bluuebunny/crossref_metadata_2025_split huggingface dataset:
RACS: rapid analysis of ChIP-Seq data for contig based genomes
Authors: Saettone Alejandro , Ponce Marcelo , Nabeel-Shah Syed , Fillingham Jeffrey 
Published: October 2019

Abstract

Background
Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA sequences on a genomic scale. ChIP-Seq generates large quantities of data that is difficult to process and analyze, particularly for organisms with a contig-based sequenced genomes that typically have minimal annotation on their associated set of genes other than their associated coordinates primarily predicted by gene finding programs. Poorly annotated genome sequence makes comprehensive analysis of ChIP-Seq data difficult and as such standardized analysis pipelines are lacking.

Results
We present a one-stop computational pipeline, “Rapid Analysis of ChIP-Seq data” (RACS), that utilizes traditional High-Performance Computing (HPC) techniques in association with open source tools for processing and analyzing raw ChIP-Seq data. RACS is an open source computational pipeline available from any of the following repositories https://bitbucket.org/mjponce/RACS or https://gitrepos.scinet.utoronto.ca/public/?a=summary&p=RACS. RACS is particularly useful for ChIP-Seq in organisms with contig-based genomes that have poor gene annotation to aid protein function discovery.To test the performance and efficiency of RACS, we analyzed ChIP-Seq data previously published in a model organism Tetrahymena thermophila which has a contig-based genome. We assessed the generality of RACS by analyzing a previously published data set generated using the model organism Oxytricha trifallax, whose genome sequence is also contig-based with poor annotation.

Conclusions
The RACS computational pipeline presented in this report is an efficient and reliable tool to analyze genome-wide raw ChIP-Seq data generated in model organisms with poorly annotated contig-based genome sequence. Because RACS segregates the found read accumulations between genic and intergenic regions, it is particularly efficient for rapid downstream analyses of proteins involved in gene expression.
SLR: a scaffolding algorithm based on long reads and contig classification
Authors: Luo Junwei , Lyu Mengna , Chen Ranran , Zhang Xiaohong , Luo Huimin , Yan Chaokun 
Published: October 2019

AbstractBackgroundScaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the problem of repetitive regions has received a great deal of attention. In the past few years, long reads sequenced by third-generation sequencing technologies (Pacific Biosciences and Oxford Nanopore) have been demonstrated to be useful for sequencing repetitive regions in genomes. Although some stand-alone scaffolding algorithms based on long reads have been presented, scaffolding still requires a new strategy to take full advantage of the characteristics of long reads.ResultsHere, we present a new scaffolding algorithm based on long reads and contig classification (SLR). Through the alignment information of long reads and contigs, SLR classifies the contigs into unique contigs and ambiguous contigs for addressing the problem of repetitive regions. Next, SLR uses only unique contigs to produce draft scaffolds. Then, SLR inserts the ambiguous contigs into the draft scaffolds and produces the final scaffolds. We compare SLR to three popular scaffolding tools by using long read datasets sequenced with Pacific Biosciences and Oxford Nanopore technologies. The experimental results show that SLR can produce better results in terms of accuracy and completeness. The open-source code of SLR is available at https://github.com/luojunwei/SLR.ConclusionIn this paper, we describes SLR, which is designed to scaffold contigs using long reads. We conclude that SLR can improve the completeness of genome assembly.
Comprehensive ensemble in QSAR prediction for drug discovery
Authors: Kwon Sunyoung , Bae Ho , Jo Jeonghee , Yoon Sungroh 
Published: October 2019

Abstract

Background
Quantitative structure-activity relationship (QSAR) is a computational modeling method for revealing relationships between structural properties of chemical compounds and biological activities. QSAR modeling is essential for drug discovery, but it has many constraints. Ensemble-based machine learning approaches have been used to overcome constraints and obtain reliable predictions. Ensemble learning builds a set of diversified models and combines them. However, the most prevalent approach random forest and other ensemble approaches in QSAR prediction limit their model diversity to a single subject.

Results
The proposed ensemble method consistently outperformed thirteen individual models on 19 bioassay datasets and demonstrated superiority over other ensemble approaches that are limited to a single subject. The comprehensive ensemble method is publicly available at http://data.snu.ac.kr/QSAR/.

Conclusions
We propose a comprehensive ensemble method that builds multi-subject diversified models and combines them through second-level meta-learning. In addition, we propose an end-to-end neural network-based individual classifier that can automatically extract sequential features from a simplified molecular-input line-entry system (SMILES). The proposed individual models did not show impressive results as a single model, but it was considered the most important predictor when combined, according to the interpretation of the meta-learning.
Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae)
Authors: Luo Hairong , Kong Xiaoyu , Chen Shixi , Shi Wei 
Published: October 2019

Abstract

Background
The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus.

Results
The 18,170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N′ gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish.

Conclusions
This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.
PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome
Authors: Teng Ke , Teng Wenjun , Wen Haifeng , Yue Yuesen , Guo Weier , Wu Juying , Fan Xifeng 
Published: October 2019

Abstract

Background
Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts.

Results
In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing.

Conclusions
This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.
Antimicrobial resistance patterns of Uropathogens isolated from adult women with acute uncomplicated cystitis
Authors: Al-Zahrani Jamaan , Al Dossari Khaled , Gabr Ahmed H. , Ahmed Abul-fotouh , Al Shahrani Saad Abdulrahman , Al-Ghamdi Sameer 
Published: October 2019

Abstract

Background
To evaluate the antibiotic resistance patterns of uropathogens isolated from adult women with acute community-acquired (CA) uncomplicated cystitis.

Results
Over a one-year period (May 2015–April 2016), the results of susceptibility testing of outpatient midstream urine samples from 5 different laboratories were prospectively evaluated. The study included only adult women with uncomplicated cystitis. The susceptibility testing in all laboratories was performed using the disk diffusion method with the VITEK-2 Compact system. The isolated uropathogens and their resistance to the tested antibiotics were evaluated. Out of 317 adult women with CA uncomplicated cystitis, 179 had a positive culture. The most commonly isolated organism was Escherichia coli (E. coli) (70.4%), followed by Klebsiella (21.2%). The overall resistance rate was highest for ampicillin (85.6%), followed by cefalotin (56.3%), trimethoprim/sulfamethoxazole (54.7%), pipracillin (51.9%), nitrofurantoin (48.8%) and aztreonam (47.4%). Isolated E. coli strains were commonly resistant to ampicillin (80.5%), trimethoprim/sulfamethoxazole (72.2%) and aztreonam (71.4%), followed by cefalotin (55.9%). The overall ciprofloxacin resistance rate was 17.9%, and the resistent was found only with E. coli (25.4%).

Conclusions
Our results may aid in the selection of proper empiric antibiotic therapy for adult women with acute CA uncomplicated cystitis.
Linkage mapping and quantitative trait loci analysis of sweetness and other fruit quality traits in papaya
Authors: Nantawan Usana , Kanchana-udomkan Chutchamas , Bar Ido , Ford Rebecca 
Published: October 2019

Abstract

Background
The identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. In this study, a genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya.

Results
For this, a linkage map was constructed comprising 219 single nucleotide polymorphism (SNP) loci across 10 linkage groups and covering 509 centiMorgan (cM). In total, 21 QTLs were identified for seven key fruit quality traits, including flesh sweetness, fruit weight, fruit length, fruit width skin freckle, flesh thickness and fruit firmness. Several QTL for flesh sweetness, fruit weight, length, width and firmness were stable across harvest years and individually explained up to 19.8% of the phenotypic variance of a particular trait. Where possible, candidate genes were proposed and explored further for their application to marker-assisted breeding.

Conclusions
This study has extended knowledge on the inheritance and genetic control for key papaya physiological and fruit quality traits. Candidate genes together with associated SNP markers represent a valuable resource for the future of strategic selective breeding of elite Australian papaya cultivars.
Tomato glycosyltransferase Twi1 plays a role in flavonoid glycosylation and defence against virus
Authors: Campos Laura , López-Gresa María Pilar , Fuertes Diana , Bellés José María , Rodrigo Ismael , Lisón Purificación 
Published: October 2019

AbstractBackgroundSecondary metabolites play an important role in the plant defensive response. They are produced as a defence mechanism against biotic stress by providing plants with antimicrobial and antioxidant weapons. In higher plants, the majority of secondary metabolites accumulate as glycoconjugates. Glycosylation is one of the commonest modifications of secondary metabolites, and is carried out by enzymes called glycosyltransferases.ResultsHere we provide evidence that the previously described tomato wound and pathogen-induced glycosyltransferase Twi1 displays in vitro activity toward the coumarins scopoletin, umbelliferone and esculetin, and the flavonoids quercetin and kaempferol, by uncovering a new role of this gene in plant glycosylation. To test its activity in vivo,Twi1-silenced transgenic tomato plants were generated and infected with Tomato spotted wilt virus. TheTwi1-silenced plants showed a differential accumulation of Twi1 substrates and enhanced susceptibility to the virus.ConclusionsBiochemical in vitro assays and transgenic plants generation proved to be useful strategies to assign a role of tomato Twi1 in the plant defence response. Twi1 glycosyltransferase showed to regulate quercetin and kaempferol levels in tomato plants, affecting plant resistance to viral infection.
Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng
Authors: Li Xue-Jiao , Yang Jian-Li , Hao Bing , Lu Ying-Chun , Qian Zhi-Long , Li Ying , Ye Shuang , Tang Jun-Rong , Chen Mo , Long Guang-Qiang , Zhao Yan , Zhang Guang-Hui , Chen Jun-Wen , Fan Wei , Yang Sheng-Chao 
Published: October 2019

Abstract

Background
Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood.

Results
A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with “plant hormone signal transduction,” “starch and sucrose metabolism,” and “phenylpropanoid biosynthesis” were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng.

Conclusion
The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.
Disease burden and associated risk factors for metabolic syndrome among adults in Ethiopia
Authors: Solomon Samrawit , Mulugeta Wudeneh 
Published: October 2019

Abstract

Background
Metabolic Syndrome (MetS) and Non-communicable diseases (NCDs) are alarmingly increasing in low-income countries. Yet, very limited is known about the prevalence and risk factors associated with MetS in Ethiopia.

Methods
A cross-sectional study was conducted among adult outpatients (N = 325) at St. Paul’s Hospital Millennium Medical College in Addis Ababa, Ethiopia. The study was conducted in accordance with STEPwise approach of the World Health Organization. MetS was defined using modified National Cholesterol Education Program’s Adult Treatment Panel III criteria. Univariate and multivariate analyses were performed.

Results
The overall prevalence of MetS was 20.3%. Among the 325 participants, 76.9% had at least one MetS components. Reduced high-density lipoprotein cholesterol was the most common MetS component at 48.6%, followed by elevated blood pressure at 36.3%, and elevated fasting glucose at 32.6%. Older age (odds ratio [OR] = 4.15; 95% confidence interval [CI] = 1.43–12.04), Amhara ethnicity (OR = 2.36; 95%CI = 1.14–4.88), overweight status (OR = 2.21; 95%CI = 1.03–4.71), higher income (OR = 3.31; 95%CI = 1.11–9.84) and higher education levels (OR = 2.19; 95%CI = 1.05–4.59) were risk factors for MetS.

Conclusion
The disease burden of MetS among Ethiopians is high, and is associated with age, weight, income, education and ethnicity. Comprehensive screening and assessment of MetS is needed along with effective preventive and treatment strategies in low-income countries, such as Ethiopia.
A comparison of the statistical performance of different meta-analysis models for the synthesis of subgroup effects from randomized clinical trials
Authors: da Costa Bruno R. , Sutton Alex J. 
Published: October 2019

Abstract

Background
When investigating subgroup effects in meta-analysis, it is unclear whether accounting in meta-regression for between-trial variation in treatment effects, but not between-trial variation in treatment interaction effects when such effects are present, leads to biased estimates, coverage problems, or wrong standard errors, and whether the use of aggregate data (AD) or individual-patient-data (IPD) influences this assessment.

Methods
Seven different models were compared in a simulation study. Models differed regarding the use of AD or IPD, whether they accounted for between-trial variation in interaction effects, and whether they minimized the risk of ecological fallacy.

Results
Models that used IPD and that allowed for between-trial variation of the interaction effect had less bias, better coverage, and more accurate standard errors than models that used AD or ignored this variation. The main factor influencing the performance of models was whether they used IPD or AD. The model that used AD had a considerably worse performance than all models that used IPD, especially when a low number of trials was included in the analysis.

Conclusions
The results indicate that IPD models that allow for the between-trial variation in interaction effects should be given preference whenever investigating subgroup effects within a meta-analysis.
Spatiotemporal multi-disease transmission dynamic measure for emerging diseases: an application to dengue and zika integrated surveillance in Thailand
Authors: Rotejanaprasert Chawarat , Lawson Andrew B. , Iamsirithaworn Sopon 
Published: October 2019

AbstractBackgroundNew emerging diseases are public health concerns in which policy makers have to make decisions in the presence of enormous uncertainty. This is an important challenge in terms of emergency preparation requiring the operation of effective surveillance systems. A key concept to investigate the dynamic of infectious diseases is the basic reproduction number. However it is difficult to be applicable in real situations due to the underlying theoretical assumptions.MethodsIn this paper we propose a robust and flexible methodology for estimating disease strength varying in space and time using an alternative measure of disease transmission within the hierarchical modeling framework. The proposed measure is also extended to allow for incorporating knowledge from related diseases to enhance performance of surveillance system.ResultsA simulation was conducted to examine robustness of the proposed methodology and the simulation results demonstrate that the proposed method allows robust estimation of the disease strength across simulation scenarios. A real data example is provided of an integrative application of Dengue and Zika surveillance in Thailand. The real data example also shows that combining both diseases in an integrated analysis essentially decreases variability of model fitting.ConclusionsThe proposed methodology is robust in several simulated scenarios of spatiotemporal transmission force with computing flexibility and practical benefits. This development has potential for broad applicability as an alternative tool for integrated surveillance of emerging diseases such as Zika.
‘Weighty issues’ in GP-led antenatal care: a qualitative study
Authors: Walker Ruth , Choi Tammie S. T. , Alexander Karyn , Mazza Danielle , Truby Helen 
Published: October 2019

Abstract

Background
Approximately 50% of women gain weight in excess of gestational weight gain (GWG) recommendations during pregnancy leading to adverse maternal and foetal outcomes and the perpetuation of the cycle of obesity. Antenatal care provided by a general practitioner (GP) in the primary care setting is an important model of care, particularly for women in regional areas where rates of overweight and obesity are highest. The aim of this study is to explore GPs’ perceptions and experiences of implementing GWG recommendations in GP-led antenatal care.

Methods
A qualitative exploratory approach recorded GPs’ experiences and insights regarding the application of GWG recommendations in practice. Data were collected via semi-structured interviews informed by the revised Theoretical Domains Framework (TDF). Deductive thematic analysis grouped coded text into TDF domains from which main themes were generated.

Results
Twenty GPs (13 female, 7 male) from metropolitan and regional Victoria, Australia participated. Codes related to at least one of 11 TDF domains. Five main themes were apparent: 1) Despite low awareness of guidelines, GWG advice is provided; 2) ‘I should do this more’; 3) Lack of everyday resources; 4) Working ‘against the odds’ at times; and 5) Optimism and reality. GPs were aware of the importance of optimal GWG however, other pregnancy-related issues are given precedence during consultations. Enablers for the implementation of GWG guidelines were practitioner-based and included GPs’ strong sense of their professional role to provide advice, and ongoing and trusting relationships with women throughout pregnancy. Barriers were mostly health system-based with limited time, remuneration, and restrictive referral pathways being limiting factors.

Conclusions
There is a need to support GPs to provide GWG advice in accordance with current national guidelines. Solutions potentially lie in strategies that promote the effective dissemination and uptake of guidelines, and changes to policy and funding within the health-system so that longer GP-led antenatal care consultations are remunerated and referrals to allied health are accessible to women who require additional support to optimise GWG.