bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial distribution of ventricular late potentials assessed by the newly developed signal‐averaged vector‐projected 187‐channel electrocardiogram in patients with old myocardial infarction
Authors: Futagawa Keisuke , Shoda Morio , Nakai Kenji , Kasanuki Hiroshi , Hagiwara Nobuhisa 
Published: December 2012

AbstractRisk stratification of lethal arrhythmias is important for the management of ischemic heart disease. Recently, we developed a novel 187‐channel signal‐averaged vector‐projected high‐resolution electrocardiograph (187‐ch SAVP‐ECG) with a Mason–Likar lead system with 10 electrodes. The purpose of this study was to examine the feasibility of a noninvasive evaluation of the spatial distribution of high‐frequency late potentials (HFLPs) in patients with myocardial infarction (MI) by using the 187‐ch SAVP‐ECG. Sixty‐four MI patients (7 women and 57 men), between the age of 39 and 84 years (mean 67.7±9.7 years), with positive ventricular late potentials defined by an X, Y, Z‐lead ECG were studied. The integrated ventricular 187‐ch SAVP‐ECG could identify the area of HFLPs that was projected virtually by mathematically calculated 187 electrograms on the body surface in all patients, and differentiate the locations of MI. The 187‐ch SAVP‐ECG can be a practical and noninvasive examination tool for identifying the location of infarction areas and possible arrhythmogenic substrates with slow conduction properties in patients with MI.
Symptom Validity Test Performance in the Huntington Disease Clinic
Authors: Sieck Barbara C. , Smith Megan M. , Duff Kevin , Paulsen Jane S. , Beglinger Leigh J. 
Published: December 2012

Abstract
Symptom validity tests (SVTs) are often used in neuropsychological assessment; however, recent studies indicate that cognitive impairment/dementia may contribute to failing scores on some effort tests. The purpose of this study was to characterize how individuals with Huntington disease (HD) perform on three SVTs and to examine the relationship between SVT performance and demographic and clinical variables. Results indicate that while the majority of HD patients passed the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) Effort Index (EI; 82% of n = 121) and the Test of Memory Malingering (92% of n = 36), failure of these SVTs was associated with poorer cognitive and adaptive functioning, and greater motor impairment. Results showed that less than one-third passed the RBANS Effort Scale (ES; 30% of n = 43) and few clinical and demographic variables were correlated with this SVT performance. Although some SVTs may be better suited to HD, cognitive ability should be considered when evaluating effort in HD.
SRmapper: a fast and sensitive genome-hashing alignment tool
Authors: Gontarz Paul M. , Berger Jennifer , Wong Chung F. 
Published: December 2012

Abstract
Summary: Modern sequencing instruments have the capability to produce millions of short reads every day. The large number of reads produced in conjunction with variations between reads and reference genomic sequences caused both by legitimate differences, such as single-nucleotide polymorphisms and insertions/deletions (indels), and by sequencer errors make alignment a difficult and computationally expensive task, and many reads cannot be aligned. Here, we introduce a new alignment tool, SRmapper, which in tests using real data can align 10s of billions of base pairs from short reads to the human genome per computer processor day. SRmapper tolerates a higher number of mismatches than current programs based on Burrows–Wheeler transform and finds about the same number of alignments in 2–8× less time depending on read length (with higher performance gain for longer read length). The current version of SRmapper aligns both single and pair-end reads in base space fastq format and outputs alignments in Sequence Alignment/Map format. SRmapper uses a probabilistic approach to set a default number of mismatches allowed and determines alignment quality. SRmapper’s memory footprint (∼2.5 GB) is small enough that it can be run on a computer with 4 GB of random access memory for a genome the size of a human. Finally, SRmapper is designed so that its function can be extended to finding small indels as well as long deletions and chromosomal translocations in future versions.
Availability: http://www.umsl.edu/∼wongch/software.html.
Contact: wongch@umsl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
Authors: McDavid Andrew , Finak Greg , Chattopadyay Pratip K. , Dominguez Maria , Lamoreaux Laurie , Ma Steven S. , Roederer Mario , Gottardo Raphael 
Published: December 2012

Abstract
Motivation: Cell populations are never truly homogeneous; individual cells exist in biochemical states that define functional differences between them. New technology based on microfluidic arrays combined with multiplexed quantitative polymerase chain reactions now enables high-throughput single-cell gene expression measurement, allowing assessment of cellular heterogeneity. However, few analytic tools have been developed specifically for the statistical and analytical challenges of single-cell quantitative polymerase chain reactions data.
Results: We present a statistical framework for the exploration, quality control and analysis of single-cell gene expression data from microfluidic arrays. We assess accuracy and within-sample heterogeneity of single-cell expression and develop quality control criteria to filter unreliable cell measurements. We propose a statistical model accounting for the fact that genes at the single-cell level can be on (and a continuous expression measure is recorded) or dichotomously off (and the recorded expression is zero). Based on this model, we derive a combined likelihood ratio test for differential expression that incorporates both the discrete and continuous components. Using an experiment that examines treatment-specific changes in expression, we show that this combined test is more powerful than either the continuous or dichotomous component in isolation, or a t-test on the zero-inflated data. Although developed for measurements from a specific platform (Fluidigm), these tools are generalizable to other multi-parametric measures over large numbers of events.
Availability: All results presented here were obtained using the SingleCellAssay R package available on GitHub (http://github.com/RGLab/SingleCellAssay).
Contact: rgottard@fhcrc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma
Authors: Chen Jia-Shing , Hung Wei-Shiang , Chan Hsiang-Han , Tsai Shaw-Jenq , Sun H. Sunny 
Published: December 2012

Abstract
Motivation: Cancer development is a complex and heterogeneous process. It is estimated that 5–10% of human genes probably contribute to oncogenesis, whereas current experimentally validated cancer genes only cover 1% of the human genome. Thus hundreds of cancer genes may still remain to be identified. To search for new genes that play roles in carcinogenesis and facilitate cancer research, we developed a systematic workflow to use information saved in a previously established tumor-associated gene (TAG) database.
Results: By exploiting the information of conserved protein domains from the TAG, we identified 183 potential new TAGs. As a proof-of-concept, one predicted oncogene, fyn-related kinase (FRK), which shows an aberrant digital expression pattern in liver cancer cells, was selected for further investigation. Using 68 paired hepatocellular carcinoma samples, we found that FRK was up-regulated in 52% of cases (P &lt; 0.001). Tumorigenic assays performed in Hep3B and HepG2 cell lines revealed a significant correlation between the level of FRK expression and invasiveness, suggesting that FRK is a positive regulator of invasiveness in liver cancer cells.
Conclusion: These findings implied that FRK is a multitalented signal transduction molecule that produces diverse biological responses in different cell types in various microenvironments. In addition, our data demonstrated the accuracy of computational prediction and suggested that other predicted TAGs can be potential targets for future cancer research.
Availability: The TAG database is available online at the Bioinformatics Center website: http://www.binfo.ncku.edu.tw/TAG/.
Contact: hssun@mail.ncku.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling
Authors: Järvstråt Linnea , Johansson Mikael , Gullberg Urban , Nilsson Björn 
Published: December 2012

Abstract
Summary: Graphical Gaussian models (GGMs) are a promising approach to identify gene regulatory networks. Such models can be robustly inferred by solving the sparse inverse covariance selection (SICS) problem. With the high dimensionality of genomics data, fast methods capable of solving large instances of SICS are needed.
We developed a novel network modeling tool, Ultranet, that solves the SICS problem with significantly improved efficiency. Ultranet combines a range of mathematical and programmatical techniques, exploits the structure of the SICS problem and enables computation of genome-scale GGMs without compromising analytic accuracy.
Availability and implementation: Ultranet is implemented in C++ and available at www.broadinstitute.org/ultranet.
Contact: bnilsson@broadinstitute.org or bjorn.nilsson@med.lu.se
Supplementary information: Supplementary data are available at Bioinformatics online.
OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets
Authors: Maguire Eamonn , González-Beltrán Alejandra , Whetzel Patricia L. , Sansone Susanna-Assunta , Rocca-Serra Philippe 
Published: December 2012

Abstract
Motivation: Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players.
Results: OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process.
Availability: OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton.
Contact: isatools@googlegroups.com
Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities
Authors: Piro Rosario M. , Molineris Ivan , Di Cunto Ferdinando , Eils Roland , König Rainer 
Published: December 2012

Abstract
Motivation: The computational evaluation of candidate genes for hereditary disorders is a non-trivial task. Several excellent methods for disease-gene prediction have been developed in the past 2 decades, exploiting widely differing data sources to infer disease-relevant functional relationships between candidate genes and disorders. We have shown recently that spatially mapped, i.e. 3D, gene expression data from the mouse brain can be successfully used to prioritize candidate genes for human Mendelian disorders of the central nervous system.
Results: We improved our previous work 2-fold: (i) we demonstrate that condition-independent transcription factor binding affinities of the candidate genes’ promoters are relevant for disease-gene prediction and can be integrated with our previous approach to significantly enhance its predictive power; and (ii) we define a novel similarity measure—termed Relative Intensity Overlap—for both 3D gene expression patterns and binding affinity profiles that better exploits their disease-relevant information content. Finally, we present novel disease-gene predictions for eight loci associated with different syndromes of unknown molecular basis that are characterized by mental retardation.
Contact: r.piro@dkfz.de or rmpiro@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
The Rationality of Being Guided by Rules
Authors: McClennen Edward F. 
Published: December 2012

AbstractThis article addresses a fundamental dilemma facing the claim that it is rational to be guided by rules. Either the practical verdict issued by a rule is the same as that favored by the balance of reasons, in which case the rule is redundant or the verdicts differ, in which case the rule should be abandoned. This article argues that this dilemma can be resolved by revising the account of practical reasoning to accord with the prescriptions of a resolute choice model. Agents in societies in which people resolutely follow, for example, a rule to keep their commitments to return favors fare better than agents in societies that lack a commitment mechanism or in which costs are incurred to enforce it.
The New York Constitution and the Federal System
Authors: Galie Peter 
Published: December 2012

Abstract
This article addresses the establishment of New York Constitution and the American federal system. The New York Constitution demonstrates a framework for governance, distributes and limits powers, and protects individual rights. Constitutional change in the state has led or been reflected in dominant movements in American politics—Jacksonian democracy, Progressive reform, Depression-era activist government. The roots of constitutional government in New York are embedded in the state's colonial history, which is rooted in English constitutional and common law. In New York after 1821, voters could vote directly on whether to approve a constitutional amendment. The constitution of 1846 has been called the “People's Constitution.” Constitutional commissions would come to play an important role in state constitutional reform. State constitutions shape collective public identities and character. The state's constitution is an imperfect document, generally acknowledged in need of reform.
Public Opinion Polling and New York Politics and Governance
Authors: Levy Donald , Koning Ashley 
Published: December 2012

Abstract
This article describes public opinion polling as well as politics and governance in New York. The interaction between the polls, press, politicians, and public creates a constant, continual, and reciprocal interplay along six distinct paths (4P process). The 4P process is a core element of the manner in which modern representative democracy works. This process is developed over time as polling grew to maturity while politicians and the press experimented with its utility and implications and addressed the costs of using polling. Polling has become integral to governing. Furthermore, it examined four cases from the two survey models, comparing and contrasting the different parts of each survey in order to determine the effects of forced-choice questions versus intensity scales. Identifying ambivalence significantly lessened support and opposition for each major issue that New Yorkers faced.
Politics and the News Media in the Empire State
Authors: Muzzio Douglas 
Published: December 2012

Abstract
This article considers politics and the news media in New York. News coverage of election campaigns in New York and throughout the country tends to focus on nonpolicy matters. The news media is widely addressed as a central actor in U.S. politics and government. The news influences how people think about politics. A major change in New York state (and other news) coverage is the altered role of the Associated Press (AP). The cutbacks in newspapers' state coverage reflect the crisis and transformation of U.S. news organizations. The future of the “news media”—specifically the so-called mainstream or traditional media of newspapers, TV, radio—is evolution or death. During the first three months of 2010, Albany proved even more bizarre than it had been over the prior five years, a considerable feat. Albany 2012 seems a different place than it was in 2009–10.
New York State's “Foreign Policy”
Authors: Friedman Kathryn Bryk 
Published: December 2012

Abstract
This article investigates a unique aspect of New York State governance—its engagement in foreign policymaking. It also discusses some of the ways in which state officials collaborate and build relationships with foreign governments and, particularly in the case of Canada, provincial counterparts in economic, political, cultural, and environmental spheres. It is shown that New York State legislators engage in foreign policymaking on issues that directly affect their constituents, although admittedly to a minimal degree when compared to their executive and judicial counterparts. The New York State judiciary has contributed to the growing body of international human rights law. It then turns to local government engagement in foreign policy. New York foreign policy takes place in social, political, cultural, economic, and environmental sectors touching virtually every corner of the globe. It is suggested that New York State has nothing to lose from strengthened engagement on the global stage.
Higher Education in New York State
Authors: Steck Henry 
Published: December 2012

Abstract
This article introduces New York's complex postsecondary sector. It then turns to the question of state financial support, and the broader character of the structure of higher education in New York State. It also discusses the two sectors and argues that the conceptualization of two distinct sectors—one “public” and one “private”—should be framed quite differently. A major goal of the State University of New York (SUNY) and the City University of New York (CUNY) is an assurance that any future tuition increases be used for the campuses and not to help close a state budget gap. The increase in tuition to fill budget gaps produces a paradoxical situation: as tuition rises, student aid provided by the state increases per student. As New York's three major higher education sectors faced the future, they were acutely aware that hard times would continue well into the future.
Introduction
Authors: Bradley Ben , Feldman Fred , Johansson Jens 
Published: December 2012

Abstract
This chapter discusses the theme of this book, which is the philosophical aspect of death. The book answers questions about what death is and why it matters that help define the growing interdisciplinary subfield of philosophy of death. It analyzes the views of ancient Greek philosophers including Socrates, Plato, Aristotle, and Epicurus about death; investigates how death is related to various concepts including disintegration of personality, personal identity, and pleasure; and explores the concept of immortality, the wrongness of killing, and the significance of death for animals.
The Evil of Death
Authors: Sider Theodore 
Published: December 2012

AbstractThis chapter examines the evil of death in the context of metaphysics. It explains that fundamental metaphysics is a search for the fundamental reality that underlies ordinary facts, and contends that the relationship between theses of fundamental metaphysics and questions of value is not a straightforward one. The chapter discusses two metaphysical views about the nature of time, four-dimensionalism, and presentism, and suggests that presentism is consistent with the idea that death is evil because it deprives the deceased of the goods of life.
Education and the Poor
Authors: Barrow Lisa , Schanzenbach Diane Whitmore 
Published: December 2012

AbstractThis article presents a basic theoretic framework to explain differences in educational inputs and outcomes. Using several data sets, it documents wide disparities in educational outcomes (educational attainment, test scores, and cognitive skills). As income rises, educational outcomes improve. Highly aggregated measures of school inputs indicate small differences according to income. Average spending per pupil, measured at the school district level, is approximately the same for nonpoor students and for free-lunch students. Average class sizes are also approximately the same across high- and low-poverty schools. The big differences across high- and low-poverty schools are in teacher characteristics, facilities, and school crime rates. Low-poverty schools have more experienced teachers, less teacher turnover, fewer crimes, and more specialized facilities. Parental educational attainment and time spent with children are positively correlated with income. These input differences significantly impact outcome differences. Policies designed to address differences in educational inputs and outcomes are reviewed.
Is Poverty Incompatible with Asset Accumulation?
Authors: McKernan Signe-Mary , Ratcliffe Caroline , Williams Shanks Trina 
Published: December 2012

AbstractThis article examines whether poverty is incompatible with asset accumulation. It considers whether the poor can and do save and whether they are able to build up assets over time. It presents data from household surveys, as well as from programs targeted at helping families accumulate assets. Presenting and evaluating the state of knowledge provides a new lens on whether the current income-based safety net could better serve poor families by having an asset-building component. The conventional thinking is that families that are income-poor cannot save. The article shows that this thinking is inaccurate; poverty does not have to be incompatible with asset accumulation.
Leadership and Followership from a Social Cognition Perspective: A Dual Process Account
Authors: Brown Douglas J. 
Published: December 2012

AbstractThis chapter explores the leadership literature through the lens of a dual processing perspective, indicating that human cognition consists of an automatic system (System 1) and a conscious system (System 2). In particular, it addresses follower and leader information processing from the dual-process paradigm. It is observed that quick, nonconscious processing plays a tremendous role in leadership and followership. The nature, acquisition, retention, and retrieval of information in System 1 follow a connectionist architecture, and function in accordance with the properties that have been typically attributed to schematic knowledge. The ability to engage System 2 has been compared to a muscle, which needs time to recover. In general, the data indicate that leadership scholars may want to consider mental events through the lens of an old, yet increasingly dominant, human-information-processing paradigm: the dual-process model.
Leadership in Context and Context in Leadership Studies
Authors: Shamir Boas 
Published: December 2012

AbstractThis chapter evaluates the “state of the science” of leadership studies with respect to the issue of context, describes some of the limitations of studies of leadership in specific contexts, and offers some suggestions about the incorporation of context into leadership theories. Studies of leadership in specific contexts, especially when they are written by authors who are highly informed about general leadership theories, have the potential to contribute to general theories. The group context identifies the characteristics of the elected or endorsed leader. Leadership aims to obtain acceptance of the interpretation favored by the leader. The general point is that studies of leadership in specific contexts or roles have to be complemented by theory-based comparative studies of leadership in different contexts, whether such studies explore hypotheses derived inductively from context-specific studies or hypotheses derived deductively from extensions of leadership theories.