bluuebunny/crossref_metadata_2025_split huggingface dataset:
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation
Authors: Chen Ting-Wen , Gan Ruei-Chi , Fang Yi-Kai , Chien Kun-Yi , Liao Wei-Chao , Chen Chia-Chun , Wu Timothy H. , Chang Ian Yi-Feng , Yang Chi , Huang Po-Jung , Yeh Yuan-Ming , Chiu Cheng-Hsun , Huang Tzu-Wen , Tang Petrus 
Published: August 2017

AbsatractAlong with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/. This new web-based annotator will shed light on field studies involving organisms without a reference genome.
Towards a new paleotemperature proxy from reef coral occurrences
Authors: Lauchstedt Andreas , Pandolfi John M. , Kiessling Wolfgang 
Published: August 2017

AbstractGlobal mean temperature is thought to have exceeded that of today during the last interglacial episode (LIG, ~ 125,000 yrs b.p.) but robust paleoclimate data are still rare in low latitudes. Occurrence data of tropical reef corals may provide new proxies of low latitude sea-surface temperatures. Using modern reef coral distributions we developed a geographically explicit model of sea surface temperatures. Applying this model to coral occurrence data of the LIG provides a latitudinal U-shaped pattern of temperature anomalies with cooler than modern temperatures around the equator and warmer subtropical climes. Our results agree with previously published estimates of LIG temperatures and suggest a poleward broadening of the habitable zone for reef corals during the LIG.
T-bet, but not Gata3, overexpression is detrimental in a neurotropic viral infection
Authors: Sato Fumitaka , Kawai Eiichiro , Martinez Nicholas E. , Omura Seiichi , Park Ah-Mee , Takahashi Satoru , Yoh Keigyou , Tsunoda Ikuo 
Published: August 2017

AbstractIntracerebral Theiler’s murine encephalomyelitis virus (TMEV) infection in mice induces inflammatory demyelination in the central nervous system. Although C57BL/6 mice normally resistant to TMEV infection with viral clearance, we have previously demonstrated that RORγt-transgenic (tg) C57BL/6 mice, which have Th17-biased responses due to RORγt overexpression in T cells, became susceptible to TMEV infection with viral persistence. Here, using T-bet-tg C57BL/6 mice and Gata3-tg C57BL/6 mice, we demonstrated that overexpression of T-bet, but not Gata3, in T cells was detrimental in TMEV infection. Unexpectedly, T-bet-tg mice died 2 to 3 weeks after infection due to failure of viral clearance. Here, TMEV infection induced splenic T cell depletion, which was associated with lower anti-viral antibody and T cell responses. In contrast, Gata3-tg mice remained resistant, while Gata3-tg mice had lower IFN-γ and higher IL-4 production with increased anti-viral IgG1 responses. Thus, our data identify how overexpression of T-bet and Gata3 in T cells alters anti-viral immunity and confers susceptibility to TMEV infection.
Self-powered Real-time Movement Monitoring Sensor Using Triboelectric Nanogenerator Technology
Authors: Jin Liangmin , Tao Juan , Bao Rongrong , Sun Li , Pan Caofeng 
Published: August 2017

AbstractThe triboelectric nanogenerator (TENG) has great potential in the field of self-powered sensor fabrication. Recently, smart electronic devices and movement monitoring sensors have attracted the attention of scientists because of their application in the field of artificial intelligence. In this article, a TENG finger movement monitoring, self-powered sensor has been designed and analysed. Under finger movements, the TENG realizes the contact and separation to convert the mechanical energy into electrical signal. A pulse output current of 7.8 μA is generated by the bending and straightening motions of the artificial finger. The optimal output power can be realized when the external resistance is approximately 30 MΩ. The random motions of the finger are detected by the system with multiple TENG sensors in series. This type of flexible and self-powered sensor has potential applications in artificial intelligence and robot manufacturing.
Computational approaches for investigating interfacial adhesion phenomena of polyimide on silica glass
Authors: Min Kyoungmin , Rammohan Aravind R. , Lee Hyo Sug , Shin Jaikwang , Lee Sung Hoon , Goyal Sushmit , Park Hyunhang , Mauro John C. , Stewart Ross , Botu Venkatesh , Kim Hyunbin , Cho Eunseog 
Published: August 2017

AbstractThis manuscript provides a comprehensive study of adhesion behavior and its governing mechanisms when polyimide undergoes various modes of detachment from silica glass. Within the framework of steered molecular dynamics, we develop three different adhesion measurement techniques: pulling, peeling, and sliding. Such computational methodologies can be applied to investigate heterogeneous materials with differing interfacial adhesion modes. Here, a novel hybrid potential involving a combination of the INTERFACE force field in conjunction with ReaxFF and including Coulombic and Lennard-Jones interactions is employed to study such interfaces. The studies indicate that the pulling test requires the largest force and the shortest distance to detachment as the interfacial area is separated instantaneously, while the peeling test is observed to exhibit the largest distance for detachment because it separates via line-by-line adhesion. Two kinds of polyimides, aromatic and aliphatic type, are considered to demonstrate the rigidity dependent adhesion properties. The aromatic polyimide, which is more rigid due to the stronger charge transfer complex between chains, requires a greater force but a smaller distance at detachment than the aliphatic polyimide for all of the three methodologies.
Acoustic allometry revisited: morphological determinants of fundamental frequency in primate vocal production
Authors: Garcia Maxime , Herbst Christian T. , Bowling Daniel L. , Dunn Jacob C. , Fitch W. Tecumseh 
Published: August 2017

AbstractA fundamental issue in the evolution of communication is the degree to which signals convey accurate (“honest”) information about the signaler. In bioacoustics, the assumption that fundamental frequency (fo) should correlate with the body size of the caller is widespread, but this belief has been challenged by various studies, possibly because larynx size and body size can vary independently. In the present comparative study, we conducted excised larynx experiments to investigate this hypothesis rigorously and explore the determinants offo. Using specimens from eleven primate species, we carried out an inter-specific investigation, examining correlations between the minimumfoproduced by the sound source, body size and vocal fold length (VFL). We found that, across species, VFL predicted minimumfomuch better than body size, clearly demonstrating the potential for decoupling between larynx size and body size in primates. These findings shed new light on the diversity of primate vocalizations and vocal morphology, highlighting the importance of vocal physiology in understanding the evolution of mammal vocal communication.
3-Mercaptopyruvate sulfurtransferase produces potential redox regulators cysteine- and glutathione-persulfide (Cys-SSH and GSSH) together with signaling molecules H2S2, H2S3 and H2S
Authors: Kimura Yuka , Koike Shin , Shibuya Norihiro , Lefer David , Ogasawara Yuki , Kimura Hideo 
Published: August 2017

AbstractCysteine-persulfide (Cys-SSH) is a cysteine whose sulfhydryl group is covalently bound to sulfur (sulfane sulfur). Cys-SSH and its glutathione (GSH) counterpart (GSSH) have been recognized as redox regulators, some of which were previously ascribed to cysteine and GSH. However, the production of Cys-SSH and GSSH is not well understood. Here, we show that 3-mercaptopyruvate sulfurtransferase (3MST) produces Cys-SSH and GSSH together with the potential signaling molecules hydrogen per- and tri-sulfide (H2S2 and H2S3). Cys-SSH and GSSH are produced in the brain of wild-type mice but not in those of 3MST-KO mice. The levels of total persulfurated species in the brain of 3MST-KO mice are less than 50% of that in the brain of wild-type mice. Purified recombinant 3MST and lysates of COS cells expressing 3MST showed that Cys-SSH and GSSH were produced in the presence of physiological concentrations of cysteine and glutathione, while those with longer sulfur chains, Cys-SSnH and GSSnH, were produced in the presence of lower than physiological concentrations of cysteine and glutathione. The present study provides new insights into the production and physiological roles of these persulfurated species as well as the therapeutic targets for diseases in which these molecules are involved.
Sex-Specific Routes To Immune Senescence In Drosophila melanogaster
Authors: Kubiak Marco , Tinsley Matthew C. 
Published: August 2017

AbstractAnimal immune systems change dramatically during the ageing process, often accompanied by major increases in pathogen susceptibility. However, the extent to which senescent elevations in infection mortality are causally driven by deteriorations in canonical systemic immune processes is unclear. We studied Drosophila melanogaster and compared the relative contributions of impaired systemic immune defences and deteriorating barrier defences to increased pathogen susceptibility in aged flies. To assess senescent changes in systemic immune response efficacy we injected one and four-week old flies with the entomopathogenic fungus Beauveria bassiana and studied subsequent mortality; whereas to include the role of barrier defences we infected flies by dusting the cuticle with fungal spores. We show that the processes underlying pathogen defence senescence differ between males and females. Both sexes became more susceptible to infection as they aged. However, we conclude that for males, this was principally due to deterioration in barrier defences, whereas for females systemic immune defence senescence was mainly responsible. We discuss the potential roles of sex-specific selection on the immune system and behavioural variation between males and females in driving these different senescent trends.
Mapping the Spatial Distribution and Characteristics of Lineaments Using Fractal and Multifractal Models: A Case Study from Northeastern Yunnan Province, China
Authors: Ni Chunzhong , Zhang Shitao , Chen Zhong , Yan Yongfeng , Li Yujian 
Published: August 2017

AbstractThis study describes the fractal dimensions of the spatial distributions of lineaments as an index of the complexity of faults, and the results could provide new insights into the migration of ore-bearing fluid. The Segment Tracing Algorithm method is employed to extract the lineaments in northeast Yunnan Province from a remote sensing image. Box-counting fractal and multifractal models are used to analyze the fractal and multifractal spatial distribution characteristics of the linear structures. The different directions of the linear structure fractal dimensions are similar in the study area. The fractal dimensions of all lineaments, northeast trending lineaments and northwest trending lineaments are 1.98, 1.94 and 1.95, respectively. The dimensions of four large ore deposit fields, Kuangshanchang, Qilinchang, Maozu, and Lemachang, are 1.93, 1.92, 1.95, and 1.93, respectively. The fractal dimensions of these four fields are greater than those of the South China lineaments. The super-large and large ore deposits are consistent with fractal dimensions with high values. The scale index and the singular index show nonlinear relationships with any real number, and the fractal dimension spectrum has a unimodal curve. This study provides a useful reference for deposit exploration in areas with topographies similar to that in northeastern Yunnan.
Integrated Analysis of Copy Number Variations and Gene Expression Profiling in Hepatocellular carcinoma
Authors: Zhou Chenhao , Zhang Wentao , Chen Wanyong , Yin Yirui , Atyah Manar , Liu Shuang , Guo Lei , Shi Yi , Ye Qinghai , Dong Qiongzhu , Ren Ning 
Published: August 2017

AbstractHepatocellular carcinoma (HCC) is one of the top three cancer killers worldwide. To identify CNV-driven differentially expressed genes (DEGs) in HBV related HCC, this study integrated analysis of copy number variations (CNVs) and gene expression profiling. Significant genes in regions of CNVs were overlapped with those obtained from the expression profiling. 93 CNV-driven genes exhibiting increased expression in the duplicated regions and 45 showing decreased expression in the deleted regions were obtained, which duplications and deletions were mainly documented at chromosome 1 and 4. Functional and pathway enrichment analyses were performed using DAVID and KOBAS, respectively. They were mainly enriched in metabolic process and cell cycle. Protein-protein interaction (PPI) network was constructed by Cytoscape, then four hub genes were identified. Following, survival analyses indicated that only high NPM1 expression was significantly and independently associated with worse survival and increased recurrence in HCC patients. Moreover, this correlation remained significant in patients with early stage of HCC. In addition, we showed that NPM1 was overexpressed in HCC cells and in HCC versus adjacent non-tumor tissues. In conclusion, these results showed that integrated analysis of genomic and expression profiling might provide a powerful potential for identifying CNV-driven genes in HBV related HCC pathogenesis.
SRSF1 suppresses selection of intron-distal 5′ splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein
Authors: Ahsan Khalid Bin , Masuda Akio , Rahman Mohammad Alinoor , Takeda Jun-ichi , Nazim Mohammad , Ohkawara Bisei , Ito Mikako , Ohno Kinji 
Published: August 2017

AbstractDok-7 is a non-catalytic adaptor protein that facilitates agrin-induced clustering of acetylcholine receptors (AChR) at the neuromuscular junction. Alternative selection of 5′ splice sites (SSs) of DOK7 intron 4 generates canonical and frame-shifted transcripts. We found that the canonical full-length Dok-7 enhanced AChR clustering, whereas the truncated Dok-7 did not. We identified a splicing cis-element close to the 3′ end of exon 4 by block-scanning mutagenesis. RNA affinity purification and mass spectrometry revealed that SRSF1 binds to the cis-element. Knocking down of SRSF1 enhanced selection of the intron-distal 5′ SS of DOK7 intron 4, whereas MS2-mediated artificial tethering of SRSF1 to the identified cis-element suppressed it. Isolation of an early spliceosomal complex revealed that SRSF1 inhibited association of U1 snRNP to the intron-distal 5′ SS, and rather enhanced association of U1 snRNP to the intron-proximal 5′ SS, which led to upregulation of the canonical DOK7 transcript. Integrated global analysis of CLIP-seq and RNA-seq also indicated that binding of SRSF1 immediately upstream to two competing 5′ SSs suppresses selection of the intron-distal 5′ SS in hundreds of human genes. We demonstrate that SRSF1 critically regulates alternative selection of adjacently placed 5′ SSs by modulating binding of U1 snRNP.
eIF4B phosphorylation at Ser504 links synaptic activity with protein translation in physiology and pathology
Authors: Bettegazzi Barbara , Bellani Serena , Roncon Paolo , Guarnieri Fabrizia Claudia , Bertero Alice , Codazzi Franca , Valtorta Flavia , Simonato Michele , Grohovaz Fabio , Zacchetti Daniele 
Published: August 2017

AbstractNeuronal physiology requires activity-driven protein translation, a process in which translation initiation factors are key players. We focus on eukaryotic initiation factor 4B (eIF4B), a regulator of protein translation, whose function in neurons is undetermined. We show that neuronal activity affects eIF4B phosphorylation and identify Ser504 as a phosphorylation site regulated by casein kinases and sensitive to the activation of metabotropic glutamate receptors. Ser504 phosphorylation increases eIF4B recruitment to the pre-initiation complex and influences eIF4B localization at synapses. Moreover, Ser504 phosphorylation modulates the translation of protein kinase Mζ. Therefore, by sensing synaptic activity, eIF4B could adjust translation to neuronal needs, promoting adaptive changes in synaptic plasticity. We also show that Ser504 phosphorylation is increased in vivo in a rat model of epilepsy during epileptogenesis i.e. when translation drives maladaptive synaptic changes. We propose eIF4B as a mediator between neuronal activity and translation, with relevance in the control of synaptic plasticity.
RERT: A Novel Regression Tree Approach to Predict Extrauterine Disease in Endometrial Carcinoma Patients
Authors: Vezzoli Marika , Ravaggi Antonella , Zanotti Laura , Miscioscia Rebecca Angelica , Bignotti Eliana , Ragnoli Monica , Gambino Angela , Ruggeri Giuseppina , Calza Stefano , Sartori Enrico , Odicino Franco 
Published: August 2017

AbstractSome aspects of endometrial cancer (EC) preoperative work-up are still controversial, and debatable are the roles played by lymphadenectomy and radical surgery. Proper preoperative EC staging can help design a tailored surgical treatment, and this study aims to propose a new algorithm able to predict extrauterine disease diffusion. 293 EC patients were consecutively enrolled, and age, BMI, children’s number, menopausal status, contraception, hormone replacement therapy, hypertension, histological grading, clinical stage, and serum HE4 and CA125 values were preoperatively evaluated. In order to identify before surgery the most important variables able to classify EC patients based on FIGO stage, we adopted a new statistical approach consisting of two-steps: 1) Random Forest with its relative variable importance; 2) a novel algorithm able to select the most representative Regression Tree (RERT) from an ensemble method. RERT, built on the above mentioned variables, provided a sensitivity, specificity, NPV and PPV of 90%, 76%, 94% and 65% respectively, in predicting FIGO stage > I. Notably, RERT outperformed the prediction ability of HE4, CA125, Logistic Regression and single cross-validated Regression Tree. Such algorithm has great potential, since it better identifies the true early-stage patients, thus providing concrete support in the decisional process about therapeutic options to be performed.
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study
Authors: Hu Xue-Jia , Li Tuan , Wang Yang , Xiong Yao , Wu Xian-Hui , Zhang De-Lin , Ye Zhi-Qiang , Wu Yun-Dong 
Published: August 2017

AbstractAs an ancient protein family, the WD40 repeat proteins often play essential roles in fundamental cellular processes in eukaryotes. Although investigations of eukaryotic WD40 proteins have been frequently reported, prokaryotic ones remain largely uncharacterized. In this paper, we report a systematic analysis of prokaryotic WD40 proteins and detailed comparisons with eukaryotic ones. About 4,000 prokaryotic WD40 proteins have been identified, accounting for 6.5% of all WD40s. While their abundances are less than 0.1% in most prokaryotes, they are enriched in certain species from Cyanobacteria and Planctomycetes, and participate in various functions such as prokaryotic signal transduction and nutrient synthesis. Comparisons show that a higher proportion of prokaryotic WD40s tend to contain multiple WD40 domains and a large number of hydrogen bond networks. The observation that prokaryotic WD40 proteins tend to show high internal sequence identity suggests that a substantial proportion of them (~20%) should be formed by recent or young repeat duplication events. Further studies demonstrate that the very young WD40 proteins, i.e., Highly-Repetitive WD40s, should be of higher stability. Our results have presented a catalogue of prokaryotic WD40 proteins, and have shed light on their evolutionary origins.
Deep-level phylogeny of Cicadomorpha inferred from mitochondrial genomes sequenced by NGS
Authors: Song Nan , Cai Wanzhi , Li Hu 
Published: August 2017

AbstractRecent development and advancement of next-generation sequencing (NGS) technologies have enabled the determination of mitochondrial genome (mitogenome) at extremely efficiency. In this study, complete or partial mitogenomes for 19 cicadomorphan species and six fulgoroid species were reconstructed by using the method of high-throughput sequencing from pooled DNA samples. Annotation analyses showed that the mitogenomes obtained have the typical insect mitogenomic content and structure. Combined with the existing hemipteran mitogenomes, a series of datasets with all 37 mitochondrial genes (up to 14,381 nt total) under different coding schemes were compiled to test previous hypotheses of deep-level phylogeny of Cicadomorpha. Thirty-seven species representing Cicadomorpha constituted the ingroup. A taxon sampling with nine species from Fulgoroidea and six from Heteroptera comprised the outgroup. The phylogenetic reconstructions congruently recovered the monophyly of each superfamily within Cicadomorpha. Furthermore, the hypothesis (Membracoidea + (Cicadoidea + Cercopoidea)) was strongly supported under the heterogeneous CAT model.
Selection for energy efficiency drives strand-biased gene distribution in prokaryotes
Authors: Gao Na , Lu Guanting , Lercher Martin J. , Chen Wei-Hua 
Published: August 2017

AbstractLagging-strand genes accumulate more deleterious mutations. Genes are thus preferably located on the leading strand, an observation known as strand-biased gene distribution (SGD). Despite of this mechanistic understanding, a satisfactory quantitative model is still lacking. Replication-transcription-collisions induce stalling of the replication machinery, expose DNA to various attacks, and are followed by error-prone repairs. We found that mutational biases in non-transcribed regions can explain ~71% of the variations in SGDs in 1,552 genomes, supporting the mutagenesis origin of SGD. Mutational biases introduce energetically cheaper nucleotides on the lagging strand, and result in more expensive protein products; consistently, the cost difference between the two strands explains ~50% of the variance in SGDs. Protein costs decrease with increasing gene expression. At similar expression levels, protein products of leading-strand genes are generally cheaper than lagging-strand genes; however, highly-expressed lagging genes are still cheaper than lowly-expressed leading genes. Selection for energy efficiency thus drives some genes to the leading strand, especially those highly expressed and essential, but certainly not all genes. Stronger mutational biases are often associated with low-GC genomes; as low-GC genes encode expensive proteins, low-GC genomes thus tend to have stronger SGDs to alleviate the stronger pressure on efficient energy usage.