bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploiting Graphoelements and Convolutional Neural Networks with Long Short Term Memory for Classification of the Human Electroencephalogram
Authors: Nejedly P. , Kremen V. , Sladky V. , Cimbalnik J. , Klimes P. , Plesinger F. , Viscor I. , Pail M. , Halamek J. , Brinkmann B. H. , Brazdil M. , Jurak P. , Worrell G. 
Published: August 2019

AbstractThe electroencephalogram (EEG) is a cornerstone of neurophysiological research and clinical neurology. Historically, the classification of EEG as showing normal physiological or abnormal pathological activity has been performed by expert visual review. The potential value of unbiased, automated EEG classification has long been recognized, and in recent years the application of machine learning methods has received significant attention. A variety of solutions using convolutional neural networks (CNN) for EEG classification have emerged with impressive results. However, interpretation of CNN results and their connection with underlying basic electrophysiology has been unclear. This paper proposes a CNN architecture, which enables interpretation of intracranial EEG (iEEG) transients driving classification of brain activity as normal, pathological or artifactual. The goal is accomplished using CNN with long short-term memory (LSTM). We show that the method allows the visualization of iEEG graphoelements with the highest contribution to the final classification result using a classification heatmap and thus enables review of the raw iEEG data and interpret the decision of the model by electrophysiology means.
Global distribution modelling, invasion risk assessment and niche dynamics of Leucanthemum vulgare (Ox-eye Daisy) under climate change
Authors: Ahmad Rameez , Khuroo Anzar A. , Charles Bipin , Hamid Maroof , Rashid Irfan , Aravind N. A. 
Published: August 2019

AbstractIn an era of climate change, biological invasions by alien species represent one of the main anthropogenic drivers of global environmental change. The present study, using an ensemble modelling approach, has mapped current and future global distribution of the invasive Leucanthemum vulgare (Ox-eye Daisy) and predicted the invasion hotspots under climate change. The current potential distribution of Ox-eye Daisy coincides well with the actual distribution records, thereby indicating robustness of our model. The model predicted a global increase in the suitable habitat for the potential invasion of this species under climate change. Oceania was shown to be the high-risk region to the potential invasion of this species under both current and future climate change scenarios. The results revealed niche conservatism for Australia and Northern America, but contrastingly a niche shift for Africa, Asia, Oceania and Southern America. The global distribution modelling and risk assessment of Ox-eye Daisy has immediate implications in mitigating its invasion impacts under climate change, as well as predicting the global invasion hotspots and developing region-specific invasion management strategies. Interestingly, the contrasting patterns of niche dynamics shown by this invasive plant species provide novel insights towards disentangling the different operative mechanisms underlying the process of biological invasions at the global scale.
Metabolomics-based biomarker discovery for bee health monitoring: A proof of concept study concerning nutritional stress in Bombus terrestris
Authors: Wang Luoluo , Meeus Ivan , Rombouts Caroline , Van Meulebroek Lieven , Vanhaecke Lynn , Smagghe Guy 
Published: August 2019

AbstractBee pollinators are exposed to multiple natural and anthropogenic stressors. Understanding the effects of a single stressor in the complex environmental context of antagonistic/synergistic interactions is critical to pollinator monitoring and may serve as early warning system before a pollination crisis. This study aimed to methodically improve the diagnosis of bee stressors using a simultaneous untargeted and targeted metabolomics-based approach. Analysis of 84 Bombus terrestris hemolymph samples found 8 metabolites retained as potential biomarkers that showed excellent discrimination for nutritional stress. In parallel, 8 significantly altered metabolites, as revealed by targeted profiling, were also assigned as candidate biomarkers. Furthermore, machine learning algorithms were applied to the above-described two biomarker sets, whereby the untargeted eight components showed the best classification performance with sensitivity and specificity up to 99% and 100%, respectively. Based on pathway and biochemistry analysis, we propose that gluconeogenesis contributed significantly to blood sugar stability in bumblebees maintained on a low carbohydrate diet. Taken together, this study demonstrates that metabolomics-based biomarker discovery holds promising potential for improving bee health monitoring and to identify stressor related to energy intake and other environmental stressors.
Successful cloning of a superior buffalo bull
Authors: Selokar Naresh L. , Sharma Papori , Saini Monika , Sheoran Suman , Rajendran Rasika , Kumar Dharmendra , Sharma Rakesh Kumar , Motiani Rajender K. , Kumar Pradeep , Jerome A , Khanna Sudhir , Yadav Prem Singh 
Published: August 2019

AbstractSomatic cell nuclear transfer (SCNT) technology provides an opportunity to multiply superior animals that could speed up dissemination of favorable genes into the population. In the present study, we attempted to reproduce a superior breeding bull of Murrah buffalo, the best dairy breed of buffalo, using donor cells that were established from tail-skin biopsy and seminal plasma. We studied several parameters such as cell cycle stages, histone modifications (H3K9ac and H3K27me3) and expression of developmental genes in donor cells to determine their SCNT reprogramming potentials. We successfully produced the cloned bull from an embryo that was produced from the skin-derived cell. Growth, blood hematology, plasma biochemistries, and reproductive organs of the produced cloned bull were found normal. Subsequently, the bull was employed for semen production. Semen parameters such as CASA (Computer Assisted Semen Analysis) variables and in vitro fertilizing ability of sperms of the cloned bull were found similar to non-cloned bulls, including the donor bull. At present, we have 12 live healthy progenies that were produced using artificial insemination of frozen semen of the cloned bull, which indicate that the cloned bull is fertile and can be utilized in the buffalo breeding schemes. Taken together, we demonstrate that SCNT can be used to reproduce superior buffalo bulls.
Glider observations of interleaving layers beneath the Kuroshio primary velocity core east of Taiwan and analyses of underlying dynamics
Authors: Jan Sen , Wang Shih-Hong , Yang Kai-Chieh , Yang Yiing Jang , Chang Ming-Huei 
Published: August 2019

AbstractSubmesoscale interleaving layers are caused by lateral intrusions of dissimilar water masses in frontal zones, which are significant processes in shaping physical, biogeochemical, and ecological parameters in the ocean. Possible interleaving layers were sometimes observed by ship-based conductivity-temperature-depth (CTD) surveys with coarse spacing between adjacent stations in the Kuroshio region east of Taiwan but have never been examined dynamically. Here we show the characteristics of interleaving layers observed by a Seaglider with two repeated hydrographic surveys along a triangle track east of Taiwan from December 2016 to March 2017. Salinity profiles indicate that prominent interleaving layers appeared in the intermediate layer (approximately 500–800 m) with vertical and horizontal length scales of O(50) m and O(10–100) km, respectively, during our observations. A dipole eddy pair and a relatively large anticyclonic eddy impinged on the Kuroshio during the first and second surveys, respectively, which brought certain impacts on the interleaving motion as the eddy potentially altered the density slope across the Kuroshio. The associated instability analysis and the Turner angle suggest that the double diffusive instability is the primary driving mechanism for the development of interleaving layers.
Diagnostic accuracy of interferon-gamma-induced protein 10 for differentiating active tuberculosis from latent tuberculosis: A meta-analysis
Authors: Qiu Xia , Tang Ying , Zou Rong , Zeng Yan , Yue Yan , Li Wenxing , Qu Yi , Mu Dezhi 
Published: August 2019

AbstractTuberculin skin test and interferon-gamma release assay are not good at differentiating active tuberculosis from latent tuberculosis. Interferon-gamma-induced protein 10 (IP-10) has been widely used to detect tuberculosis infection. However, its values of discriminating active and latent tuberculosis is unknown. To estimate the diagnostic potential of IP-10 for differentiating active tuberculosis from latent tuberculosis, we searched PubMed, Web of Science, Embase, the Cochrane Library, CNKI, Wanfang, VIP and CBM databases. Eleven studies, accounting for 706 participants (853 samples), were included. We used a bivariate diagnostic random-effects model to conduct the primary data. The overall pooled sensitivity, specificity, negative likelihood rate, positive likelihood rate, diagnostic odds ratio and area under the summary receiver operating characteristic curve were 0.72 (95% CI: 0.68–0.76), 0.83 (95% CI: 0.79–0.87), 0.32 (95% CI: 0.22–0.46), 4.63 (95% CI: 2.79–7.69), 17.86 (95% CI: 2.89–38.49) and 0.8638, respectively. This study shows that IP-10 is a potential biomarker for differentiating active tuberculosis from latent tuberculosis.
High-resolution crystal structure of arthropod Eiger TNF suggests a mode of receptor engagement and altered surface charge within endosomes
Authors: Bertinelli Mattia , Paesen Guido C. , Grimes Jonathan M. , Renner Max 
Published: August 2019

AbstractThe tumour necrosis factor alpha (TNFα) superfamily of proteins are critical in numerous biological processes, such as in development and immunity. Eiger is the sole TNFα member described in arthropods such as in the important model organismDrosophila. To date there are no structural data on any Eiger protein. Here we present the structure of the TNF domain of Eiger from the fall armywormSpodoptera frugiperda(SfEiger) to 1.7 Å from a serendipitously obtained crystal without prior knowledge of the protein sequence. Our structure confirms that canonical trimerization is conserved from ancestral TNFs and points towards a mode of receptor engagement. Furthermore, we observe numerous surface histidines on SfEiger, potentially acting as pH switches following internalization into endosomes. Our data contributes to the genome annotation ofS. frugiperda, a voracious agricultural pest, and can serve as a basis for future structure-function investigations of the TNF system in related arthropods such asDrosophila.
Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences
Authors: Lakin Steven M. , Kuhnle Alan , Alipanahi Bahar , Noyes Noelle R. , Dean Chris , Muggli Martin , Raymond Rob , Abdo Zaid , Prosperi Mattia , Belk Keith E. , Morley Paul S. , Boucher Christina 
Published: August 2019

AbstractThe characterization of antimicrobial resistance genes from high-throughput sequencing data has become foundational in public health research and regulation. This requires mapping sequence reads to databases of known antimicrobial resistance genes to determine the genes present in the sample. Mapping sequence reads to known genes is traditionally accomplished using alignment. Alignment methods have high specificity but are limited in their ability to detect sequences that are divergent from the reference database, which can result in a substantial false negative rate. We address this shortcoming through the creation of Meta-MARC, which enables detection of diverse resistance sequences using hierarchical, DNA-based Hidden Markov Models. We first describe Meta-MARC and then demonstrate its efficacy on simulated and functional metagenomic datasets. Meta-MARC has higher sensitivity relative to competing methods. This sensitivity allows for detection of sequences that are divergent from known antimicrobial resistance genes. This functionality is imperative to expanding existing antimicrobial gene databases.
TRAF6 maintains mammary stem cells and promotes pregnancy-induced mammary epithelial cell expansion
Authors: Yamamoto Mizuki , Abe Chiho , Wakinaga Sakura , Sakane Kota , Yumiketa Yo , Taguchi Yuu , Matsumura Takayuki , Ishikawa Kosuke , Fujimoto Jiro , Semba Kentaro , Miyauchi Maki , Akiyama Taishin , Inoue Jun-ichiro 
Published: August 2019

AbstractReceptor activator of nuclear factor (NF)-κB (RANK) signaling promotes pregnancy-dependent epithelial cell differentiation and expansion for mammary gland development, which requires NF-κB pathway-dependent Cyclin D1 induction and inhibitor of DNA binding 2 (Id2) pathway-dependent anti-apoptotic gene induction. However, the roles of tumor necrosis factor receptor-associated factor 6 (TRAF6) remain unclear despite its requirement in RANK signaling. Here we show that TRAF6 is crucial for both mammary stem cell maintenance and pregnancy-induced epithelial cell expansion. TRAF6 deficiency impairs phosphoinositide 3-kinase (PI3K)/AKT and canonical NF-κB pathways, whereas noncanonical NF-κB signaling remains functional. Therefore, we propose that TRAF6 promotes cell proliferation by activating PI3K/AKT signaling to induce retinoblastoma phosphorylation in concert with noncanonical NF-κB pathway-dependent Cyclin D1 induction. Furthermore, TRAF6 inhibits apoptosis by activating canonical NF-κB signaling to induce anti-apoptotic genes with the Id2 pathway. Therefore, proper orchestration of TRAF6-dependent and -independent RANK signals likely establishes mammary gland formation.
Dual wettability on diarylethene microcrystalline surface mimicking a termite wing
Authors: Nishimura Ryo , Hyodo Kengo , Mayama Hiroyuki , Yokojima Satoshi , Nakamura Shinichiro , Uchida Kingo 
Published: August 2019

AbstractThe termite wing has a specific property of wetting in contact with a water droplet: it adsorbs water mist, whereas larger water droplets are bounced on the surface. This is owing to the survival strategy of termites. Here, we reproduce the termite wing’s dual wettability by a photoinduced crystal growth technique. Upon UV irradiation to a microcrystalline surface of a mixture of two diarylethenes, two types of needle-shaped crystals of distinctly different sizes are observed to grow. The surface shows behavior akin to the termite wing’s dual wettability. The bouncing ability of a water droplet is attributed to the smaller-sized needle crystals, whereas the adhesive property is owing to the larger-sized ones, explaining the microstructures of the termite wing. Considering dissipation energy and adhesion energy, the bouncing ability and dual wettability can be explained theoretically. The surface could potentially be used in water harvesting applications.
High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans
Authors: Xu Youqin , Chen Lina , Liu Mengyi , Lu Yanfang , Yue Yanwei , Liu Yue , Chen Honghao , Xie Fuliang , Zhang Chao 
Published: August 2019

AbstractThis study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including gene ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and kyoto encyclopedia of genes and genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and glutathione S-transferase (GST) gene families which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45) and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as regulators of IR response and represent promising markers of IR exposure.
Challenges and future of precision medicine strategies for breast cancer based on a database on drug reactions
Authors: Zhang Xiping , Yang Hongjian , Zhang Ruiping 
Published: August 2019

Abstract
Breast cancer (BC) is a malignancy with the highest incidence in women. Great progress has been made in research related to traditional precision medicine for BC. However, many reports have suggested that patients with BC have not benefited a lot from such progress. Thus, we analyze traditional precision medicine strategies for BC, sum up their limitations and challenges, and preliminarily propose future orientations of precision medicine strategies based on a database on drug reaction of patients with BC. According to related research, traditional precision medicine strategies for BC, which are based on molecular subtypes, perform pertinent treatments, new drug research and development according to molecular typing results. Nevertheless, these strategies still have some deficiencies. First, there are very few patients with each molecular subtype, the match ratio of drugs is low. Second, these strategies can not solve the problem of poor drug sensitivity resulting from heterogeneity. The main strategy we put forward in the present paper is based on patients’ varying drug reactions. Focusing on treating existing patients and maximizing the utilization of existing drugs, it is expected to not have deficiencies of traditional precision medicine for BC, including low match rate and poor therapeutic efficacy arising from tumor heterogeneity of BC.
BMSC-derived exosomes carrying microRNA-122-5p promote proliferation of osteoblasts in osteonecrosis of the femoral head
Authors: Liao Wen , Ning Yu , Xu Hai-Jia , Zou Wen-Zhong , Hu Jing , Liu Xiang-Zhong , Yang Yi , Li Zhang-Hua 
Published: August 2019

Abstract
Mesenchymal stem cells (MSCs) with multipotential differentiation capacity can differentiate into bone cells under specific conditions and can be used to treat osteonecrosis (ON) of the femoral head (ONFH) through cell transplantation. The current study aims to explore the role of bone marrow (BM) MSCs (BMSCs)-derived exosomes carrying microRNA-122-5p (miR-122-5p) in ONFH rabbit models.
First, rabbit models with ONFH were established. ONFH-related miRNAs were screened using the Gene Expression Omnibus (GEO) database. A gain-of-function study was performed to investigate the effect of miR-122-5p on osteoblasts and BMSCs and effects of exosomes carrying miR-122-5p on ONFH. Co-culture experiments for osteoblasts and BMSCs were performed to examine the role of exosomal miR-122-5p in osteoblast proliferation and osteogenesis. The target relationship between miR-122-5p and Sprouty2 (SPRY2) was tested.
MiR-122, significantly decreased in ONFH in the GSE89587 expression profile, was screened. MiR-122-5p negatively regulated SPRY2 and elevated the activity of receptor tyrosine kinase (RTK), thereby promoting the proliferation and differentiation of osteoblasts. In vivo experiments indicated that bone mineral density (BMD), trabecular bone volume (TBV), and mean trabecular plate thickness (MTPT) of femoral head were increased after over-expressing miR-122-5p in exosomes. Significant healing of necrotic femoral head was also observed.
Exosomes carrying over-expressed miR-122-5p attenuated ONFH development by down-regulating SPRY2 via the RTK/Ras/mitogen-activated protein kinase (MAPK) signaling pathway. Findings in the present study may provide miR-122-5p as a novel biomarker for ONFH treatment.
DNA methylation in satellite repeats disorders
Authors: Francastel Claire , Magdinier Frédérique 
Published: August 2019

AbstractDespite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements.Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.
New advances in extracting and learning from protein–protein interactions within unstructured biomedical text data
Authors: Caufield J. Harry , Ping Peipei 
Published: August 2019

Abstract
Protein–protein interactions, or PPIs, constitute a basic unit of our understanding of protein function. Though substantial effort has been made to organize PPI knowledge into structured databases, maintenance of these resources requires careful manual curation. Even then, many PPIs remain uncurated within unstructured text data. Extracting PPIs from experimental research supports assembly of PPI networks and highlights relationships crucial to elucidating protein functions. Isolating specific protein–protein relationships from numerous documents is technically demanding by both manual and automated means. Recent advances in the design of these methods have leveraged emerging computational developments and have demonstrated impressive results on test datasets. In this review, we discuss recent developments in PPI extraction from unstructured biomedical text. We explore the historical context of these developments, recent strategies for integrating and comparing PPI data, and their application to advancing the understanding of protein function. Finally, we describe the challenges facing the application of PPI mining to the text concerning protein families, using the multifunctional 14-3-3 protein family as an example.
12 Gbit/s three‐tap FFE half‐rate transmitter with low jitter clock buffering scheme
Authors: Park K. , Oh T. 
Published: August 2019

A 12 Gbit/s feed‐forward equalisation (FFE) transmitter has been designed in 65 nm CMOS process. The three‐tap/half‐rate high‐speed tap signal generation technique for the segmented FFE driver is presented. A clock buffer scheme to make the equivalent signal transition for each segmented unit contributes to a low jitter performance. The measurement results show 9.31 ps RMS jitter at 12 Gbit/s after equalisation and the horizontal eye‐opening is 0.204 UI at BER. The prototype transmitter occupies and consumes 1.58 pJ/bit.