers’ Role Overload
Authors: Polenick Courtney A , Stanz Sarah D , Leggett Amanda N , Maust Donovan T , Hodgson Nancy A , Kales Helen C 
Published: September 2018

Abstract

Background and Objectives
Managing medications can be stressful for spousal caregivers, but little is known about particular aspects of medication management that are most consequential for caregiving outcomes. We examined care stressors and resources related to medication management, their associations with role overload among spousal caregivers, and whether these links vary by care recipients’ number of chronic health conditions and dementia status.

Research Design and Methods
This cross-sectional study included 377 spousal caregivers of adults aged 65 and older from the 2011 National Health and Aging Trends Study and National Study of Caregiving. Linear regressions were estimated to evaluate how medication-related stressors (ordering medication, keeping track of medications, giving injections) and resources (medication reminder systems, shared medication management within the spousal dyad) are associated with caregivers’ role overload. Care recipients’ number of chronic health conditions and dementia status were considered as moderators. Models controlled for caregivers’ sociodemographic characteristics, chronic health conditions, and other care tasks.

Results
Caregivers who administered injections reported more role overload, whereas those who worked with care recipients to jointly manage medications reported less role overload. Keeping track of medications was linked to caregivers’ greater role overload when care recipients had 5 or more chronic health conditions. Finally, care recipients’ use of medication reminder systems was linked to less role overload for caregivers of a partner with dementia.

Discussion and Implications
Devising strategies to assist spousal caregivers in the more onerous components of medication management and promote resources that mitigate medication-related stress may improve caregiver well-being.
Bevacizumab at first recurrence after standard radio-chemotherapy is associated with improved overall survival in glioblastoma patients with large tumor burden
Authors: Nguyen Huy Tram , Nguyen Nhung , Liu Liang Yen , Dovek Laura , Lenchner Daniel , Harris Robert , Ozer Byram , Ravelo Arliene , Sommer Nicolas , Sim Myung Shin , Elashoff Robert , Green Richard , Nghiemphu Phioanh Leia , Cloughesy Timothy Francis , Ellingson Benjamin , Lai Albert 
Published: September 2018

Abstract

Background
Since its approval for use in recurrent glioblastoma (GBM), the survival benefit of bevacizumab (Bev) remains to be demonstrated. To address this issue, we retrospectively examined survival from first recurrence in patients treated with Bev, lomustine (CCNU), or Bev/CCNU.

Methods
We identified 168 primary GBM patients diagnosed at UCLA and Kaiser Permanente LA who received upfront radio-chemotherapy, followed by Bev and/or CCNU at first recurrence. Three patient groups, contemporaneously diagnosed from 2009 through 2015, were identified: (1) patients treated with Bev alone (n = 49), (2) CCNU alone (CCNU 09-15) (n = 36), and (3) Bev/CCNU (n = 53). Another CCNU control group (n = 30) diagnosed from 2001 through 2004 (CCNU 01-04) was also derived. We measured tumor size at first recurrence treatment initiation, using bidimensional (2D) and volumetric (3D) techniques, and analyzed overall survival (OS) from first recurrence.

Results
Among the entire cohort, larger tumor size at first recurrence was associated with poorer survival. The CCNU 01-04 group had similar tumor size as the Bev arms and low Bev crossover (7%). Treatment with Bev was associated with improved survival in patients with large tumor 2D measurements: Median OS for Bev and Bev/CCNU groups were 6.71 mo (n = 27) and 6.97 mo (n = 36) vs 4.03 mo (n = 10) in CCNU 01-04. Analysis by 3D measurement yielded similar results. Interestingly, the CCNU 09-15 group showed the highest survival, likely due to smaller tumor size and crossover to Bev (69%).

Conclusion
Survival advantage from Bev treatment was observed only among patients with large tumor burden as determined by either 2D or 3D measurement.
What Was the Holocaust?
Authors: Mastroianni George R. 
Published: September 2018

Abstract
Chapter 1 provides a brief historical summary of the Holocaust, beginning with relevant events in Germany in the years leading up to the initiation of mass killing that accompanied the invasion of Russia in June 1941. While Auschwitz dominates the popular conception of what the Holocaust was, much of the killing was accomplished not with Zyklon B but with bullets and engine exhaust gas, and much of it occurred during the relatively short interval between early 1942 and mid-1943. The Holocaust was a complicated enterprise distributed over time and space that was “more” than it is in the popular mind in almost every way: more than Jews, more than Auschwitz, more than the Gestapo and Schutzstaffel (SS), more than Nazis, more even than Germans.
The Holocaust
Authors: Mastroianni George R. 
Published: September 2018

Abstract
Chapter 2 traces the history of psychological thinking about Hitler, the Nazi accession to power, and, eventually, the Holocaust. Explanations of these phenomena took several forms. Some focused on putative psychopathology, either of Nazi leaders or Germans as a whole; some focused on particular German cultural and social adaptations that were thought to produce particularly obedient and authoritarian individuals; still others emphasized the interaction of some or all of these factors with long-term, large-scale historical and cultural processes. Gordon Allport saw prejudice and racism as central to understanding the Holocaust. After Stanley Milgram’s studies appeared in the early 1960s, genocidal behavior was largely seen by psychologists as an obedient response to situational pressures. Recent decades have brought greater diversity in social psychological explanations of perpetrator behavior in the Holocaust and in genocide more generally.
Personality
Authors: Mastroianni George R. 
Published: September 2018

Abstract
Chapter 5 considers the role of personality in the Holocaust. The idea that psychopathology or insanity characterized the individual leaders of the Third Reich or the German population was simply not supported by the evidence. Perhaps these leaders, or even the German population as a whole, were not characterized by a psychological disorder but were nevertheless different from other people in some important way. The authoritarian personality, a construct derived from Freudian thought, was suggested as a possible explanation. German child-rearing practices were implicated in the production of this personality, which was thought to be related to perpetrator behavior. Defining and measuring the authoritarian personality has posed some challenges, and researchers have not convincingly tied authoritarian traits to perpetrator behavior. The concept of “national character,” a kind of societal-level personality, has similarly been difficult to define and connect to perpetrator behavior. Personality approaches have also been applied to the study of rescuers.
Cognition and Memory
Authors: Mastroianni George R. 
Published: September 2018

Abstract
Chapter 7 treats human thinking and remembering as adaptive processes employing shortcuts that sometimes favor efficiency over accuracy. Humans (and animals) achieve adaptive success partly by categorizing and classifying the myriad stimuli to which they are exposed and developing patterns of differential response to the various categories. While this tendency to categorical thinking can promote adaptive success under some circumstances, it can also lead to pernicious consequences such as stereotyping, prejudice, and racism. Such thinking was promoted and encouraged by the Nazis. Memory is also characterized by shortcuts: we really reconstruct our past experiences more than we recall them. Humans are susceptible to many different kinds of memory errors and failures. Because so much of what we know about the Holocaust is derived from memories, understanding how memory works is vital to making sense of this crucial source of information.
The Psychology of the Holocaust in Perspective
Authors: Mastroianni George R. 
Published: September 2018

Abstract
Chapter 12 attempts to address the questions many of us ask about the behavior of perpetrators and others during the Holocaust in light of the material presented in the preceding eleven chapters. Is the potential for genocidal behavior universal? Could anyone become a mass murderer under the right circumstances? Is the potential for genocide greater in more modern societies? Of Mind and Murder is not intended to offer definitive answers to any of these questions but to hopefully summarize and contextualize much previous work on the psychology of the Holocaust in ways that might stimulate fruitful discussions of these and other important questions.
Jury Selection in the Post-Batson Era
Authors: O’Brien Barbara , Grosso Catherine M. 
Published: September 2018

Abstract
In Batson v. Kentucky (1986), the US Supreme Court sought to eradicate racial discrimination in jury selection by prohibiting the exercise of peremptory strikes based on race. This chapter reviews the evidence that Batson has failed to protect jurors from race-based strikes and the reasons for this failure. The test for establishing racial discrimination set forth in Batson suffers from design flaws that make its enforcement difficult given common psychological mechanisms at work in the decision-making process and which may be exacerbated by the jury selection process itself. Batson seeks to remedy only intentional discrimination. Moreover, its capacity to ensure diverse juries is limited by the stages of jury selection that precede its application. Enforcing Batson effectively is critical to the system’s integrity, but no simple solutions exist to remedy the stubborn persistence of racial bias in jury selection. All of this suggests that measures are needed to strengthen Batson’s protections.
In the Aftermath of Ferguson
Authors: Cole Lindsey M. 
Published: September 2018

Abstract
This chapter examines the impact of police on juror perceptions and decision-making, both before and after Ferguson. It first reviews the existing literature describing the role of police in court, including police as witnesses and the effect of police and court legitimacy on jurors and jury deliberation. Next, it describes the events in Ferguson and the resulting national attention and rise of social movements and then discusses the effects of Ferguson and social media coverage on changing public attitudes toward and perceived legitimacy of the police. The chapter also explores how common police practices, such as testilying and the blue wall of silence, might further impact juror trust in police and legal institutions in the aftermath of Ferguson. The chapter closes with several policy recommendations and future research directions to address Ferguson’s impact on the courts and juries.
The Impact of Legally Relevant Media Exposure on Criminal Juror Decision-Making
Authors: Groscup Jennifer L. 
Published: September 2018

Abstract
Exposure to various forms of media can potentially impact decision-making by jurors in criminal trials. Cases like the highly publicized Casey Anthony trial, in which jurors’ media exposure might have affected the verdict, highlight the importance of understanding what messages jurors receive from the media and how those messages might influence their perceptions of trial participants and evidence. This chapter first explores research on the content of legally relevant news media, reality television, and scripted television dramas to better understand the messages the media might be delivering. Next, it reviews research suggesting how various media sources influence the development of legally relevant attitudes and, in turn, juror decision-making. The chapter then investigates the media’s direct influence on juror decision-making, focusing particularly on the CSI Effect. Finally, it discusses recommendations for jury system reform that might decrease media influence as well as future research directions.
Neuroscience and Jury Decision-Making
Authors: Hunter Shelby , Schweitzer N. J. , Ware Jillian M. 
Published: September 2018

Abstract
This chapter examines the emerging use of neuroscience evidence in criminal trials and its influence on jury decision-making. It begins with a look at the prevalence of neuroscience expert evidence in criminal cases, finding a rapid increase in its use both in and outside of the United States. It then looks at the broader research on how the lay public is persuaded by neuroscience-derived information, followed by an examination of the relatively young literature on the specific (and often paradoxical) impact of neuroscience and neuroimagery on jurors’ judgments of criminal defendants. The chapter concludes with some caveats about the current state of neuroscience with respect to the legal system and some recommendations for future research.
Public Health and Law
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
This chapter introduces and defines basic concepts used throughout the book and within the fields of public health and law. The chapter explores the focus on population-level data, rather than individual-level information, as public health’s primary lens. It defines health disparities, the social determinants of health, and the three levels of prevention to exemplify public health’s broad perspective, which looks beyond healthcare to more systemic causes of illness and disease. It also defines law and its role in shaping behaviors and environments at all levels—federal, state, local, tribal, and international—and introduces examples for how law may be used to impact the public’s health.
Ethics in Transdisciplinary Practice
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
This chapter defines the three basic meanings of ethics: as a way of defining the “Good,” as a set of basic principles that emerge from ethical deliberation, and as a way of establishing standards to interact with professionals outside a given field. The chapter explores professional ethical codes from law, medicine, and public health and identifies ways in which ethics are supported or enforced through law.
Constitutional Limitations
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
This chapter introduces the 14th Amendment’s Equal Protection Clause by discussing its history, judicials interpretations, and application to public health issues. It reviews the fundamental equal protection doctrine—similarly situation person must not receive disparate treatment. It also describes the definitions and usage of suspect and quasi-suspect classes and the levels of scrutiny courts may apply to while reviewing equal protection claims. Using cases such as Craig v. Boren and City of New York v. New St. Mark’s Baths to illustrate, the chapter also examines the application of the equal protection clause to public health issues. The chapter highlights factors that have historically led to equal protection violations by public health officials.
Constitutional Limitations
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
This chapter reviews the impact of the First and Second Amendments to the US Constitution on the exercise of the police power for public health. The chapter reviews how the courts have applied the First Amendment’s Free Speech Clause to regulate commercial speech and identifies the standards courts use to assess whether public health laws unconstitutionally burden religious practice. Finally, the chapter explains the limitations imposed on gun control measures by the Second Amendment and the interplay of law and politics in the regulation of firearms.
Strategic Considerations in Creating a Legal Proposal
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
Chapter 15 reviews the importance of strategy and research in the formation and drafting of a proposed public health law, including assessing potential support and opposition. The chapter dictates an iterative process whereby the proposal’s drafter should first seek to understand his or her own proposal and its goals, explore the values-and practical-based interests behind why anyone would care about the legal proposal, identify groups of people and individuals who sympathize with or oppose the interests or burdens underlying all aspects of the proposal, research the history and positions of these groups, and anticipate challenges to the proposed enactment and implementation.
How to Write a Law
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
This chapter defines the process of drafting a law, beginning with understanding the goal of the law, then moving through the steps of incorporating the existing science and law, capturing the goal, the rules of conduct, and intervention in organized language and structure, which differs depending on whether the law is a regulation or a statute, and soliciting expert and stakeholder feedback. The chapter also covers technical drafting issues, such as legal definitions, cross-references, use of consistent terminology, and the use and placement of modifiers.
Models of Regulation
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
This chapter defines regulation and identifies its three generic elements: a standard of behavior, means of monitoring whether the standard is being practiced, and means of incentivizing those who have not adopted the behavior to do so. The chapter introduces the various actors within and outside of government who may practice the elements of regulation and reviews the theory of responsive regulation and enforcement. The chapter ends with an exploration of the challenges to effective regulation.
Defending Lawsuits
Authors: Burris Scott , Berman Micah L. , Penn, and Matthew , Holiday Tara Ramanathan 
Published: September 2018

Abstract
Chapter 20 explores the strategic reasons why entities may challenge public health laws, and uses the R.J. Reynolds Tobacco Company v. FDA case to walk through the steps of a legal challenge to a public health law. The chapter also identifies the attorneys involved in defending public health laws on behalf of local, state, and federal government entities and explains how legal technical assistance from public health organizations can support their efforts. Finally, the chapter defines the role of amicus curiae briefs and how they may effectively contribute to the defense of public health laws and regulations.