bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spondylodiscitis with Extensive Spine Involvement—Case Report
Authors: Faleiro Rodrigo , Sales Marcos , Garcia Luiz , Moraes Vítor , Fontoura Renato , Mendonça Bernardo 
Published: June 2016

AbstractSpondylodiscitis consists of an inflammatory process of infectious origin that affects primarily the intervertebral disc and spreads to the adjacent vertebral bodies, often evolving into osteomyelitis, with consequent associated neurological damage. The diagnosis is often delayed, with an average of 2 to 6 months between the appearance of the first symptoms and the confirmation of the disease. Therefore, the laboratorial and imaging exams play an important role in the diagnosis of spondylodiscitis, as well as in the orientation for the treatment to be followed (conservative or surgical). We report a case of extensive involvement of the spine and discuss about the epidemiology of the disease, its diagnosis, and therapeutic principles.
Einstellungen zu Entscheidungen am Lebensende und Pflegebedürftigkeit: Ergebnisse einer repräsentativen Befragung der österreichischen Bevölkerung (50+)
Authors: Stolz E. , Rásky É. , Freidl W. 
Published: June 2016

Zusammenfassung
Hintergrund und Ziel: Bisherige Befragungen der Bevölkerung hinsichtlich Einstellungen zu Entscheidungen am Lebensende klammern die Pflegebedürftigkeit im Alter und den Einfluss von Sorgen hinsichtlich des Alter(n)s aus. Ziel der vorliegenden Arbeit ist die Präsentation erster Ergebnisse einer aktuellen Befragung zu diesem Thema.
Methode: Eine bundesweite repräsentative Querschnittsbefragung von Österreichern über 50 Jahren (n=968) wurde 2015 durchgeführt.
Ergebnisse: 29,0% der Befragten gaben an als schwer pflegebedürftige ältere Person nicht weiterleben zu wollen. In diesem Zusammenhang befürworteten den von der pflegebedürftigen älteren Person gewünschten Verzicht auf lebensverlängernde Maßnahmen 48,5%, den assistierten Suizid 41,7% und die aktive Sterbehilfe 34,1%. Sorgen hinsichtlich des Alter(n)s sind weit verbreitet (53,7–83,0%). Personen, die hinsichtlich des Alter(n)s sehr besorgt sind, befürworteten assistierten Suizid und aktive Sterbehilfe eher als weniger Besorgte.
Schlussfolgerung: Weitverbreitete Sorgen bezogen auf das Alter(n) und negative Vorstellungen hinsichtlich Pflegebedürftigkeit im Alter sollten im Rahmen von Informationskampagnen thematisiert werden.
One-Year Follow-up of Children and Adolescents with Major Depressive Disorder: Relationship between Clinical Variables and Abcb1 Gene Polymorphisms
Authors: Blázquez A. , Gassó P. , Mas S. , Plana M. , Lafuente A. , Lázaro L. 
Published: June 2016

Abstract
Introduction: Differences in response to fluoxetine (FLX) may be influenced by certain genes that are involved in FLX transportation (ABCB1). We examined remission and recovery from the index episode in a cohort of patients treated with FLX, and also investigated associations between genetic variants in ABCB1 and remission, recovery, and suicide risk.
Methods: This was a naturalistic 1-year follow-up study of 46 adolescents diagnosed with major depressive disorder (MDD). At 12 months they underwent a diagnostic interview with the K-SADS-PL.
Results: It was found that remission was around 69.5% and recovery 56.5%. Remission and recovery were associated with lower scores on the CDI at baseline, with fewer readmissions and suicide attempts, and with lower scores on the CGI and higher scores on the GAF scale. No relationship was found between ABCB1 and remission or recovery. However, a significant association was observed between the G2677T ABCB1 polymorphism and suicide attempts.
Conclusion: Other factors such as stressful events, family support, and other genetic factors are likely to be involved in MDD outcome.
Die Zukunft der medizinisch–rehabilitativen Versorgung im Kontext der Multimorbidität – Teil I: Begriffsbestimmung, Versorgungsfragen und Herausforderungen
Authors: Seger W. , Cibis W. , Deventer A. , Grotkamp S. , Lübke N. , Schönle P.-W. , Schmidt-Ohlemann M. , Schubert M. 
Published: June 2016

Zusammenfassung
Hintergrund: Multimorbide Personen mit 2 und mehr chronischen Krankheiten mit sozialmedizinischer Relevanz, rücken immer mehr in den Vordergrund der rehabilitativen Versorgung.
Methodik: Nach Klärung der Begriffsbestimmung von Multimorbidität im rehabilitativen Kontext und orientierender Literaturauswertung zu deren Prävalenz und Folgen wurden ausgehend von einem kasuistischen Beispiel besondere Anforderungen und allgemeine Herausforderungen für die Leistungsgestaltung sowie für die rehabilitative Versorgung herausgearbeitet und im Ärztlichen Sachverständigenrat der Bundesarbeitsgemeinschaft für Rehabilitation (BAR) konsentiert.
Ergebnis: Der Handlungsbedarf bei multimorbiden Versicherten reicht von der funktionsbezogenen, individuellen Bedarfsermittlung über die Zuweisungspraxis, Rehabilitationsdurchführung und -nachsorge bis zur Reintegration der Rehabilitanden in den Sozialraum.
Psychosoziale Belastungen, Stressempfinden und Stressbewältigung von Studierenden der Sozialen Arbeit: Ergebnisse einer quantitativen Studie
Authors: Kriener C. , Schwertfeger A. , Deimel D. , Köhler T. 
Published: June 2016

ZusammenfassungIm Rahmen der vorliegenden quantitativen Untersuchung wurden die Daten von 746 Studierenden der Sozialen Arbeit hinsichtlich ihres aktuellen Stresserlebens, erlebter psychosozialer Belastungsfaktoren sowie deren Nutzung spezifischer Bewältigungsverfahren erhoben. Zum Einsatz kam die Perceived Stress Scale (PSS) sowie das Trierer Inventar zum Chronischen Stress (TICS). Die Ergebnisse zeigen, dass ein Drittel der Studierenden unter viel bis extrem viel Stress leidet. Ein Viertel fühlt sich deutlich überfordert und sozial überlastet. Psychosozialen Belastungen durch prägende Ereignisse in der Biografie (z. B. Tod oder psychische Erkrankung von nahen Angehörigen) sind weit mehr als die Hälfte der Studierenden ausgesetzt. Trotz deutlicher Belastungen hat nur ein Viertel schon einmal professionelle Unterstützung in Anspruch genommen. Studierende, die vorwiegend funktionale Bewältigungsstrategien nutzen, weisen u. a. ein geringeres Stressempfinden und geringere Überforderung als Studierende auf, die vorwiegend dysfunktionale Bewältigungsstrategien nutzen. Dieses theoretisch häufig beschriebene und empirisch fundierte Wissen sollte gewinnbringend im Hochschulkontext genutzt werden: Die vermehrte Implementierung von Seminaren zur Stressbewältigung im Studium liegt nahe – das Erlernen funktionaler Bewältigungsstrategien kann zu einer deutlichen Reduktion von Stress und Belastungen unter Studierenden beitragen. Zudem sollten niedrigschwellige psychosoziale Unterstützungsangebote implementiert und ausgebaut werden.
A Virtue Analysis of Recreational Marijuana Use
Authors: Sullivan Ezra , Austriaco Nicanor 
Published: June 2016

Several empirical studies suggest that recreational marijuana is popularly perceived as an essentially harmless rite of passage that ends as young people settle into their careers and their adult intimate relationships. Is this perception accurate? To answer this question, we evaluate the morality of recreational marijuana use from a virtue perspective guided by the theological synthesis of St. Thomas Aquinas. Since the medical data reveals that recreational marijuana use is detrimental to the well-being of the user, we conclude that it is a vicious activity, an instance of the vice of intoxication, and as such would be morally illicit. Lay summary: In contrast to its medical use, the recreational use of marijuana cannot be justified for at least three reasons. First, as scientists have amply documented, it harms the organic functioning of the human body. Second, it impedes our ability to reason and in so doing does harm to us. Finally, it has lasting detrimental effects on the user and his neighbor, even when it occurs in a casual setting. Intoxication is always contrary to the integral good of the person. Thus, the use of marijuana is never warranted even for good, non-medical reasons.
A Philosophical Assessment of TK's Autopsy Report: Implications for the Debate over the Brain Death Criteria
Authors: Austriaco Nicanor Pier Giorgio 
Published: June 2016

In recent years, there has been increasing evidence that the totally brain-dead patient is able to continue to live and to maintain some integrated functions, albeit with the necessary assistance of mechanical ventilation. Several years ago, the autopsy report of a totally brain-dead patient named TK who was kept on life support for nearly twenty years was published in the Journal of Child Neurology. He remains the individual kept on life support the longest after suffering total brain failure. In this essay, I argue that the clinical data described in the autopsy report demonstrate that TK's long-term survival after total brain failure supports the claim acknowledged by the President's Council on Bioethics that the brain-dead patient retains his bodily integrity. As such, he is not dead. He is still a living, though severely disabled, human organism, a human person made in the image and likeness of God. Lay summary: Traditionally, the presence or absence of bodily integration has been used to definitively discern the presence or absence of life in the human being where decomposition of the body is the surest sign of death. The autopsy report of a patient named TK who was brain-dead for nearly twenty years demonstrates that brain-dead patients retain their bodily integrity. As such, TK and other brain-dead patients are not dead. They are living, though severely disabled, human organisms, who are human persons made in the image and likeness of God.
Permanent versus determinant: Not via saturations
Authors: Bürgisser Peter , Ikenmeyer Christian , Hüttenhain Jesko 
Published: June 2016

Let

D
e

t
n

Det_n

denote the closure of the

G
l

n
2

(

C

)

\mathrm {Gl}_{n^2}(\mathbb {C})

-orbit of the determinant polynomial

d
e
t

n

\mathrm {det}_n

with respect to linear substitution. The highest weights (partitions) of irreducible

G
l

n
2

(

C

)

\mathrm {Gl}_{n^2}(\mathbb {C})

-representations occurring in the coordinate ring of

D
e

t
n

Det_n

form a finitely generated monoid

S
(
D
e

t
n

)

S(Det_n)

. We prove that the saturation of

S
(
D
e

t
n

)

S(Det_n)

contains all partitions

λ
\lambda

with length at most

n
n

and size divisible by

n
n

. This implies that representation theoretic obstructions for the permanent versus determinant problem must be holes of the monoid

S
(
D
e

t
n

)

S(Det_n)

.
Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction
Authors: He Dan , Kuhn David , Parida Laxmi 
Published: June 2016

AbstractGiven a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait prediction is usually represented as linear regression models. In many cases, for the same set of samples and markers, multiple traits are observed. Some of these traits might be correlated with each other. Therefore, modeling all the multiple traits together may improve the prediction accuracy. In this work, we view the multitrait prediction problem from a machine learning angle: as either a multitask learning problem or a multiple output regression problem, depending on whether different traits share the same genotype matrix or not. We then adapted multitask learning algorithms and multiple output regression algorithms to solve the multitrait prediction problem. We proposed a few strategies to improve the least square error of the prediction from these algorithms. Our experiments show that modeling multiple traits together could improve the prediction accuracy for correlated traits.Availability and implementation: The programs we used are either public or directly from the referred authors, such as MALSAR ( http://www.public.asu.edu/~jye02/Software/MALSAR/ ) package. The Avocado data set has not been published yet and is available upon request.Contact: dhe@us.ibm.com
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for
de novo
metabolic pathway reconstruction
Authors: Tabei Yasuo , Yamanishi Yoshihiro , Kotera Masaaki 
Published: June 2016

Abstract
Motivation : Metabolic pathways are an important class of molecular networks consisting of compounds, enzymes and their interactions. The understanding of global metabolic pathways is extremely important for various applications in ecology and pharmacology. However, large parts of metabolic pathways remain unknown, and most organism-specific pathways contain many missing enzymes. Results: In this study we propose a novel method to predict the enzyme orthologs that catalyze the putative reactions to facilitate the de novo reconstruction of metabolic pathways from metabolome-scale compound sets. The algorithm detects the chemical transformation patterns of substrate–product pairs using chemical graph alignments, and constructs a set of enzyme-specific classifiers to simultaneously predict all the enzyme orthologs that could catalyze the putative reactions of the substrate–product pairs in the joint learning framework. The originality of the method lies in its ability to make predictions for thousands of enzyme orthologs simultaneously, as well as its extraction of enzyme-specific chemical transformation patterns of substrate–product pairs. We demonstrate the usefulness of the proposed method by applying it to some ten thousands of metabolic compounds, and analyze the extracted chemical transformation patterns that provide insights into the characteristics and specificities of enzymes. The proposed method will open the door to both primary (central) and secondary metabolism in genomics research, increasing research productivity to tackle a wide variety of environmental and public health matters.
Availability and Implementation :
Contact : maskot@bio.titech.ac.jp
RNAiFold2T: Constraint Programming design of thermo-IRES switches
Authors: Garcia-Martin Juan Antonio , Dotu Ivan , Fernandez-Chamorro Javier , Lozano Gloria , Ramajo Jorge , Martinez-Salas Encarnacion , Clote Peter 
Published: June 2016

Abstract
Motivation: RNA thermometers (RNATs) are cis -regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation.
Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site ( thermo -IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements.
Availability: RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold , which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine.
Contact: clote@bc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction
Authors: Cui Xuefeng , Lu Zhiwu , Wang Sheng , Jing-Yan Wang Jim , Gao Xin 
Published: June 2016

Abstract
Motivation : Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information.
Method : We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration.
Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.
Availability and implementation: Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx .
Contact : xin.gao@kaust.edu.sa
Supplementary information : Supplementary data are available at Bioinformatics online.
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks
Authors: Glicksberg Benjamin S. , Li Li , Badgeley Marcus A. , Shameer Khader , Kosoy Roman , Beckmann Noam D. , Pho Nam , Hakenberg Jörg , Ma Meng , Ayers Kristin L. , Hoffman Gabriel E. , Dan Li Shuyu , Schadt Eric E. , Patel Chirag J. , Chen Rong , Dudley Joel T. 
Published: June 2016

Abstract
Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL).
Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes.
Contacts : rong.chen@mssm.edu or joel.dudley@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
RADIS:analysis ofRAD-seq data for interspecific phylogeny
Authors: Cruaud Astrid , Gautier Mathieu , Rossi Jean-Pierre , Rasplus Jean-Yves , Gouzy Jérôme 
Published: June 2016

AbstractIn an attempt to make the processing of RAD-seq data easier and allow rapid and automated exploration of parameters/data for phylogenetic inference, we introduce the perl pipeline RADIS. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilized.Availability and implementation: RADIS is written in perl, designed to run on Linux and Unix platforms. RADIS and its manual are freely available from http://www1.montpellier.inra.fr/CBGP/software/RADIS/.Contact: astrid.cruaud@supagro.inra.frSupplementary information: Supplementary data are available at Bioinformatics online.
@MInter: automated text-mining of microbial interactions
Authors: Lim Kun Ming Kenneth , Li Chenhao , Chng Kern Rei , Nagarajan Niranjan 
Published: June 2016

AbstractMotivation: Microbial consortia are frequently defined by numerous interactions within the community that are key to understanding their function. While microbial interactions have been extensively studied experimentally, information regarding them is dispersed in the scientific literature. As manual collation is an infeasible option, automated data processing tools are needed to make this information easily accessible.Results: We present @MInter, an automated information extraction system based on Support Vector Machines to analyze paper abstracts and infer microbial interactions. @MInter was trained and tested on a manually curated gold standard dataset of 735 species interactions and 3917 annotated abstracts, constructed as part of this study. Cross-validation analysis showed that @MInter was able to detect abstracts pertaining to one or more microbial interactions with high specificity (specificity = 95%, AUC = 0.97). Despite challenges in identifying specific microbial interactions in an abstract (interaction level recall = 95%, precision = 25%), @MInter was shown to reduce annotator workload 13-fold compared to alternate approaches. Applying @MInter to 175 bacterial species abundant on human skin, we identified a network of 357 literature-reported microbial interactions, demonstrating its utility for the study of microbial communities.Availability and implementation: @MInter is freely available at https://github.com/CSB5/atminter.Contact: nagarajann@gis.a-star.edu.sgSupplementary information: Supplementary data are available at Bioinformatics online.