bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAMUEL HOWARD AND THE MUSIC FOR THE INSTALLATION OF THE DUKE OF GRAFTON AS CHANCELLOR OF CAMBRIDGE UNIVERSITY, 1769
Authors: HOWARD ALAN 
Published: August 2017

ABSTRACTSamuel Howard (?1710–1782) has long been a familiar inhabitant of the diligent footnotes of Handel biographers. A choirboy in the Chapel Royal, he was a member of Handel's chorus and the composer of much theatre music of his own; he later became organist of both St Bride's, Fleet Street and nearby St Clement Danes, Strand, where he was buried in 1782. His most significant and ambitious work is his fine orchestrally accompanied anthem ‘This is the day which the Lord hath made’, published posthumously in 1792 with an impressive title page detailing the performance of the work ‘at St Margaret's Church before the governors of the Westminster Infirmary, in the Two Universities, and upon many other Publick Occasions in different parts of the Kingdom’. This article confirms for the first time that this work originated as Howard's doctoral exercise; contemporary press reports and information in the University archives make clear that the composer's doctorate was linked to the provision of music for the Duke of Grafton's installation as Chancellor of Cambridge University in 1769. Surviving information about this event offers a glimpse of musical life in Cambridge on a comparable scale to the much better reported proceedings upon similar occasions in Oxford. This evidence then serves as a starting-point from which to consider Howard's later prominence as a director of high-profile public performances in London and the provinces.
Contribution of C1485T mutation in the HBx gene to human and murine hepatocarcinogenesis
Authors: Hagiwara Satoru , Nishida Naoshi , Park Ah-Mee , Komeda Yoriaki , Sakurai Toshiharu , Watanabe Tomohiro , Kudo Masatoshi 
Published: August 2017

AbstractAlthough Hepatitis B virus (HBV) X gene mutations are frequently detected in HBV-related human hepatocellular carcinoma (HCC) patients, causative HBx mutations in the development of HCC have not yet been determined. We herein identified C1485T and C1653T mutations in the HBx gene as independent risk of HCC for HBV through the analysis using serum from chronic hepatitis B patients. We generated transgenic mice expressing wild-type (WT-HBxTg) and mutant (C1485T-HBxTg) HBx to assess the carcinogenic potential of mutated HBx. C1485T-HBxTg mice were more susceptible to diethylnitrosamine-induced hepatocarcinogenesis than WT-HBxTg mice and control non-Tg mice. The promotion of hepatocarcinogenesis in C1485T-HBxTg mice was accompanied by the activation of β-catenin and Jun N-terminal kinase (JNK) signaling pathways as well as the production of reactive oxygen species, whereas the activation of nuclear factor-kappa B in the livers of C1485T-HBxTg mice was attenuated. These results demonstrate that the HBx C1485T mutation contributes to human and murine hepatocarcinogenesis.
Ameliorative effects of melatonin on dark-induced leaf senescence in gardenia (Gardenia jasminoides Ellis): leaf morphology, anatomy, physiology and transcriptome
Authors: Zhao Daqiu , Wang Rong , Meng Jiasong , Li Zhiyuan , Wu Yanqing , Tao Jun 
Published: August 2017

AbstractCut gardenia (Gardenia jasminoides Ellis) foliage is widely used as a vase material or flower bouquet indoors; however, insufficient indoor light accelerates its senescence, which shortens its viewing time. In this study, applying melatonin to delay gardenia leaf senescence when exposed to extremely low light condition (darkness), and the results showed that 1.0 mM was the effective concentration. At this concentration, chlorophyll contents and chlorophyll fluorescence parameters (Fv/Fm, Fv/F0 and Y(II)) increased, while the carotenoid and flavonoid contents decreased. Meanwhile, stress physiological indices decreased in response to exogenous melatonin application, whereas an increase in glutamine synthetase activity, water and soluble protein contents was observed. Moreover, exogenous melatonin application also reduced leaf programmed cell death under darkness, increased the endogenous melatonin level, expression levels of tryptophan decarboxylase gene, superoxide dismutase and catalase activities and the ascorbate–glutathione cycle, and maintained more intact anatomical structures. Furthermore, transcriptome sequencing revealed that various biological processes responded to exogenous melatonin application, including carbohydrate metabolism, amino acid metabolism, lipid metabolism, plant hormone signal transduction and pigment biosynthesis. Consequently, dark-induced leaf senescence in gardenia was significantly delayed. These results provided a better understanding for improving the ornamental value of cut gardenia foliage using melatonin.
An overview of multi-task learning
Authors: Zhang Yu , Yang Qiang 
Published: August 2017

AbstractAs a promising area in machine learning, multi-task learning (MTL) aims to improve the performance of multiple related learning tasks by leveraging useful information among them. In this paper, we give an overview of MTL by first giving a definition of MTL. Then several different settings of MTL are introduced, including multi-task supervised learning, multi-task unsupervised learning, multi-task semi-supervised learning, multi-task active learning, multi-task reinforcement learning, multi-task online learning and multi-task multi-view learning. For each setting, representative MTL models are presented. In order to speed up the learning process, parallel and distributed MTL models are introduced. Many areas, including computer vision, bioinformatics, health informatics, speech, natural language processing, web applications and ubiquitous computing, use MTL to improve the performance of the applications involved and some representative works are reviewed. Finally, recent theoretical analyses for MTL are presented.
GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies
Authors: Wei Runmin , Wang Jingye , Jia Erik , Chen Tianlu , Ni Yan , Jia Wei 
Published: August 2017

AbstractLeft-censored missing values commonly exist in targeted metabolomics datasets and can be considered as missing not at random (MNAR). Improper data processing procedures for missing values will cause adverse impacts on subsequent statistical analyses. However, few imputation methods have been developed and applied to the situation of MNAR in the field of metabolomics. Thus, a practical left-censored missing value imputation method is urgently needed. We have developed an iterative Gibbs sampler based left-censored missing value imputation approach (GSimp). We compared GSimp with other three imputation methods on two real-world targeted metabolomics datasets and one simulation dataset using our imputation evaluation pipeline. The results show that GSimp outperforms other imputation methods in terms of imputation accuracy, observation distribution, univariate and multivariate analyses, and statistical sensitivity. The R code for GSimp, evaluation pipeline, vignette, real-world and simulated targeted metabolomics datasets are available at:https://github.com/WandeRum/GSimp.Author summaryMissing values caused by the limit of detection/quantification (LOD/LOQ) were widely observed in mass spectrometry (MS)-based targeted metabolomics studies and could be recognized as missing not at random (MNAR). MNAR leads to biased parameter estimations and jeopardizes following statistical analyses in different aspects, such as distorting sample distribution, impairing statistical power, etc. Although a wide range of missing value imputation methods was developed for –omics studies, a limited number of methods was designed appropriately for the situation of MNAR currently. To alleviate problems caused by MNAR and facilitate targeted metabolomics studies, we developed a Gibbs sampler based missing value imputation approach, called GSimp, which is public-accessible on GitHub. And we compared our method with existing approaches using an imputation evaluation pipeline on real-world and simulated metabolomics datasets to demonstrate the superiority of our method from different perspectives.
Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements
Authors: Mumbach Maxwell R. , Satpathy Ansuman T. , Boyle Evan A. , Dai Chao , Gowen Benjamin G. , Cho Seung Woo , Nguyen Michelle L. , Rubin Adam J. , Granja Jeffrey M. , Kazane Katelynn R. , Wei Yuning , Nguyen Trieu , Greenside Peyton G. , Corces M. Ryan , Tycko Josh , Simeonov Dimitre R. , Suliman Nabeela , Li Rui , Xu Jin , Flynn Ryan A. , Kundaje Anshul , Khavari Paul A. , Marson Alexander , Corn Jacob E. , Quertermous Thomas , Greenleaf William J. , Chang Howard Y. 
Published: August 2017

ABSTRACTThe challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here, we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naïve T cells to T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a four-fold increase of potential target genes for autoimmune and cardiovascular diseases.
A large, open source dataset of stroke anatomical brain images and manual lesion segmentations
Authors: Liew Sook-Lei , Anglin Julia M. , Banks Nick W. , Sondag Matt , Ito Kaori L. , Kim Hosung , Chan Jennifer , Ito Joyce , Jung Connie , Khoshab Nima , Lefebvre Stephanie , Nakamura William , Saldana David , Schmiesing Allie , Tran Cathy , Vo Danny , Ard Tyler , Heydari Panthea , Kim Bokkyu , Aziz-Zadeh Lisa , Cramer Steven C. , Liu Jingchun , Soekadar Surjo , Nordvik Jan-Egil , Westlye Lars T. , Wang Junping , Winstein Carolee , Yu Chunshui , Ai Lei , Koo Bonhwang , Craddock R. Cameron , Milham Michael , Lakich Matthew , Pienta Amy , Stroud Alison 
Published: August 2017

AbstractStroke is the leading cause of adult disability worldwide, with up to two-thirds of individuals experiencing long-term disabilities. Large-scale neuroimaging studies have shown promise in identifying robust biomarkers (e.g., measures of brain structure) of long-term stroke recovery following rehabilitation. However, analyzing large rehabilitation-related datasets is problematic due to barriers in accurate stroke lesion segmentation. Manually-traced lesions are currently the gold standard for lesion segmentation on T1-weighted MRIs, but are labor intensive and require anatomical expertise. While algorithms have been developed to automate this process, the results often lack accuracy. Newer algorithms that employ machine-learning techniques are promising, yet these require large training datasets to optimize performance. Here we present ATLAS (Anatomical Tracings of Lesions After Stroke), an open-source dataset of 304 T1-weighted MRIs with manually segmented lesions and metadata. This large, diverse dataset can be used to train and test lesion segmentation algorithms and provides a standardized dataset for comparing the performance of different segmentation methods. We hope ATLAS release 1.1 will be a useful resource to assess and improve the accuracy of current lesion segmentation methods.
Multi-reference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets
Authors: Ammar Constantin , Berchtold Evi , Csaba Gergely , Schmidt Andreas , Imhof Axel , Zimmer Ralf 
Published: August 2017

AbstractSpectral libraries play a central role in the analysis of data-independent-acquisition (DIA) proteomics experiments. A main assumption in current spectral library tools is that a single characteristic intensity pattern (CIP) suffices to describe the fragmentation of a peptide in a particular charge state (peptide charge pair). However, we find that this is often not the case. We carry out a systematic evaluation of spectral variability over public repositories and in-house datasets. We show that spectral variability is widespread and partly occurs under fixed experimental conditions. Using clustering of preprocessed spectra, we derive a limited number of Multiple Characteristic Intensity Patterns (MCIPs) for each peptide charge pair, which allow almost complete coverage of our heterogeneous dataset without affecting the false discovery rate. We show that a MCIP library derived from public repositories performs in most cases similar to a “custom-made” spectral library, which has been acquired under identical experimental conditions as the query spectra. We apply the MCIP approach to a DIA data set and observe a significant increase in peptide recognition. We propose the MCIP approach as an easy-to-implement addition to current spectral library search engines and as a new way to utilize the data stored in spectral repositories.
BBSome trains remove activated GPCRs from cilia by enabling passage through the transition zone
Authors: Ye Fan , Nager Andrew R. , Nachury Maxence V. 
Published: August 2017

AbstractA diffusion barrier at the transition zone enables the compartmentalization of signaling molecules by cilia. The BBSome and the small GTPase Arl6, which triggers BBSome coat polymerization, are required for the exit of activated signaling receptors from cilia, but how diffusion barriers are crossed when membrane proteins exit cilia remains to be determined. Here we found that activation of the ciliary GPCRs Smoothened and SSTR3 drove the Arl6-dependent assembly of large, highly processive and cargo-laden retrograde BBSome trains. Single-molecule imaging revealed that the assembly of BBSome trains enables the lateral transport of ciliary GPCRs across the transition zone. Yet, the removal of activated GPCRs from cilia was inefficient because a second, periciliary diffusion barrier was infrequently crossed. We conclude that exit from cilia is a two-step process in which BBSome/Arl6 trains first moves activated GPCRs through the transition zone before a periciliary barrier can be crossed.SummaryUpon activation, GPCRs must exit cilia for appropriate signal transduction. Using bulk imaging of BBSome and single molecule imaging of GPCRs, Ye et al. demonstrate that retrograde BBSome trains assemble on-demand upon GPCR activation and ferry GPCRs across the transition zone. Yet, ciliary exit often fails because of a second diffusion barrier.
Opposite effects of lateralised transcranial alpha versus gamma stimulation on spatial attention
Authors: Wöstmann Malte , Vosskuhl Johannes , Obleser Jonas , Herrmann Christoph S. 
Published: August 2017

AbstractSpatial attention relatively increases the power of neural 10-Hz alpha oscillations in the hemisphere ipsilateral to attention. The functional roles of lateralised oscillations for attention are unclear. Here, 20 human participants performed a dichotic listening task under continuous transcranial alternating current stimulation (tACS) at alpha (10 Hz, vs sham) or gamma (47 Hz, vs sham) frequency, targeting left temporo-parietal cortex. Participants attended to four spoken numbers presented to one ear, while ignoring numbers on the other ear. As predicted, we found that alpha-tACS contralateral to the attended ear decreased recall of attended targets. Notably, gamma-tACS reversed the effect. Results provide a proof of concept that externally amplified oscillations can enhance spatial attention and facilitate attentional selection of speech. Furthermore, opposite effects of alpha versus gamma oscillations support the view that, across modalities, states of high alpha are incommensurate with active neural processing as reflected by states of high gamma.
Seamless Multiscale Modeling of Coagulation Using Dissipative Particle Dynamics
Authors: Yazdani Alireza , Li Zhen , Humphrey Jay D. , Karniadakis George Em 
Published: August 2017

AbstractWe propose a new multiscale framework that seamlessly integrates four key components of blood clotting namely, blood rheology, cell mechanics, coagulation kinetics and transport of species and platelet adhesive dynamics. We use transport dissipative particle dynamics (tDPD), which is the extended form of original DPD, as the base solver, while a coarse-grained representation of blood cell’s membrane accounts for its mechanics. Our results show the dominant effect of blood flow and high Peclet numbers on the reactive transport of the chemical species signifying the importance of membrane bound reactions on the surface of adhered platelets. This new multiscale particle-based methodology helps us probe synergistic mechanisms of thrombus formation, and can open new directions in addressing other biological processes from sub-cellular to macroscopic scales.
Dramatic evolution of body length due to post-embryonic changes in cell size in a newly discovered close relative ofC. elegans
Authors: Woodruff Gavin C. , Phillips Patrick C. 
Published: August 2017

AbstractUnderstanding morphological diversity—and morphological constrainto—has been a central question in evolutionary biology since its inception. Nematodes of the genusCaenorhabditis, which contains the well-studied model systemC. elegans, display remarkable morphological consistency in the face of extensive genetic divergence. Here, we provide a description of the broad developmental patterns of a recently discovered species,C.sp. 34, which was isolated from fresh figs in Okinawa and which is among the closest known relatives ofC. elegans.C.sp. 34 displays an extremely large body size and can grow to be nearly twice as long asC. elegansand all other known members of the genus. Observations of the timing of developmental milestones reveal thatC.sp. 34 develops about twice as slowly asC. elegans. Measurements of embryo and larval size show that the size difference betweenC.sp. 34 andC. elegansis largely due to post-embryonic events, particularly during the transition from larval to adult stages. This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells. The overall difference in body size is therefore largely attributable to changes in cell size via increased cytoplasmic volume. Because of its close relationship toC. elegans, the distinctness ofC.sp. 34 provides an ideal system for the detailed analysis of evolutionary diversification. The context of over forty years ofC. elegansdevelopmental genetics also reveals clues into how natural selection and developmental constraint act jointly to promote patterns of morphological stasis and divergence in this group.
Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)
Authors: Parks Matthew , Nakov Teofil , Ruck Elizabeth , Wickett Norman J. , Alverson Andrew J. 
Published: August 2017

ABSTRACTPremise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.
Epigenomic and 3D genome architecture in naïve and primed human embryonic stem cell states
Authors: Battle Stephanie L. , Jayavelu Naresh Doni , Azad Robert N. , Hesson Jennifer , Ahmed Faria N. , Zoller Joseph A. , Mathieu Julie , Ruohola-Baker Hannele , Ware Carol B. , David Hawkins R. 
Published: August 2017

ABSTRACTDuring mammalian embryogenesis changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the pre-implantation blastocyst (naïve) and post-implantation epiblast (primed), our data demonstrate that a substantial portion of known human enhancers are pre-marked by H3K4me1 in naïve cells, providing an enhanced open chromatin state in naïve pluripotency. The naïve enhancer repertoire occupies nine percent of the genome, three times that of primed cells, and can exist in broad chromatin domains over fifty kilobases. Enhancer chromatin states are largely poised. Seventy-seven percent of naïve enhancers are decommissioned in a stepwise manner as cells become primed. While primed topological associated domains are unaltered upon differentiation, naïve domains expand across primed boundaries, impacting three dimensional genome architecture. Differential topological associated domain edges coincide with naïve H3K4me1 enrichment. Our results suggest that naïve-derived cells have a chromatin landscape reflective of early embryogenesis.