bluuebunny/crossref_metadata_2025_split huggingface dataset:
If these data could talk
Authors: Pasquier Thomas , Lau Matthew K. , Trisovic Ana , Boose Emery R. , Couturier Ben , Crosas Mercè , Ellison Aaron M. , Gibson Valerie , Jones Chris R. , Seltzer Margo 
Published: September 2017

AbstractIn the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software have enabled the rapid implementation of novel methods to manage and analyze the growing flood of data. However, it has become apparent that many scientific fields exhibit distressingly low rates of reproducibility. Although there are many dimensions to this issue, we believe that there is a lack of formalism used when describing end-to-end published results, from the data source to the analysis to the final published results. Even when authors do their best to make their research and data accessible, this lack of formalism reduces the clarity and efficiency of reporting, which contributes to issues of reproducibility. Data provenance aids both reproducibility through systematic and formal records of the relationships among data sources, processes, datasets, publications and researchers.
Nectin-3 modulates the structural plasticity of dentate granule cells and long-term memory
Authors: Wang X-X , Li J-T , Xie X-M , Gu Y , Si T-M , Schmidt M V , Wang X-D 
Published: September 2017

AbstractNectin-3, a cell adhesion molecule enriched in hippocampal neurons, has been implicated in stress-related cognitive disorders. Nectin-3 is expressed by granule cells in the dentate gyrus (DG), but it remains unclear whether nectin-3 in DG modulates the structural plasticity of dentate granule cells and hippocampus-dependent memory. In this study, we found that DG nectin-3 expression levels were developmentally regulated and reduced by early postnatal stress exposure in adult mice. Most importantly, knockdown of nectin-3 levels in all DG neuron populations by adeno-associated virus (AAV) mimicked the cognitive effects of early-life stress, and impaired long-term spatial memory and temporal order memory. Moreover, AAV-mediated DG nectin-3 knockdown increased the density of doublecortin-immunoreactive differentiating cells under proliferation and calretinin-immunoreactive immature neurons, but markedly decreased calbindin immunoreactivity, indicating that nectin-3 modulates the differentiation and maturation of adult-born DG granule cells. Using retrovirus to target newly generated DG neurons, we found that selective nectin-3 knockdown in new DG neurons also impaired long-term spatial memory. In addition, suppressing nectin-3 expression in new DG neurons evoked a reduction of dendritic spines, especially thin spines. Our data indicate that nectin-3 expressed in DG neurons may modulate adult neurogenesis, dendritic spine plasticity and the cognitive effects of early-life stress.
Rheumatic Diseases and Molecular Physical Medicine – New Aspects
Authors: Lange Uwe , Müller-Ladner Ulf , Dischereit Gabriel 
Published: September 2017

AbstractA multimodal treatment of rheumatic diseases without physical medicine is incomplete. However, the mechanisms underlying the beneficial effects of physical medicine are only partially understood. Modern molecular medicine offers new insights into pivotal mechanisms and mediators of the inflammatory process and into interactions between cells of the immune system and bone cells. Investigating the potential influences of different methods of physical medicine on the central regulatory processes of inflammatory rheumatic diseases is of great interest, highly fascinating and opens up new avenues of research for the future. This article focuses on the novel results of molecular physical medicine in rheumatic diseases and osteoporosis.
Prävention von Gehirnerschütterungen im Juniorenfußball – Ist eine Abschaffung des Kopfballspiels notwendig?
Authors: Krutsch Volker , Krutsch Werner , Jansen Petra , Hoffmann Helmut , Angele Peter , Lehmann Jennifer , Loose Oliver , Gänsslen Axel , Nerlich Michael , Weber Johannes 
Published: September 2017

ZusammenfassungFußball wird als beliebteste Sportart weltweit von einer Großzahl von Verletzungen begleitet. Zu den seltenen Verletzungen, mit zum Teil schwerwiegenden Folgen, zählen Schädelhirntraumen, deren Verletzungsmechanismen im Fußball multifaktoriell sind. Der Ball gehört im Rahmen des Kopfballspiels zu den seltenen Auslösern einer Kopfverletzung im Fußball. Kurz-, mittel- und langfristige Folgen von Kopfbällen im Fußball sind insgesamt nur unzureichend untersucht und es sind kaum praktische Fallbeispiele mit schwerwiegenden Folgen bekannt. Das seit dem November 2015 bestehende Kopfballverbot im Juniorenfußball der USA ist unter Berücksichtigung der Angst und des hohen Risikos für Schädelhirntraumen bei den beliebtesten amerikanischen Sportarten wie American Football oder Eishockey für den US-Sport im Allgemeinen nachvollziehbar, jedoch sollte diese Entscheidung zum Kopfballverbot im Fußball aufgrund fehlender wissenschaftlicher Daten und anderen Erfahrungen aus der Praxis in Europa nicht ungeprüft übernommen werden. Vielmehr sind andere Präventionsmaßnahmen für Schädelhirntraumen und weitere Verletzungen im Juniorenfußball notwendig und wozu die Anpassung der Ballgrößen für Juniorenfußballer gehört und bereits Alltag ist. Das Regelwerk so zu ändern, dass der Kopfball im Juniorenfußball gänzlich abgeschafft wird, ist nach Meinung der Autoren deswegen nicht zwingend erforderlich. Weitere Studien sind hier für eine Vereinheitlichung des weltweiten Fußballsports notwendig.
Ernährungsmedizinische Aspekte in der Rheumatologie
Authors: Adam Olaf 
Published: September 2017

ZusammenfassungFür die Entzündungshemmung durch Omega-3-Fettsäuren haben Metaanalysen den Evidenzgrad IA ermittelt. Darüber hinaus belegen GCP-Studien (GCP: Good Clinical Practice) den zusätzlichen Effekt der antiinflammatorischen Ernährung auf die Gelenkentzündung, den Bedarf an nicht steroidalen Antirheumatika und Glukokortikoiden und sogar auf die Manifestation der Arteriosklerosefolgen.Komponenten der antiinflammatorischen Ernährung sind die Senkung der Arachidonsäurezufuhr durch eine vegetarisch ausgerichtete Kost und die optimale Versorgung mit Antioxidanzien, Spurenelementen, sekundären Pflanzenstoffen und Mineralstoffen. Die Überprüfung der Zufuhr der Arachidonsäure und der Eicosapentaensäure mittels des fokussierten Food-Frequency-Questionnaire sollte durch die Bestimmung des Fettsäurespektrums in den Erythrozytenlipiden ergänzt werden. Zusätzlich sind die Begleit- und Folgeerkrankungen, körperlichen Einschränkungen sowie soziale und psychische Belastungen zu berücksichtigen, die in Kooperation mit Ergo-, Psycho- und Physiotherapeuten therapiert werden.Die Ernährungstherapie kann die Pharmakotherapie nicht ersetzen, sondern soll diese unterstützen und hilft, als eine wichtige adjuvante Behandlung, den Therapieerfolg zu verbessern und die Compliance des Patienten zu fördern.Prostaglandine sind an allen entzündlich-rheumatischen Prozessen beteiligt. Sie entstehen aus der Omega-6-Arachidonsäure, die im Körper gebildet werden kann, aber hauptsächlich mit der Nahrung zugeführt wird. Deshalb ist die richtige Ernährung bei Rheuma ein wichtiger Eckpfeiler der Therapie. Um die Patientenbetreuung zu optimieren, empfiehlt sich eine fächerübergreifende Zusammenarbeit von Spezialisten.
Uzara, Xysmalobium undulatum – eine afrikanische Arzneipflanze
Authors: Sosnowski Paul , Melzig Matthias 
Published: September 2017

ZusammenfassungXysmalobium undulatum (L.) R.Br., Uzara, ist seit Jahrhunderten ein bekanntes Phytopharmakon in der südafrikanischen Stammesmedizin. Die Anwendungsgebiete erstrecken sich von der Behandlung einer Diarrhoe, Spasmen der glatten Muskulatur bis hin zur Wundbehandlung. Das Inhaltsstoffspektrum (u. a. herzwirksame Steroidglykoside vom Cardenolid-Typ, Pregnenolon, Sistosterole, Gerbstoffe, Flavonoide) bietet die Grundlage für das Indikationsspektrum dieser Arzneipflanze. In Deutschland empfiehlt die Kommission E als Indikationsgebiet für die Droge Uzarawurzel (Uzarae radix) lediglich die Anwendung bei unspezifischen, akuten Durchfallerkrankungen.
Aloe vera-Gel – eine Literaturrecherche
Authors: Ochmann Knut , Beer André-Michael 
Published: September 2017

ZusammenfassungAuf dem Gebiet der Phytotherapie hat die innerliche Anwendung der Aloe vera-Pflanze wegen ihres laxierenden Effekts zur Behandlung von Obstipation ihren festen Platz. Weitere Indikationen verknüpft man derzeit vornehmlich mit dem Blattmark (Gel), das von alters her zur topischen Applikation bei Wunden und Verbrennungen zum Einsatz kommt. Für mehrere Anwendungsgebiete hält der Markt das Gel in Nahrungsergänzungsmitteln bereit. Diese Literaturrecherche klinischer Studien, basierend auf den gängigen Datenbanken, zeigt, dass zwar nicht wenige Studien hinsichtlich einer Vielzahl von Indikationen die Wirksamkeit und Sicherheit des Aloe vera-Gels nachweisen, dass aber gleichwohl dringender Forschungsbedarf besteht.
Omega-3-Fettsäuren bei Herzinsuffizienz
Authors: von Schacky Clemens 
Published: September 2017

ZusammenfassungHerzinsuffizienz ist der häufigste Grund für Krankenhausaufnahmen in Deutschland. Die beiden Omega-3-Fettsäuren Eicosapentaensäure (EPA) und
Docosahexaensäure (DHA) aus Meeresfisch und ähnlichen Quellen, nicht aber die pflanzliche Alpha-Linolensäure, werden in den Leitlinien bei
Herzinsuffizienz mit eingeschränkter linksventrikulärer Funktion empfohlen. Die Empfehlungen basieren auf Epidemiologie, Wirkmechanismen und
einer großen Interventionsstudie mit klinischen Endpunkten. Die Aufnahme von EPA und DHA ist von Person zu Person sehr variabel, und die
klinischen Wirkungen korrelieren nicht mit der Dosis, sondern mit ihren Spiegeln in Erythrozyten. Daher empfiehlt sich eine zielgerichtete
Therapie auf Basis einer standardisierten Fettsäureanalytik der Erythrozyten, die auch bei Herzinsuffizienz die umfangreichste
wissenschaftliche Datenbasis hat: der HS-Omega-3 Index® mit einem Zielbereich von 8–11 %.
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features
Authors: Rogers Mark F , Shihab Hashem A , Mort Matthew , Cooper David N , Gaunt Tom R , Campbell Colin 
Published: September 2017

AbstractSummaryWe present FATHMM-XF, a method for predicting pathogenic point mutations in the human genome. Drawing on an extensive feature set, FATHMM-XF outperforms competitors on benchmark tests, particularly in non-coding regions where the majority of pathogenic mutations are likely to be found.Availability and implementationThe FATHMM-XF web server is available at http://fathmm.biocompute.org.uk/fathmm-xf/, and as tracks on the Genome Tolerance Browser: http://gtb.biocompute.org.uk. Predictions are provided for human genome version GRCh37/hg19. The data used for this project can be downloaded from: http://fathmm.biocompute.org.uk/fathmm-xf/Supplementary informationSupplementary data are available at Bioinformatics online.
DART: a fast and accurate RNA-seq mapper with a partitioning strategy
Authors: Lin Hsin-Nan , Hsu Wen-Lian 
Published: September 2017

Abstract

Motivation
In recent years, the massively parallel cDNA sequencing (RNA-Seq) technologies have become a powerful tool to provide high resolution measurement of expression and high sensitivity in detecting low abundance transcripts. However, RNA-seq data requires a huge amount of computational efforts. The very fundamental and critical step is to align each sequence fragment against the reference genome. Various de novo spliced RNA aligners have been developed in recent years. Though these aligners can handle spliced alignment and detect splice junctions, some challenges still remain to be solved. With the advances in sequencing technologies and the ongoing collection of sequencing data in the ENCODE project, more efficient alignment algorithms are highly demanded. Most read mappers follow the conventional seed-and-extend strategy to deal with inexact matches for sequence alignment. However, the extension is much more time consuming than the seeding step.

Results
We proposed a novel RNA-seq de novo mapping algorithm, call DART, which adopts a partitioning strategy to avoid the extension step. The experiment results on synthetic datasets and real NGS datasets showed that DART is a highly efficient aligner that yields the highest or comparable sensitivity and accuracy compared to most state-of-the-art aligners, and more importantly, it spends the least amount of time among the selected aligners.

Availability and implementation
https://github.com/hsinnan75/DART

Supplementary information
Supplementary data are available at Bioinformatics online.
Was Planet 9 captured in the Sun’s natal star-forming region?
Authors: Parker Richard J. , Lichtenberg Tim , Quanz Sascha P. 
Published: September 2017

Abstract
The presence of an unseen ‘Planet 9’ on the outskirts of the Solar system has been invoked to explain the unexpected clustering of the orbits of several Edgeworth–Kuiper Belt Objects. We use N-body simulations to investigate the probability that Planet 9 was a free-floating planet (FFLOP) that was captured by the Sun in its birth star formation environment. We find that only 1–6 per cent of FFLOPs are ensnared by stars, even with the most optimal initial conditions for capture in star-forming regions (one FFLOP per star, and highly correlated stellar velocities to facilitate capture). Depending on the initial conditions of the star-forming regions, only 5–10 of 10 000 planets are captured on to orbits that lie within the constraints for Planet 9. When we apply an additional environmental constraint for Solar system formation – namely the injection of short-lived radioisotopes into the Sun’s protoplanetary disc from supernovae – we find the probability for the capture of Planet 9 to be almost zero.
Surgical Management of Intrinsic Tumors of the Facial Nerve
Authors: Prasad Sampath Chandra , Laus Melissa , Dandinarasaiah Manjunath , Piccirillo Enrico , Russo Alessandra , Taibah Abdelkader , Sanna Mario 
Published: September 2017

Abstract

BACKGROUND
Intrinsic tumors of the facial nerve are a rare entity. Dealing with this subset of tumors is challenging both in terms of decision making and surgical intervention.

OBJECTIVE
To review the outcomes of surgical management of facial nerve tumors and cable nerve graft interpositioning.

METHODS
A retrospective analysis was performed at a referral center for skull base pathology. One hundred fifteen patients who were surgically treated for facial nerve tumors were included. In case of nerve interruption during surgery, the cable nerve interpositioning technique was employed wherein the facial nerve palsy lasted for less than 1-yr duration. In cases of facial nerve palsy lasting for greater than 1 yr, the nerve was restituted by a hypoglossal facial coaptation.

RESULTS
Various degrees of progressive paralysis were seen in 84 (73%) cases. Sixty nine (60%) of the tumors involved multiple segments of the facial nerve. Sixty-two (53.9%) tumors involved the geniculate ganglion. Seventy four (64.3%) of the cases were schwannomas. Hearing preservation surgeries were performed in 60 (52.1%). Ninety one (79.1%) of the nerves that were sectioned in association with tumor removal were restituted primarily by interposition cable grafting. The mean preoperative House-Brackmann grading of the facial nerve was 3.6. The mean immediate postoperative grading was 5.4, which recovered to a mean of 3.4 at the end of 1 yr.

CONCLUSION
In patients with good facial nerve function (House-Brackmann grade I-II), a wait-and-scan approach is recommended. In cases where the facial nerve has been interrupted during surgery, the cable nerve interpositioning technique is a convenient and well-accepted procedure for immediate restitution of the nerve.
Assessment of the impact of shared data on the scientific literature
Authors: Milham Michael P. , Craddock R. Cameron , Fleischmann Michael , Son Jake , Clucas Jon , Xu Helen , Koo Bonhwang , Krishnakumar Anirudh , Biswal Bharat B. , Castellanos F. Xavier , Colcombe Stan , Di Martino Adriana , Zuo Xi-Nian , Klein Arno 
Published: September 2017

AbstractData sharing is increasingly recommended as a means of accelerating science by facilitating collaboration, transparency, and reproducibility. While few oppose data sharing philosophically, a range of barriers deter most researchers from implementing it in practice (e.g., workforce and infrastructural demands, sociocultural and privacy concerns, lack of standardization). To justify the significant effort required for sharing data (e.g., organization, curation, distribution), funding agencies, institutions, and investigators need clear evidence of benefit. Here, using the International Neuroimaging Data-sharing Initiative, we present a brain imaging case study that provides direct evidence of the impact of open sharing on data use and resulting publications over a seven-year period (2010-2017). We dispel the myth that scientific findings using shared data cannot be published in high-impact journals and demonstrate rapid growth in the publication of such journal articles, scholarly theses, and conference proceedings. In contrast to commonly used ‘pay to play’ models, we demonstrate that openly shared data can increase the scale (i.e., sample size) of scientific studies conducted by data contributors, and can recruit scientists from a broader range of disciplines. These findings suggest the transformative power of data sharing for accelerating science and underscore the need for the scientific ecosystem to embrace the challenge of implementing data sharing universally.
The genome ofTrichoplusia ni, an agricultural pest and novel model for small RNA biology
Authors: Fu Yu , Yang Yujing , Zhang Han , Farley Gwen , Wang Junling , Quarles Kaycee A. , Weng Zhiping , Zamore Phillip D. 
Published: September 2017

AbstractThe cabbage looper,Trichoplusia ni(Lepidoptera: Noctuidae), is a destructive insect pest that feeds on a wide range of plants. The High Five cell line (Hi5), originally derived fromT. niovaries, is often used for efficient expression of recombinant proteins. Here, we report a draft assembly of the 368.2 MbT. nigenome, with 90.6% of all bases assigned to one of its 28 chromosomes and predicted 14,037 predicted protein-coding genes. Manual curation of gene families involved in chemoreception and detoxification revealsT. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Using male and female genome sequences, we define Z-linked and repeat-rich W-linked sequences. Transcriptome and small RNA data fromT. nithorax, ovary, testis, and Hi5 cells reveal distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding core small RNA pathway proteins. siRNAs target both endogenous transposons and the exogenous TNCL virus. Surprisingly,T. nisiRNAs are not 2´-O-methylated. Five piRNA-producing loci account for 34.9% piRNAs in the ovary, 49.3% piRNAs in the testis, and 44.0% piRNAs in Hi5 cells. Nearly all of the W chromosome is devoted to piRNA production: >76.0% of bases in the assembled W produce piRNAs in ovary. To enable use of theT. nigermline-derived Hi5 cell line as a model system, we have established efficient genome editing and single-cell cloning protocols. Taken together, theT. nigenome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo.
What the structural-functional connectome reveals about brain aging: The key role of the fronto-striatal-thalamic circuit and the rejuvenating impact of physical activity
Authors: Bonifazi P. , Erramuzpe A. , Diez I. , Gabilondo I. , Boisgontier M.P. , Pauwels L. , Stramaglia S. , Swinnen S.P. , Cortes J.M. 
Published: September 2017

AbstractPhysiological ageing affects brain structure and function impacting its morphology, connectivity and performance. However, at which extent brain-connectivity metrics reflect the age of an individual and whether treatments or lifestyle factors such as physical activity influence the age-connectivity match is still unclear. Here, we assessed the level of physical activity and collected brain images from healthy participants (N=155) ranging from 10 to 80 years to build functional (resting-state) and structural (tractography) connectivity matrices that were combined as connectivity descriptors. Connectivity descriptors were used to compute a maximum likelihood age estimator that was optimized by minimizing the mean absolute error. The connectivity-based estimated age, i.e. the brain-connectome age (BCA), was compared to the chronological age (ChA). Our results were threefold. First, we showed that ageing widely affects the structural-functional connectivity of multiple structures, such as the anterior part of the default mode network, basal ganglia, thalamus, insula, cingulum, hippocampus, parahippocampus, occipital cortex, fusiform, precuneus and temporal pole. Second, our analysis showed that the structure-function connectivity between basal ganglia and thalamus to orbitofrontal and frontal areas make a major contribution to age estimation. Third, we found that high levels of physical activity reduce BCA as compared to ChA, and vice versa, low levels increment it. In conclusion, the BCA model results highlight the impact of physical activity and the key role played by the connectivity between basal ganglia and thalamus to frontal areas on the process of healthy aging. Notably, the same methodology can be generally applied both to evaluate the impact of other factors and therapies on brain ageing, and to identify the structural-functional brain connectivity correlate of other biomarkers than ChA.
ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota
Authors: Batut Bérénice , Gravouil Kévin , Defois Clémence , Hiltemann Saskia , Brugère Jean-François , Peyretaillade Eric , Peyret Pierre 
Published: September 2017

AbstractBackgroundNew generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.FindingsWe therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides a curated collection of tools to explore and visualize taxonomic and functional information from raw amplicon, metagenomic or metatranscriptomic sequences. To guide different analyses, several customizable workflows are included. All workflows are supported by tutorials and Galaxy interactive tours to guide the users through the analyses step by step. ASaiM is implemented as Galaxy Docker flavour. It is scalable to many thousand datasets, but also can be used a normal PC. The associated source code is available under Apache 2 license athttps://github.com/ASaiM/frameworkand documentation can be found online (http://asaim.readthedocs.io/)ConclusionsBased on the Galaxy framework, ASaiM offers sophisticated analyses to scientists without command-line knowledge. ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.