bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intragenic differential expression in archaea transcriptomes revealed by computational analysis of tiling microarrays
Authors: Khan Atlas , Vêncio Ricardo Z. N. 
Published: July 2017

AbstractRecent advances, in high-throughput technologies allows whole transcriptome analysis, providing a complete and panoramic view of intragenic differential expression in eukaryotes. However, intragenic differential expression in prokaryotes still mystery and incompletely understood. In this study, we investigated and collected the evidence for intragenic differential expression in several archaeal transcriptomes such as,Halobacterium salinarumNRC-1,Pyrococcus furiosus, Methanococcus maripaludis, andSulfolobus solfataricus, based on computational methods; specifically, by well-known self-organizing map (SOM) for cluster analysis, which transforms high dimensional data into low dimensional. We found 104 (3.86%) of genes in Halobacterium salinarum NRC-1, 59 (2.56%) of genes inPyrococcus furiosus,43 (2.41%) of genesMethanococcus maripaludisand 13 (0.42%) of genes inSulfolobus solfataricushave two or more clusters, i.e., showed the intragenic differential expression at different conditions.
Genome-wide profiling of transcribed enhancers during macrophage activation
Authors: Denisenko Elena , Guler Reto , Mhlanga Musa , Suzuki Harukazu , Brombacher Frank , Schmeier Sebastian 
Published: July 2017

AbstractMacrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well-known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in mouse macrophages, their time kinetics and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers and find that genes associated to many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli-specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue to further elucidate enhancer regulation in macrophages.
Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing
Authors: Mito Mari , Kadota Mitsutaka , Tanaka Kaori , Furuta Yasuhide , Abe Kuniya , Iwasaki Shintaro , Nakagawa Shinichi 
Published: July 2017

AbstractBackgroundThe nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq).ResultsFLAG-tagged histone H2B, a constitutive chromatin component, was first expressed inCamk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3—an active promoter mark—allowed us to survey neuron-specific coding and non-coding transcripts. Indeed, tChIP-Seq identified hundreds of genes associated with neuronal functions and genes with unknown functions expressed in cortical neurons.ConclusionstChIP-Seq thus provides a versatile approach to investigating the epigenetic modifications of particular cell typesin vivo.
RiceTSV3Encoding Obg-like GTPase Protein is Essential for Chloroplast Development during the Early Leaf Stage under Cold Stress
Authors: Lin Dongzhi , Jiang Quan , Ma Xiaojing , Zheng Kailun , Gong Xiaodi , Teng Sheng , Xu Jianlong , Dong Yanjun 
Published: July 2017

ABSTRACTThe Spo0B-associated GTP-binding (Obg) proteins occupy a wide variety of roles in the viability of nearly all bacteria. Its detailed roles in higher plants have not yet been elucidated. A novel rice thermo-sensitive virescent mutanttsv3was identified in this study that displayed albino phenotype at 20°C before the 3-leaf stage while being normal green at 32°C or even at 20°C after the 4-leaf stage. The mutant phenotype was aligned with altered chlorophyll (Chl) content and chloroplast development. Map-based cloning and complementation test showed thatTSV3encoded a kind of small GTP binding protein. Subcellular localization revealed that TSV3 was in chloroplast.TSV3transcripts were highly expressed in leaves and weak or undetectable in other tissues, suggesting the tissue-specific expression. Intsv3mutant, the transcriptional levels of certain genes associated with biogenesis of chloroplast ribosomes 50S subunit were severely decreased at the 3-leaf-stage under cold stress, but could be recovered to normal levels at a higher temperature (32°C). The observations from this study indicated that the rice nuclear-encodedTSV3plays important roles in chloroplast development at early leaf stage under cold stress.
C-State: An interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search
Authors: Sowpati Divya Tej , Srivastava Surabhi , Dhawan Jyotsna , Mishra Rakesh K 
Published: July 2017

AbstractBackgroundComparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge.ResultsWe developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript- based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge.ConclusionsC-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.
Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species
Authors: Förster Daniel W. , Bull James K. , Lenz Dorina , Autenrieth Marijke , Paijmans Johanna L. A. , Kraus Robert H. S. , Nowak Carsten , Bayerl Helmut , Kühn Ralph , Saveljev Alexander P. , Sindičić Magda , Hofreiter Michael , Schmidt Krzysztof , Fickel Jörns 
Published: July 2017

ABSTRACTHybridization capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. A cross-species approach makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for non-model organisms, for which often noa prioriknowledge exists regarding these loci. Here, we have adopted cross-species capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a non-model organism, the Eurasian lynxLynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic catFelis catus). In this manner, we were able to survey intraspecific variation at hundreds of nuclear loci across the European range ofL. lynx. A large set of bi-allelic candidate SNPs was then tested in a high throughput SNP-genotyping platform (Fluidigm), which we reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with additional samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (incl. the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
confFuse: high-confidence fusion gene detection across tumor entities
Authors: Huang Zhiqin , Jones David T.W. , Wu Yonghe , Lichter Peter , Zapatka Marc 
Published: July 2017

ABSTRACTBackgroundFusion genes play an important role in the tumorigenesis of many cancers. Next-generation sequencing (NGS) technologies have been successfully applied in fusion gene detection for the last several years, and a number of NGS-based tools have been developed for identifying fusion genes during this period. Most fusion gene detection tools based on RNA-seq data report a large number of candidates (mostly false positives), making it hard to prioritize candidates for experimental validation and further analysis. Selection of reliable fusion genes for downstream analysis becomes very important in cancer research. We therefore developed confFuse, a scoring algorithm to reliably select high-confidence fusion genes which are likely to be biologically relevant.ResultsConfFuse takes multiple parameters into account in order to assign each fusion candidate a confidence score, of which score ≥8 indicates high-confidence fusion gene predictions. These parameters were manually curated based on our experience and on certain structural motifs of fusion genes. Compared with alternative tools, based on 96 published RNA-seq samples from different tumor entities, our method can significantly reduce the number of fusion candidates (301 high-confidence from 8,083 total predicted fusion genes) and keep high detection accuracy (recovery rate 85.7%). Validation of 18 novel, high-confidence fusions detected in three breast tumor samples resulted in a 100% validation rate.ConclusionsConfFuse is a novel downstream filtering method that allows selection of highly reliable fusion gene candidates for further downstream analysis and experimental validations. confFuse is available athttps://github.com/Zhiqin-HUANG/confFuse.
Advanced processing and analysis of conventional confocal microscopy generated scanning FCS data
Authors: Waithe Dominic , Schneider Falk , Chojnacki Jakub , Clausen Mathias , Shrestha Dilip , de la Serna Jorge Bernardino , Eggeling Christian 
Published: July 2017

AbstractScanning Fluorescence Correlation Spectroscopy (scanning FCS) is a variant of conventional point FCS that allows molecular diffusion at multiple locations to be measured simultaneously. It enables disclosure of potential spatial heterogeneity in molecular diffusion dynamics and also the acquisition of a large amount of FCS data at the same time, providing large statistical accuracy. Here, we optimize the processing and analysis of these large-scale acquired sets of FCS data. On one hand we present FoCuS-scan, scanning FCS software that provides an end-to-end solution for processing and analysing scanning data acquired on commercial turnkey confocal systems. On the other hand, we provide a thorough characterisation of large-scale scanning FCS data over its intended time-scales and applications and propose a unique solution for the bias and variance observed when studying slowly diffusing species. Our manuscript enables researchers to straightforwardly utilise scanning FCS as a powerful technique for measuring diffusion across a broad range of physiologically relevant length scales without specialised hardware or expensive software.
A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
Authors: Goldman Mary , Zhang Junjun , Fonseca Nuno A. , Cortés-Ciriano Isidro , Xiang Qian , Craft Brian , Piñeiro-Yáñez Elena , O’Connor Brian D , Bazant Wojciech , Barrera Elisabet , Muñoz-Pomer Alfonso , Petryszak Robert , Füllgrabe Anja , Al-Shahrour Fatima , Keays Maria , Haussler David , Weinstein John N. , Huber Wolfgang , Valencia Alfonso , Park Peter J. , Papatheodorou Irene , Zhu Jingchun , Ferretti Vincent , Vazquez Miguel ,   on behalf of the PCAWG Portals and Visualization Working Group,   the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Published: July 2017

AbstractThe Pan-Cancer Analysis of Whole Genomes (PCAWG) project has generated, to our knowledge, the largest whole-genome cancer sequencing resource to date. Here we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper: The ICGC Data Portal, UCSC Xena, Expression Atlas, PCAWG-Scout, and Chromothripsis Explorer. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, as well as demonstrate how the tools can be used together to more deeply understand tumor biology. Together, these tools enable researchers to dynamically query complex genomics data and integrate external information, enabling and enhancing PCAWG data interpretation. More information on these tools and their capabilities is available from The PCAWG Data Portals and Visualizations Page (http://docs.icgc.org/pcawg).
Temperature and Light Effects on Germination ofPeronospora effusaSporangia
Authors: Choudhury Robin Alan , McRoberts Neil 
Published: July 2017

AbstractSpinach downy mildew, caused by the biotrophic oomycetePeronospora effusa, is an economically important disease that is found in all spinach growing regions of the US. To effectively predict disease risk we need to understand the response ofP. effusato different environmental conditions. We conducted several germination assays, exposingP. effusasporangia to different temperature and lighting conditions. Between 5 and 25°C under constant darkness, germination ofP. effusasporangia on water agar declined. These results were qualitatively different from a previous study ofP. effusagermination that found a bimodal response curve, with increased germination at lower and higher temperatures. Time course studies revealed that sporangia consistently germinated within the first twelve hours of plating, regardless of incubation temperature. Sporangia exposed to blue light had significantly reduced germination when compared with those exposed to red, yellow, or no light. Light intensity and color significantly impacted germination, although the effect of color varied by light intensity.
Chitosan membranes applied on the prostatic neurovascular bundles after nerve‐sparing robot‐assisted radical prostatectomy: a phase II study
Authors: Porpiglia Francesco , Bertolo Riccardo , Fiori Cristian , Manfredi Matteo , De Cillis Sabrina , Geuna Stefano 
Published: July 2017

ObjectiveTo evaluate the feasibility and the safety of applying chitosan membrane (ChiMe) on the neurovascular bundles (NVBs) after nerve‐sparing robot‐assisted radical prostatectomy (NS‐RARP). The secondary aim of the study was to report preliminary data and in particular potency recovery data.Patients and MethodsThis was a single‐centre, single‐arm prospective study, enrolling all patients with localised prostate cancer scheduled for RARP with five‐item version of the International Index of Erectile Function scores of >17, from July 2015 to September 2016. All patients underwent NS‐RARP with ChiMe applied on the NVBs. The demographics, perioperative, postoperative and complications data were evaluated. Potency recovery data were evaluated in particular and any sign/symptom of local allergy/intolerance to the ChiMe was recorded and evaluated.ResultsIn all, 140 patients underwent NS‐RARP with ChiMe applied on the NVBs. Applying the ChiMe was easy in almost all the cases, and did not compromise the safety of the procedure. None of the patients reported signs of intolerance/allergy attributable to the ChiMe and potency recovery data were encouraging.ConclusionIn our experience, ChiMe applied on the NVBs after NS‐RARP was feasible and safe, without compromising the duration, difficulty or complication rate of the ‘standard’ procedure. No patients had signs of intolerance/allergy attributable to the ChiMe and potency recovery data were encouraging. A comparative cohort would have added value to the study. The present paper was performed before Conformité Européene (CE)‐mark achievement.
Chronic spinal cord injury causes upregulation of serotonin (5‐HT)2A and 5‐HT2C receptors in lumbosacral cord motoneurons
Authors: Cao Nailong , Ni Jianshu , Wang Xiaohu , Tu Hongjian , Gu Baojun , Si Jiemin , Wu Gang , Andersson Karl‐Erik 
Published: July 2017

ObjectivesTo investigate whether the voiding dysfunction caused by spinal cord injury (SCI) in rats can be improved by i.v. administration of the serotonin (5‐HT)2A/2C receptor agonist 2,5‐dimethoxy‐4‐iodophenyl‐2‐aminopropanehydrochloride (DOI), and to discuss whether the mechanism can be ascribed to 5‐HT2A and 5‐HT 2C receptor upregulation in lumbosacral cord motoneurons.Materials and MethodsFemale Sprague–Dawley rats were divided into two groups (SCI group vs normal control [NC] group). Under urethane anaesthesia, cystometry was performed to examine the variation in urodynamic variables before and after successive intrathecal (i.t.) administration of various doses of DOI into the lumbosacral cord. Changes in 5‐HT2A and ‐2C receptors in the lumbosacral cord were also investigated using immunohistochemical staining and Western blot analysis.ResultsCompared with NC rats, the SCI rats had higher bladder capacity and post‐void residual urine volume, and lower voiding efficiency. After SCI, DOI improved voiding efficiency, probably via external urethral sphincter (EUS) activity. Immunohistochemical staining and Western blot analysis showed that 5‐HT2A and ‐2C receptors were upregulated in lumbosacral cord motoneurons.ConclusionIn rats with SCI, DOI can improve voiding efficiency; this may be attributable to 5‐HT2A and ‐2C receptor upregulation in lumbosacral cord motoneurons controlling EUS activity.
A brief psychological intervention for mothers of children with food allergy can change risk perception and reduce anxiety: Outcomes of a randomized controlled trial
Authors: Boyle R. J. , Umasunthar T. , Smith J. G. , Hanna H. , Procktor A. , Phillips K. , Pinto C. , Gore C. , Cox H. E. , Warner J. O. , Vickers B. , Hodes M. 
Published: July 2017

SummaryBackgroundMothers of children with food allergy have increased anxiety, which may be influenced by healthcare professionals’ communication of risk.ObjectiveTo evaluate a brief psychological intervention for reducing anxiety in mothers of children with food allergy.MethodsTwo hundred mothers of children with food allergy were recruited from allergy clinics. A computer‐generated randomization list was used to allocate participants to a single‐session cognitive behavioural therapy intervention including a risk communication module, or standard care. Anxiety and risk perception were assessed at 6 weeks and 1 year. Primary outcome was state anxiety at 6 weeks. Secondary outcomes included state anxiety at 1 year, risk perception at 6 weeks and 1 year, and salivary cortisol response to a simulated anaphylaxis scenario at 1 year.ResultsWe found no significant difference in the primary outcome state anxiety at 6 weeks, with mean 31.9 (SD 10.2) intervention, 34.0 (10.2) control; mean difference 2.1 (95% CI −0.9, 5.0; P=.17). There was significantly reduced state anxiety at 6 weeks in the intervention group, in the subgroup of participants with moderate/high anxiety at enrolment (103/200, 52%), with mean 33.0 (SD 9.3) intervention, 37.8 (SD 10.0) control; mean difference 4.8 (95% CI 0.9, 8.7; P=.016; Cohen's d effect size 0.50). The psychological intervention also reduced risk perception and salivary cortisol response (P=.032; effect size 0.36).ConclusionWe found evidence that a brief psychological intervention which incorporates accurate risk information may impact on anxiety, risk perception and physiological stress response in mothers of children with food allergy.
Pregnancy after laparoscopic ventral mesh rectopexy: implications and outcomes
Authors: Hogan A. M. , Tejedor P. , Lindsey I. , Jones O. , Hompes R. , Gorissen K. J. , Cunningham C. 
Published: July 2017

AbstractAimSurgical management of rectal prolapse varies considerably. Most surgeons are reluctant to use ventral mesh rectopexy in young women until they have completed their family. The aim of the present study was to review outcomes of pregnancy following laparoscopic ventral mesh rectopexy from a tertiary referral centre over a 10‐year period (2006–2016) and to review the impact on pelvic floor symptoms.MethodWe undertook a retrospective review of a prospectively compiled database of patients who had undergone laparoscopic ventral rectopexy in a single centre over a 10‐year period. Pelvic floor symptom scores (Vaizey for incontinence and Longo for obstructive defaecation) were collected at initial presentation (pre‐intervention), post‐intervention and after child birth.ResultsIn all, 954 rectopexies were performed over this 10‐year period. 225 (24%) patients were women and under 45 years of age (taken as an arbitrary cut‐off for decreased likelihood of pregnancy). Eight (4%) of these patients became pregnant following rectopexy. The interval between rectopexy and delivery was 42 months (21–50). Six patients delivered live babies by elective lower segment caesarean section and two by spontaneous vaginal delivery. Six were first babies and two were second. No mesh related adverse outcome was reported. No difference in pelvic floor symptoms was demonstrated on comparison of post‐rectopexy and post‐delivery scores.ConclusionThis study provides the first description in the English language literature of safe delivery by elective lower segment caesarean section or spontaneous vaginal delivery following laparoscopic ventral mesh rectopexy. No adverse impact on pelvic floor related quality of life was detected.
Outcomes of patients diagnosed with acute myeloid leukemia after solid organ transplantation
Authors: Lontos Konstantinos , Agha Mounzer , Raptis Anastasios , Hou Jing‐Zhou , Farah Rafic , Redner Robert L. , Im Annie , Dorritie Kathleen A. , Sehgal Alison , Rossetti James , Saul Melissa , Gooding William E. , Humar Abhinav , Boyiadzis Michael 
Published: July 2017

AbstractOrgan transplant recipients are at an increased risk for subsequent cancer including acute myeloid leukemia (AML). Treatment of AML following solid transplantation represents a clinical challenge as most patients have significant comorbidities at the time of AML diagnosis. In this study, we evaluated the treatment and outcomes of patients who developed AML following solid organ transplantation at our institution and reviewed the literature on outcomes for these patients. The study cohort consisted of 14 patients (median age 66 years, range 52‐77 years) with newly diagnosed AML following solid organ transplantation. The median interval time between solid organ transplantation and AML diagnosis was 72 months (range 15‐368 months). Seven patients received standard induction chemotherapy, four patients received intermediate type therapy, and the remaining three patients were deemed not fit for therapy and received palliative and supportive care. Six of the 11 treated patients (55%) achieved complete remission (CR). The median overall survival (OS) for all patients was 6 months. The median OS for the patients who achieved complete remission after therapy was 17 months and 2 months for the remaining patients. Despite initial CR, relapse rates are still high, suggesting that alternative strategies for post‐remission therapies are warranted.