bluuebunny/crossref_metadata_2025_split huggingface dataset:
ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types
Authors: Steinfeld Israel , Navon Roy , Creech Michael L. , Yakhini Zohar , Tsalenko Anya 
Published: January 2015

Abstract
Summary: ENViz (Enrichment Analysis and Visualization) is a Cytoscape app that performs joint enrichment analysis of two types of sample matched datasets in the context of systematic annotations. Such datasets may be gene expression or any other high-throughput data collected in the same set of samples. The enrichment analysis is done in the context of pathway information, gene ontology or any custom annotation of the data. The results of the analysis consist of significant associations between profiled elements of one of the datasets to the annotation terms (e.g. miR-19 was associated to the cell-cycle process in breast cancer samples). The results of the enrichment analysis are visualized as an interactive Cytoscape network.
Availability and implementation: ENViz is publically available in the Cytoscape App Store (http://apps.cytoscape.org/apps/enviz). For additional information please visit the tool website: http://www.agilent.com/labs/research/compbio/enviz/
Contact: israel_steinfeld@agilent.com
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
Authors: Xin Hongyi , Greth John , Emmons John , Pekhimenko Gennady , Kingsford Carl , Alkan Can , Mutlu Onur 
Published: January 2015

Abstract
Motivation: Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend based mappers differ by significantly more errors than what is typically allowed. Such error-abundant sequence pairs needlessly waste resources and severely hinder the performance of read mappers. Therefore, it is crucial to develop a fast and accurate filter that can rapidly and efficiently detect error-abundant string pairs and remove them from consideration before more computationally expensive methods are used.
Results: We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence pairs using bit-parallel and SIMD-parallel operations. SHD only filters string pairs that contain more errors than a user-defined threshold, making it fully comprehensive. It also maintains high accuracy with moderate error threshold (up to 5% of the string length) while achieving a 3-fold speedup over the best previous algorithm (Gene Myers’s bit-vector algorithm). SHD is compatible with all mappers that perform sequence alignment for verification.
Availability and implementation: We provide an implementation of SHD in C with Intel SSE instructions at: https://github.com/CMU-SAFARI/SHD.
Contact: hxin@cmu.edu, calkan@cs.bilkent.edu.tr or onur@cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Experimental myositis inducible with transfer of dendritic cells presenting a skeletal muscle C protein-derived CD8 epitope peptide
Authors: Okiyama Naoko , Hasegawa Hisanori , Oida Takatoku , Hirata Shinya , Yokozeki Hiroo , Fujimoto Manabu , Miyasaka Nobuyuki , Kohsaka Hitoshi 
Published: January 2015

AbstractIt is suggested that polymyositis, an autoimmune inflammatory myopathy, is mediated by autoaggressive CD8 T cells. Skeletal muscle C protein is a self-antigen that induces C protein-induced myositis, a murine model of polymyositis. To establish a new murine model of myositis inducible with a single CD8 T-cell epitope peptide that derives from the C protein, three internet-based prediction systems were employed to identify 24 candidate peptides of the immunogenic fragment of the C protein and bind theoretically to major histocompatibility complex class I molecules of C57BL/6 (B6) mice. RMA-S cell assay revealed that a HILIYSDV peptide, amino acid position 399–406 of the C protein, had the highest affinity to the H2-Kb molecules. Transfer of mature bone marrow-derived dendritic cells pulsed with HILIYSDV induced myositis in naive B6 mice. This myositis was suppressed by anti-CD8-depleting antibodies but not by anti-CD4-depleting antibodies. Because this myositis model is mediated by CD8 T cells independently of CD4 T cells, it should be a useful tool to investigate pathology of polymyositis and develop therapies targeting CD8 T cells.
Association between sHLA-G and HLA-G 14-bp deletion/insertion polymorphism in Crohn’s disease
Authors: Zidi Inès , Ben Yahia Hamza , Bortolotti Daria , Mouelhi Leila , Laaribi Ahmed Baligh , Ayadi Shema , Zidi Nour , Houissa Fatma , Debbech Radhouane , Boudabous Abdellatif , Najjar Taoufik , Di Luca Dario , Rizzo Roberta 
Published: January 2015

Abstract
The aim of this study was to evaluate the association between the HLA-G 14-bp deletion/insertion (Del/Ins) polymorphism and soluble (s) HLA-G production in patients with Crohn’s disease (CD). We analyzed also the sHLA-G molecules by ELISA and western blot in plasma samples. Among unselected patients, the 14-bp Del/Ins polymorphism was not significantly associated with increased CD risk neither for alleles (P = 0.371) nor for genotypes (P = 0.625). However, a significant association was reported between the 14-bp Del/Ins polymorphism and CD, in particular in young-onset CD patients for alleles [P = 0.020, odds ratio (OR) = 2.438, 95% confidence interval (CI): 1.13–5.25] but not with adult-onset CD patients. A significant association was reported concerning the genotype Ins/Ins for young-onset CD patients (P = 0.029, OR = 3.257, 95% CI: 1.08–9.77). We observed also a significant increase in sHLA-G measured by ELISA in CD patients compared to controls (P = 0.002). The 14-bp Del/Del and 14-bp Del/Ins genotypes are the high HLA-G producers. Among sHLA-Gpositive patients, 43% of subjects present dimers of HLA-G. The presence of dimers seems to be related to the advanced stages of the disease. The 14-bp Del/Ins polymorphism is associated with an increased risk of CD particularly in young-onset CD patients and controls sHLA-G plasma levels. Dimers of sHLA-G are frequent in advanced disease stages. The above findings indicate that the genetic 14-bp Del/Ins polymorphism in exon 8 of the HLA-G gene is associated with the risk of CD and suggest a role for sHLA-G as a prognostic marker for progressive disease.
New plasmid-mediated aminoglycoside 6′-N-acetyltransferase, AAC(6′)-Ian, and ESBL, TLA-3, from a Serratia marcescens clinical isolate
Authors: Jin Wanchun , Wachino Jun-ichi , Kimura Kouji , Yamada Keiko , Arakawa Yoshichika 
Published: January 2015

Abstract

Objectives
Enterobacteriaceae clinical isolates showing amikacin resistance (MIC 64 to &gt;256 mg/L) in the absence of 16S rRNA methyltransferase (MTase) genes were found. The aim of this study was to clarify the molecular mechanisms underlying amikacin resistance in Enterobacteriaceae clinical isolates that do not produce 16S rRNA MTases.

Methods
PCR was performed to detect already-known amikacin resistance determinants. Cloning experiments and sequence analyses were performed to characterize unknown amikacin resistance determinants. Transfer of amikacin resistance determinants was performed by conjugation and transformation. The complete nucleotide sequence of the plasmids was determined by next-generation sequencing technology. Amikacin resistance enzymes were purified with a column chromatography system. The enzymatic function of the purified protein was investigated by thin-layer chromatography (TLC) and HPLC.

Results
Among the 14 isolates, 9 were found to carry already-known amikacin resistance determinants such as aac(6′)-Ia and aac(6′)-Ib. Genetic analyses revealed the presence of a new amikacin acetyltransferase gene, named aac(6′)-Ian, located on a 169 829 bp transferable plasmid (p11663) of the Serratia marcescens strain NUBL-11663, one of the five strains negative for known aac(6′) genes by PCR. Plasmid p11663 also carried a novel ESBL gene, named blaTLA-3. HPLC and TLC analyses demonstrated that AAC(6′)-Ian catalysed the transfer of an acetyl group from acetyl coenzyme A onto an amine at the 6′-position of various aminoglycosides.

Conclusions
We identified aac(6′)-Ian as a novel amikacin resistance determinant together with a new ESBL gene, blaTLA-3, on a transferable plasmid of a S. marcescens clinical isolate.
A NuSTAR observation of the fast symbiotic nova V745 Sco in outburst
Authors: Orio M. , Rana V. , Page K. L. , Sokoloski J. , Harrison F. 
Published: January 2015

Abstract
The fast recurrent nova V745 Sco was observed in the 3–79 keV X-rays band with NuSTAR 10 d after the optical discovery. The measured X-ray emission is consistent with a collisionally ionized optically thin plasma at temperature of about 2.7 keV. A prominent iron line observed at 6.7 keV does not require enhanced iron in the ejecta. We attribute the X-ray flux to shocked circumstellar material. No X-ray emission was observed at energies above 20 keV, and the flux in the 3–20 keV range was about 1.6 × 10−11 erg cm−2 s−1. The emission measure indicates an average electron density of the order of 107 cm−2. The X-ray flux in the 0.3–10 keV band almost simultaneously measured with Swift was about 40 times larger, mainly due to the luminous central supersoft source emitting at energy below 1 keV. The fact that the NuSTAR spectrum cannot be fitted with a power law, and the lack of hard X-ray emission, allow us to rule out Comptonized gamma-rays, and to place an upper limit of the order of 10−11 erg cm−2 s−1 on the gamma-ray flux of the nova on the tenth day of the outburst.
The ultraluminous X-ray source NuSTAR J095551+6940.8: a magnetar in a high-mass X-ray binary
Authors: Ekşi K. Y. , Andaç İ. C. , Çıkıntoğlu S. , Gençali A. A. , Güngör C. , Öztekin F. 
Published: January 2015

Abstract
The recent detection of pulsations from the ultraluminous X-ray source (ULX) NuSTAR J095551+6940.8 in M82 by Bachetti et al. indicates that the object is an accreting neutron star in a high-mass X-ray binary (HMXB) system. The super-Eddington luminosity of the object implies that the magnetic field is sufficiently strong to suppress the scattering cross-section unless its beam is viewed at a favourable angle. We show that the torque equilibrium condition for the pulsar indicates that the dipole magnetic field of the neutron star is 6.7 × 1013 G, two orders of magnitude higher than that estimated by Bachetti et al., and further point to the possibility that even stronger magnetic fields could well be in the higher multipoles. This supports the recent view that magnetars descent from HMXBs if the magnetic field decays an order of magnitude during the process of transition.
An ultraluminous nascent millisecond pulsar
Authors: Kluźniak Włodek , Lasota Jean-Pierre 
Published: January 2015

Abstract
If the ultraluminous source (ULX) M82 X-2 sustains its measured spin-up value of $\dot{\nu }= 10^{-10}\,{\rm s^{-2}}$, it will become a millisecond pulsar in less than 105 yr. The observed (isotropic) luminosity of 1040 erg s−1 also supports the notion that the neutron star will spin up to a millisecond period upon accreting about 0.1 Mȯ – the reported hard X-ray luminosity of this ULX, together with the spin-up value, implies torques consistent with the accretion disc extending down to the vicinity of the stellar surface, as expected for low values of the stellar dipole magnetic field (B ≲ 109 G). This suggests a new channel of millisecond pulsar formation – in high-mass X-ray binaries – and may have implications for studies of gravitational waves, and possibly for the formation of low-mass black holes through accretion-induced collapse.
Spectroscopy of the Type Ia supernova 2011fe past 1000 d
Authors: Taubenberger S. , Elias-Rosa N. , Kerzendorf W. E. , Hachinger S. , Spyromilio J. , Fransson C. , Kromer M. , Ruiter A. J. , Seitenzahl I. R. , Benetti S. , Cappellaro E. , Pastorello A. , Turatto M. , Marchetti A. 
Published: January 2015

Abstract
In this Letter we present an optical spectrum of SN 2011fe taken 1034 d after the explosion, several hundred days later than any other spectrum of a Type Ia supernova (disregarding light-echo spectra and Local Group remnants). The spectrum is still dominated by broad emission features, with no trace of a light echo or interaction of the supernova ejecta with surrounding interstellar material. Comparing this extremely late spectrum to an earlier one taken 331 d after the explosion, we find that the most prominent feature at 331 d – [Fe iii] emission around 4700 Å – has entirely faded away, suggesting a significant change in the ionization state. Instead, [Fe ii] lines are probably responsible for most of the emission at 1034 d. An emission feature at 6300–6400 Å has newly developed at 1034 d, which we tentatively identify with Fe i λ6359, [Fe i] λλ6231, 6394 or [O i] λλ6300, 6364. Interestingly, the features in the 1034 d spectrum seem to be collectively redshifted, a phenomenon that we currently have no convincing explanation for. We discuss the implications of our findings for explosion models, but conclude that sophisticated spectral modelling is required for any firm statement.
Reconciling timber extraction with biodiversity conservation in tropical forests using reduced‐impact logging
Authors: Bicknell Jake E. , Struebig Matthew J. , Davies Zoe G. 
Published: January 2015

SummaryOver 20% of the world's tropical forests have been selectively logged, and large expanses are allocated for future timber extraction. Reduced‐impact logging (RIL) is being promoted as best practice forestry that increases sustainability and lowersCO2emissions from logging, by reducing collateral damage associated with timber extraction.RILis also expected to minimize the impacts of selective logging on biodiversity, although this is yet to be thoroughly tested.We undertake the most comprehensive study to date to investigate the biodiversity impacts ofRILacross multiple taxonomic groups. We quantified birds, bats and large mammal assemblage structures, using a before‐after control‐impact (BACI) design across 20 sample sites over a 5‐year period. Faunal surveys utilized point counts, mist nets and line transects and yielded >250 species. We examined assemblage responses to logging, as well as partitions of feeding guild and strata (understorey vs. canopy), and then tested for relationships with logging intensity to assess the primary determinants of community composition.Community analysis revealed little effect ofRILon overall assemblages, as structure and composition were similar before and after logging, and between logging and control sites. Variation in bird assemblages was explained by natural rates of change over time, and not logging intensity. However, when partitioned by feeding guild and strata, the frugivorous and canopy bird ensembles changed as a result ofRIL, although the latter was also associated with change over time. Bats exhibited variable changes post‐logging that were not related to logging, whereas large mammals showed no change at all.Indicator species analysis and correlations with logging intensities revealed that some species exhibited idiosyncratic responses toRIL, whilst abundance change of most others was associated with time.Synthesis and applications. Our study demonstrates the relatively benign effect of reduced‐impact logging (RIL) on birds, bats and large mammals in a neotropical forest context, and therefore, we propose that forest managers should improve timber extraction techniques more widely. IfRILis extensively adopted, forestry concessions could represent sizeable and important additions to the global conservation estate – over 4 million km2.
A method for analysing replicated point patterns in ecology
Authors: Bagchi Robert , Illian Janine B. 
Published: January 2015

Summary

Many ecological questions could gain insight from linking variation in spatial structure to explanatory variables. Although methods that make these links have been developed in the statistical literature, they have been used rarely in ecology.

We present an approach that considers point patterns from different sources (e.g. multiple plots or species) as replicates of the spatial processes of interest. Using an integrated two‐step procedure, the method uses a linear mixed‐effects modelling framework to explain variation in the spatial structure of the replicated patterns with categorical and continuous predictors.

Inferences on the strength of the relationships between the predictors and spatial structure are made on the basis of a semi‐parametric bootstrap procedure that accounts for the dependency among spatial scales and, if required, among replicates.

We illustrate the approach with three simulated examples. These demonstrate that replicated analyses can increase the performance of spatial point pattern analyses, allow analysis of sparse patterns (e.g. rare species) and help identify the drivers of variation among spatial point patterns.

The paucity of ecological studies that utilize replicated point pattern analysis may be due partly to a lack of familiarity with the methods. By highlighting the options available, we hope to encourage greater use of these methods by ecologists in the future.
Phylogeny of split‐footed lacewings (Neuroptera, Nymphidae), with descriptions of new Cretaceous fossil species from China
Authors: Shi Chaofan , Winterton Shaun L. , Ren Dong 
Published: January 2015

AbstractA phylogeny of the lacewing family Nymphidae based on morphology and DNA sequences is presented including representatives of all living genera and selected fossil genera. Widely distributed Jurassic and Cretaceous genera gave rise to recent taxa now restricted to Australasia. Two previously defined clades (i.e. Nymphinae and Myiodactylinae) were recovered and reflect the diverging adult and larval morphology of members of these two subfamilies. From Chinese Cretaceous deposits, a new genus (Spilonymphes gen. nov.) is described with one new species, as well as new species described in the genera Baissoleon Makarkin and Sialium Westwood.
EngageUC: Developing an Efficient and Ethical Approach to Biobanking Research at the University of California
Authors: Garrett Sarah B. , Koenig Barbara A. , Brown Arleen , Hult Jen R. , Boyd Elizabeth A. , Dry Sarah , Dohan Daniel ,   in collaboration with UC BRAID
Published: January 2015

AbstractBiorepositories, or biobanks, provide researchers with access to biological samples and associated data in support of translational research. Efficient operation and ethical stewardship of biobanks involves coordinated efforts among multiple stakeholders including researchers who manage and use the repository, institutional officials charged with its oversight, and patients and volunteers who contribute samples and data. As advancements in translational research increasingly involve more data derived from larger numbers of diverse samples, the size and governance challenges facing biorepositories have grown. We describe an approach to developing efficient and ethical biobank governance that includes all major stakeholders. This model provides a pathway for addressing the technical and ethical challenges that must be resolved to ensure biorepositories continue to support translational research.
Sympathoadrenal neural crest cells: The known, unknown and forgotten?
Authors: Lumb Rachael , Schwarz Quenten 
Published: January 2015

Neural crest cells (NCCs) are highly migratory progenitor cells that give rise to a vast array of differentiated cell types. One of their key derivatives is the autonomic nervous system (ANS) that is comprised in part from chromaffin cells of the adrenal medulla and organ of Zuckerkandl, the sympathetic chain and additional prevertebral ganglia such as the celiac ganglia, suprarenal ganglia and mesenteric ganglia. In this review we discuss recent advances toward our understanding of how the NCC precursors of the ANS migrate to their target regions, how they are instructed to differentiate into the correct cell types, and the morphogenetic signals controlling their development. Many of these processes remain enigmatic to developmental biologists worldwide. Taking advantage of lineage tracing mouse models one of our own aims is to address the morphogenetic events underpinning the formation of the ANS and to identify the molecular mechanisms that help to segregate a mixed population of NCCs into pathways specific for the sympathetic ganglia, sensory ganglia or adrenal medulla.
Predation pressure in Ugandan cotton fields measured by a sentinel prey method
Authors: Howe Andy G. , Nachman Gösta , Lövei Gábor L. 
Published: January 2015

AbstractPest suppression by natural enemies is an important ecosystem service, which is a valuable resource to poor smallholders in developing countries. Diverse natural enemy assemblages of arthropod predators and parasitoids are documented in various regions in Africa, but our knowledge of their impact on herbivores in agroecosystems remains limited. We conducted experiments in cotton, Gossypium hirsutum L. (Malvaceae), under typical local agronomic practices in Uganda to assess levels of predation pressure ascribed to natural enemies. We measured predation rates on artificial caterpillars made of plasticine glued to cotton plants. Predation pressure on cotton fields varied between 1.96 and 4.1% per day, but was not significantly influenced by cotton treatments (insecticide/no insecticide, monocropping/intercropping with Phaseolus spp.). Predation pressure in non‐crop habitats adjacent to cotton fields was up to 12× higher than in the fields. Marks left on the artificial caterpillars revealed that arthropods and birds were largely accountable for predation in cotton fields, whereas arthropods and small mammals were dominant in non‐cultivated habitats.
Early‐life stress induces anxiety‐like behaviors and activity imbalances in the medial prefrontal cortex and amygdala in adult rats
Authors: Ishikawa Junko , Nishimura Ryoichi , Ishikawa Akinori 
Published: January 2015

AbstractEarly‐life stress increases the prevalence of psychiatric diseases associated with emotional dysregulation. Emotional regulation requires the inhibitory influence of the medial prefrontal cortex (mPFC) on amygdalar activity, and dysfunction of this system is believed to induce anxiety. Because mPFC and amygdala have dense reciprocal connections and projections between them continue to develop until adolescence, early‐life stress may impair the function of this circuit and cause emotional dysregulation. We examined the effects of stress during circuit development on anxiety‐like behaviors, neural activities in the mPFC and amygdala, and impulse transmission in the mPFC–amygdala circuit in adult rats. Early‐life stress, unpredictable stress twice a day for 12 days following early weaning, increased anxiety‐like behaviors in the open‐field and elevated plus‐maze tests. In the open‐field test, stress altered Fos expression in the mPFC and amygdala. Compared to non‐stressed rats, which were exposed to neither unpredictable stress nor early weaning, stressed rats exhibited decreased Fos expression in the right superficial layers of the infralimbic cortex and increased Fos expression in the right basolateral amygdala and both sides of the central amygdala. Electrophysiological analysis revealed that excitatory latencies of mPFC neurons to amygdalar stimulation in stressed rats were significantly longer than control rats in the right, but not left, hemisphere. Stress had no effect on excitatory latencies of amygdalar neurons to mPFC stimulation in the mPFC–amygdala circuits in the both hemisphere. These data suggest that early‐life stress impairs the mPFC–amygdala circuit development, resulting in imbalanced mPFC and amygdala activities and anxiety‐like behaviors.