bluuebunny/crossref_metadata_2025_split huggingface dataset:
OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images
Authors: Ovchinnikova Katja , Kovalev Vitaly , Stuart Lachlan , Alexandrov Theodore 
Published: April 2020

Abstract
Background
Imaging mass spectrometry (imaging MS) is an enabling technology for spatial metabolomics of tissue sections with rapidly growing areas of applications in biology and medicine. However, imaging MS data is polluted with off-sample ions caused by sample preparation, particularly by the MALDI (matrix-assisted laser desorption/ionization) matrix application. Off-sample ion images confound and hinder statistical analysis, metabolite identification and downstream analysis with no automated solutions available.

Results
We developed an artificial intelligence approach to recognize off-sample ion images. First, we created a high-quality gold standard of 23,238 expert-tagged ion images from 87 public datasets from the METASPACE knowledge base. Next, we developed several machine and deep learning methods for recognizing off-sample ion images. The following methods were able to reproduce expert judgements with a high agreement: residual deep learning (F1-score 0.97), semi-automated spatio-molecular biclustering (F1-score 0.96), and molecular co-localization (F1-score 0.90). In a test-case study, we investigated off-sample images corresponding to the most common MALDI matrix (2,5-dihydroxybenzoic acid, DHB) and characterized properties of matrix clusters.

Conclusions
Overall, our work illustrates how artificial intelligence approaches enabled by open-access data, web technologies, and machine and deep learning open novel avenues to address long-standing challenges in imaging MS.
MI-MAAP: marker informativeness for multi-ancestry admixed populations
Authors: Chen Siqi , Ghandikota Sudhir , Gautam Yadu , Mersha Tesfaye B. 
Published: April 2020

Abstract
Background
Admixed populations arise when two or more previously isolated populations interbreed. A powerful approach to addressing the genetic complexity in admixed populations is to infer ancestry. Ancestry inference including the proportion of an individual’s genome coming from each population and its ancestral origin along the chromosome of an admixed population requires the use of ancestry informative markers (AIMs) from reference ancestral populations. AIMs exhibit substantial differences in allele frequency between ancestral populations. Given the huge amount of human genetic variation data available from diverse populations, a computationally feasible and cost-effective approach is becoming increasingly important to extract or filter AIMs with the maximum information content for ancestry inference, admixture mapping, forensic applications, and detecting genomic regions that have been under recent selection.

Results
To address this gap, we present MI-MAAP, an easy-to-use web-based bioinformatics tool designed to prioritize informative markers for multi-ancestry admixed populations by utilizing feature selection methods and multiple genomics resources including 1000 Genomes Project and Human Genome Diversity Project. Specifically, this tool implements a novel allele frequency-based feature selection algorithm, Lancaster Estimator of Independence (LEI), as well as other genotype-based methods such as Principal Component Analysis (PCA), Support Vector Machine (SVM), and Random Forest (RF). We demonstrated that MI-MAAP is a useful tool in prioritizing informative markers and accurately classifying ancestral populations. LEI is an efficient feature selection strategy to retrieve ancestry informative variants with different allele frequency/selection pressure among (or between) ancestries without requiring computationally expensive individual-level genotype data.

Conclusions
MI-MAAP has a user-friendly interface which provides researchers an easy and fast way to filter and identify AIMs. MI-MAAP can be accessed at https://research.cchmc.org/mershalab/MI-MAAP/login/.
Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing
Authors: Jiang Bingzhi , Cheng Yanbo , Cai Zhandong , Li Mu , Jiang Ze , Ma Ruirui , Yuan Yeshan , Xia Qiuju , Nian Hai 
Published: April 2020

Abstract
Background
Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) is one of the most serious limitations to soybean production worldwide. The identification of resistance gene(s) and their incorporation into elite varieties is an effective approach for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F8:11 recombinant inbred lines (RILs) derived from a cross of the resistant cultivar Guizao1 and the susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgans (cM) between adjacent bin markers in this population were used to map and explore candidate gene(s).

Results
PRR resistance in Guizao1 was found to be controlled by a single Mendelian locus and was finely mapped to a 367.371-kb genomic region on chromosome 3 harbouring 19 genes, including 7 disease resistance (R)-like genes, in the reference Willliams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed that Glyma.03 g05300 was likely involved in PRR resistance.

Conclusions
These findings from the fine mapping of a novel Rps locus will serve as a basis for the cloning and transfer of resistance genes in soybean and the breeding of P. sojae-resistant soybean cultivars through marker-assisted selection.
Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines
Authors: Powell Christian D. , Kirchoff Daniel C. , DeRouchey Jason E. , Moseley Hunter N. B. 
Published: April 2020

Abstract
Background
Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear.

Results
Protamine sequences from UniProt’s databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment.

Conclusions
High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. Also, the human protamine P1 sequence has a tyrosine substitution in a position expecting eutherian dicysteine cross-linking. Similarly, some members of the metatherian Planigales genus contain cysteine substitutions in positions expecting plausible metatherian dityrosine cross-linking. Rare cysteine-tyrosine cross-linking could explain both observations.
Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses
Authors: Liu Yue , Liu Nannan , Deng Xiong , Liu Dongmiao , Li Mengfei , Cui Dada , Hu Yingkao , Yan Yueming 
Published: April 2020

Abstract
Background
DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family.

Results
Using the recently released wheat genome database (IWGSC RefSeq v1.0), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31 T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses.

Conclusions
The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.
Dysbiosis of saliva microbiome in patients with oral lichen planus
Authors: Yu Fei Yan , Wang Qian Qian , Li Miao , Cheng Ya-Hsin , Cheng Yi-Shing Lisa , Zhou Yu , Yang Xi , Zhang Fang , Ge Xuejun , Zhao Bin , Ren Xiu Yun 
Published: April 2020

Abstract
Background
Oral microbiota is not only important for maintaining oral health but also plays a role in various oral diseases. However, studies regarding microbiome changes in oral lichen planus (OLP) are very limited. To the best of our knowledge, there has been only two studies investigating salivary microbiome changes in OLP. Therefore, the purpose of this study was to identify the characteristic microbial profile in the saliva of OLP patients, with or without erosive lesions, and compare that with recurrent aphthous ulcer (RAU), a common oral immunological disorder that also shows multiple erosive/ulcerative lesions. Whole saliva samples were collected from 20 patients with OLP (erosive E, n = 10 and non-erosive NE, n = 10), 10 patients with RAU (U) and 10 healthy controls (C). DNA was extracted from the saliva samples, and the 16S rDNA gene V4 hypervariable region was analyzed using Illumina sequencing.

Results
We obtained 4949 operational taxonomic units (OTUs) from the V4 region in all saliva samples. Community composition analysis showed a clear decreased relative abundance of genera Streptococcus and Sphingomonas in saliva from RAU patients when compared to the other three groups. Relative abundance of Lautropia and Gemella were higher in E group, whereas relative abundance of Haemophilus and Neisseria were higher in NE group when compared to C group. Abiotrophia and Oribacterium were higher in OLP (combining E and NE groups), while Eikenella and Aggregatibacter were lower when compared to C group. There was statistically significance in α-diversity between E and RAU groups(p < 0.05). Significant differences in β-diversity were detected in bacteria between E and C; NE and C; as well as E and NE groups. The LDA effect size algorithm identified the g_Haemophilus might be the potential biomarker in NE group.

Conclusions
We found that salivary microbiome in erosive OLP was significantly different from that found in RAU; and these changes may be related to the underlying disease process rather than presence of ulcerative/erosive lesions clinically. In addition, our findings in bacterial relative abundance in OLP were significantly different from the previously reported findings, which points to the need for further research in salivary microbiome of OLP.
Flowering in Persian walnut: patterns of gene expression during flower development
Authors: Hassankhah Amin , Rahemi Majid , Ramshini Hossein , Sarikhani Saadat , Vahdati Kourosh 
Published: April 2020

AbstractBackgroundFlower development and sufficient fruit set are important parameters with respect to walnut yield. Knowledge about flowering genes of fruit trees can help to conduct better molecular breeding programs. Therefore, this study was carried out to investigate the expression pattern of some flowering genes (FT,SOC1,CAL,LFYandTFL1) in Persian walnut (cv. Chandler) during the growing season and winter dormancy.ResultsThe results showed that walnut flower induction and initiation in Shahmirzad, Iran occurred in early June and late September, respectively. After meeting chilling and heat requirement, flower differentiation and anthesis occurred in late-March and mid-April to early-May, respectively. Study of flowering gene expression showed that the expression of theFTgene increased in three stages including before breaking of bud dormancy, from late March to late April (coincided with flower differentiation and anthesis) and from late May to mid-June (coincided with flower induction). LikeFT, the expression ofSOC1gene increased during flower induction and initiation (mid-May to early-August) as well as flower anthesis (mid-April to early-May).LFYandCALgenes as floral meristem identity genes are activated byFTandSOC1genes. In contrast with flowering stimulus genes,TFL1showed overexpression during winter dormancy which prevented flowering.ConclusionThe expression ofFTgene activated downstream floral meristem identity genes includingSOC1,CALandLFYwhich consequently led to release bud dormancy as well as flower anthesis and induction. Also,TFL1as a flowering inhibitor gene in walnut showed overexpression during the bud dormancy. Chilling accumulation reducedTFL1gene expression and increased the expression of flowering genes which ultimately led to overcome dormancy.
Using estimated probability of pre-diagnosis behavior as a predictor of cancer survival time: an example in esophageal cancer
Authors: Fahey Paul P. , Page Andrew , Stone Glenn , Astell-Burt Thomas 
Published: April 2020

Abstract
Background
Information on the associations between pre-diagnosis health behavior and post-diagnosis survival time in esophageal cancer could assist in planning health services but can be difficult to obtain using established study designs. We postulated that, with a large data set, using estimated probability for a behavior as a predictor of survival times could provide useful insight as to the impact of actual behavior.

Methods
Data from a national health survey and logistic regression were used to calculate the probability of selected health behaviors from participant’s demographic characteristics for each esophageal cancer case within a large cancer registry data base. The associations between survival time and the probability of the health behaviors were investigated using Cox regression.

Results
Observed associations include: a 0.1 increase in the probability of smoking 1 year prior to diagnosis was detrimental to survival (Hazard Ratio (HR) 1.21, 95% CI 1.19,1.23); a 0.1 increase in the probability of hazardous alcohol consumption 10 years prior to diagnosis was associated with decreased survival in squamous cell cancer (HR 1.29, 95% CI 1.07, 1.56) but not adenocarcinoma (HR 1.08, 95% CI 0.94,1.25); a 0.1 increase in the probability of physical activity outside the workplace is protective (HR 0.83, 95% CI 0.81,0.84).

Conclusions
We conclude that probability for health behavior estimated from demographic characteristics can provide an initial assessment of the association between pre-diagnosis health behavior and post-diagnosis health outcomes, allowing some sharing of information across otherwise unrelated data collections.
The role of a multidisciplinary team in the management of portal hypertension
Authors: Tseng Yujen , Ma Lili , Lv Minzhi , Luo Tiancheng , Liu Chengfeng , Wei Yichao , Liu Chu , Zhou Ji , Yan Zhiping , Xu Pengju , Hu Guohua , Ding Hong , Ji Yuan , Chen Shiyao , Wang Jian 
Published: April 2020

Abstract
Background
Gastroesophageal variceal hemorrhage is the most severe complication of portal hypertension, with a high mortality rate. The current recommendations for gastroesophageal varices include pharmacological treatment, endoscopic treatment, transjugular intrahepatic portosystemic shunt (TIPS) placement, and splenectomy with devascularization surgery. Multidisciplinary team (MDT) comprises of a group of medical experts and specialists across a range of disciplines, providing personalized and targeted patient care tailored to each individual’s condition, circumstances, and expectations.

Methods
Patients referred to the MDT clinic since its establishment in September 2014 were prospectively enrolled and followed-up for at least 12 months. Patient baseline characteristics, treatment methods, outcome and survival were compared to non-MDT patients retrieved from a prospectively maintained database with propensity score matching.

Results
Propensity-score matching (PSM) was carried out to balance available covariates, resulting in 58 MDT patients vs. 111 non-MDT patients. Overall survival and variceal rebleed was compared between the two groups. The rate of variceal rebleed was significantly higher in the non-MDT group, while no difference in overall survival was observed.

Conclusions
This study is the first to investigate the role of a multidisciplinary team in the management of gastroesophageal varices secondary to portal hypertension. Patients treated based on MDT clinic recommendations had a significantly lower risk for variceal rebleed.
Q fever seroprevalence in parturient women: the EQRUN cross-sectional study on Reunion Island
Authors: Jaubert Julien , Atiana Laura , Larrieu Sophie , De Vos Philippe , Somon-Payet Claudine , Porcherat Sylvaine , Mboussou Yoan , Naze Florence , Picot Sandrine , Boukerrou Malik , Robillard Pierre-Yves , Gérardin Patrick 
Published: April 2020

Abstract
Background
Q fever (Coxiella burnetii infection) has been associated with adverse perinatal outcomes. After investigating the obstetrical importance of Q fever on Reunion island and demonstrating an association between incident Q fever and miscarriage, we conducted a cross-sectional serosurvey to assess the prevalence of Coxiella burnetii infection among parturient women.

Methods
Between January 9 and July 24, 2014, within the level-4 maternity of Saint Pierre hospital and the level-1 maternity of Le Tampon, we proposed to screen all parturient women for Coxiella burnetii serology. Seropositivity was defined using indirect immunofluorescence for a dilution of phase 2 IgG titre ≥1:64. Further dilutions were chosen to discriminate recent or active infections from past or prevalent infections (< 1:128) and classify these as either possible (1:128), or probable (≥1:256). Recurrent miscarriage, stillbirth, preterm birth, small-for-gestational as well as a composite outcome of these adverse pregnancy outcomes were compared according to seropositivity using bivariate analysis or propensity score matching of seropositive and seronegative women on confounding factors.

Results
Among 1112 parturient women screened for Q fever over this 7-month period, 203 (18.3%) were seropositive. Overall weighted seroprevalence was of 20.1% (95%CI, 17.7–22.5%). Weighted seroprevalence of probable infections was 4.7% (95%CI 3.4–5.9%), while > 90% of positive serologies corresponded to past infections or false positives. Seropositivity was associated with none of the abovementioned adverse perinatal outcomes, whether in unpaired or matched analyses on propensity score.

Conclusion
The magnitude and the pattern of seroprevalence suggest that Q fever is endemic on Reunion island. In this context, we found no significant contribution of prevalent Coxiella burnetii infection to adverse pregnancy outcomes. Although reassuring, these data put in our endemic context, with a previously demonstrated increased risk of incident Q fever associated miscarriage, encourage us to protect pregnant women against the risk of new infection, periconceptional or early in pregnancy.
Ombitasvir/paritaprevir/ritonavir & dasabuvir ± ribavirin following protease inhibitors failure - a prospective multi-centre trial
Authors: Deutsch Liat , Houri Inbal , Ben-Ari Ziv , Shlomai Amir , Veitsman Ella , Cohen-Ezra Oranit , Issachar Assaf , Mor Orna , Gozlan Yael , Bruck Rafael , Menachem Yoram , Zelber-Sagi Shira , Katchman Helena , Shibolet Oren 
Published: April 2020

Abstract
Background
Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease and hepatocellular carcinoma. Treatment with first generation protease inhibitors (PI) + peg-interferon (pegIFN) and ribavirin (RBV) achieved sustained virologic response (SVR) rates of 65–75% but was associated with multiple side effects. The aim of this study was to evaluate safety and efficacy of Ombitasvir/Paritaprevir/Ritonavir and Dasabuvir (3D) ± RBV in HCV genotype 1 patients that failed previous treatment with first generation PIs.

Methods
An investigator-initiated, open-label, multi-centre clinical trial. HCV Genotype 1 patients who were previously null/partial responders or relapsers to telaprevir, boceprevir or simepravir+pegIFN/RBV and met eligibility criteria were included. 3D ± RBV were administrated for 12 or 24 weeks according to label. The primary outcome was antiviral response (SVR12); Secondary outcomes were patient reported outcomes, adverse events and resistance associated variants.

Results
Thirty-nine patients initiated treatment according to study protocol (59% men, age 54.0 ± 8.7 years, BMI 28.7 ± 4.5 kg/m2). Thirty-seven (94.9%) completed the study. Thirty-five patients had genotype 1b (9 cirrhotics) and 4 had genotype 1a (2 cirrhotics). Intention-to-treat SVR12 was 92.3% and per-protocol SVR12 was 97.3%. The rate of advanced fibrosis (FibroScan® score F3–4) declined from 46.2 to 25.7% (P = 0.045). Abnormal ALT levels declined from 84.6 to 8.6% (P < 0.001). Seven patients (17.9%) experienced serious adverse events (3 Psychiatric admissions, 1 pneumonia, 1 ankle fracture, 2 palpitations), and 12 patients (30.8%) experienced self-reported adverse events, mostly weakness.

Conclusion
3D ± RBV is safe and effective in achieving SVR among patients with HCV genotype 1 who failed previous first-generation PI treatment.

Trial registration
NCT02646111 (submitted to ClinicalTrials.gov, December 28, 2015).