bluuebunny/crossref_metadata_2025_split huggingface dataset:
The seasonal development dynamics of the yak hair cycle transcriptome
Authors: Bao Pengjia , Luo Jiayu , Liu Yanbin , Chu Min , Ren Qingmiao , Guo Xian , Tang Bolin , Ding Xuezhi , Qiu Qiang , Pan Heping , Wang Kun , Yan Ping 
Published: May 2020

Abstract
Background
Mammalian hair play an important role in mammals’ ability to adapt to changing climatic environments. The seasonal circulation of yak hair helps them adapt to high altitude but the regulation mechanisms of the proliferation and differentiation of hair follicles (HFs) cells during development are still unknown. Here, using time series data for transcriptome and hormone contents, we systematically analyzed the mechanism regulating the periodic expression of hair development in the yak and reviewed how different combinations of genetic pathways regulate HFs development and cycling.

Results
This study used high-throughput RNA sequencing to provide a detailed description of global gene expression in 15 samples from five developmental time points during the yak hair cycle. According to clustering analysis, we found that these 15 samples could be significantly grouped into three phases, which represent different developmental periods in the hair cycle. A total of 2316 genes were identified in these three consecutive developmental periods and their expression patterns could be divided into 9 clusters. In the anagen, genes involved in activating hair follicle growth are highly expressed, such as the WNT pathway, FGF pathway, and some genes related to hair follicle differentiation. In the catagen, genes that inhibit differentiation and promote hair follicle cell apoptosis are highly expressed, such as BMP4, and Wise. In the telogen, genes that inhibit hair follicle activity are highly expressed, such as DKK1 and BMP1. Through co-expression analysis, we revealed a number of modular hub genes highly associated with hormones, such as SLF2, BOP1 and DPP8. They may play unique roles in hormonal regulation of events associated with the hair cycle.

Conclusions
Our results revealed the expression pattern and molecular mechanisms of the seasonal hair cycle in the yak. The findings will be valuable in further understanding the alpine adaptation mechanism in the yak, which is important in order to make full use of yak hair resources and promote the economic development of pastoral plateau areas.
Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis
Authors: Vergun Andrey A. , Girnyk Anastasiya E. , Korchagin Vitaly I. , Semyenova Seraphima K. , Arakelyan Marine S. , Danielyan Felix D. , Murphy Robert W. , Ryskov Alexey P. 
Published: May 2020

AbstractBackgroundThe hybridization of femaleD. raddeiand maleD. valentinigave rise to the parthenogenetic Caucasian rock lizardDarevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three species yields estimates of clonal diversity and tests the hypothesis of a single origin forD. unisexualis.ResultsGenotyping and sequencing of four microsatellite-containing loci for 109 specimens ofD. unisexualis, 17D. valentini,and 45D. raddei nairensisidentified 12 presumptive clones,including one widespread and 11 rare clones. Most individuals in some localities had a rare clone. Clone-specific alleles inD. unisexualiswere compared with those of the parental species. The results inferred a single hybridization event. Post-formation mutations best explain the less common clones.ConclusionsInterspecific analyses identify alleles inherited byD. unisexualisfrom its bisexual ancestors.SNP analyses fail to reject the hypothesis of a single interspecific origin ofD. unisexualis,followed by microsatellite mutations in this initial clone. Microsatellites detect higher clonal diversity inD. unisexualiscompared to allozymes and identify the likely origins of clones.Our approach may be applicable to other unisexual species whose origins involve interspecific hybridization.
High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize
Authors: Wang Yuancong , Xu Jinyan , Ge Min , Ning Lihua , Hu Mengmei , Zhao Han 
Published: May 2020

Abstract
Background
The fluctuation of nitrogen (N) contents profoundly affects the root growth and architecture in maize by altering the expression of thousands of genes. The differentially expressed genes (DEGs) in response to N have been extensively reported. However, information about the effects of N variation on the alternative splicing in genes is limited.

Results
To reveal the effects of N on the transcriptome comprehensively, we studied the N-starved roots of B73 in response to nitrate treatment, using a combination of short-read sequencing (RNA-seq) and long-read sequencing (PacBio-sequencing) techniques. Samples were collected before and 30 min after nitrate supply. RNA-seq analysis revealed that the DEGs in response to N treatment were mainly associated with N metabolism and signal transduction. In addition, we developed a workflow that utilizes the RNA-seq data to improve the quality of long reads, increasing the number of high-quality long reads to about 2.5 times. Using this workflow, we identified thousands of novel isoforms; most of them encoded the known functional domains and were supported by the RNA-seq data. Moreover, we found more than 1000 genes that experienced AS events specifically in the N-treated samples, most of them were not differentially expressed after nitrate supply-these genes mainly related to immunity, molecular modification, and transportation. Notably, we found a transcription factor ZmNLP6, a homolog of AtNLP7-a well-known regulator for N-response and root growth-generates several isoforms varied in capacities of activating downstream targets specifically after nitrate supply. We found that one of its isoforms has an increased ability to activate downstream genes. Overlaying DEGs and DAP-seq results revealed that many putative targets of ZmNLP6 are involved in regulating N metabolism, suggesting the involvement of ZmNLP6 in the N-response.

Conclusions
Our study shows that many genes, including the transcription factor ZmNLP6, are involved in modulating early N-responses in maize through the mechanism of AS rather than altering the transcriptional abundance. Thus, AS plays an important role in maize to adapt N fluctuation.
Genome-wide association study leads to novel genetic insights into resistance to Aspergillus flavus in maize kernels
Authors: Han Guomin , Li Cuiping , Xiang Fangzhi , Zhao Qianqian , Zhao Yang , Cai Ronghao , Cheng Beijiu , Wang Xuewen , Tao Fang 
Published: May 2020

AbstractBackgroundFungus infection in staple grains affects the food storage and threatens food security. TheAspergillus flavusis known to infect multiple grains and produce mycotoxin Aflatoxin B1, which is mutagenic, teratogenic and causes immunosuppression in animals. However, the molecular mechanism of maize resistance toA. flavusis largely unknown.ResultsHere we used corn kernels to investigate resistance genes toA. flavususing genome-wide association study (GWAS) of 313 inbred lines. We characterized the resistance levels of kernels after inoculating withA. flavus. The GWAS with 558,529 SNPs identified four associated loci involving 29 candidate genes that were linked to seed development, resistance or infection, and involved in signal pathways, seed development, germination, dormancy, epigenetic modification, and antimicrobial activity. In addition, a few candidate genes were also associated with several G-protein signaling and phytohormones that might involve in synergistic work conferring different resistance during seed development. Expression of 16 genes out of 29 during kernel development was also associated with resistance levels.ConclusionsWe characterized the resistance levels of 313 maize kernels after inoculating withA. flavus, and found four associated loci and 16 candidate maize genes. The expressed 16 genes involved in kernel structure and kernel composition most likely contribute to mature maize kernels’ resistance toA. flavus, and in particular, in the development of pericarp. The linked candidate genes could be experimentally transformed to validate and manipulate fungal resistance. Thus this result adds value to maize kernels in breeding programs.
Using alcohol consumption diary data from an internet intervention for outcome and predictive modeling: a validation and machine learning study
Authors: Lindner Philip , Johansson Magnus , Gajecki Mikael , Berman Anne H. 
Published: May 2020

Abstract
Background
Alcohol use disorder (AUD) is highly prevalent and presents a large treatment gap. Self-help internet interventions are an attractive approach to lowering thresholds for seeking help and disseminating evidence-based programs at scale. Internet interventions for AUD however suffer from high attrition and since continuous outcome measurements are uncommon, little is known about trajectories and processes. The current study investigates whether data from a non-mandatory alcohol consumption diary, common in internet interventions for AUD, approximates drinks reported at follow-up, and whether data from the first half of the intervention predict treatment success.

Methods
N = 607 participants enrolled in a trial of online self-help for AUD, made an entry in the non-mandatory consumption diary (total of 9117 entries), and completed the follow-up assessment. Using multiple regression and a subset of calendar data overlapping with the follow-up, scaling factors were derived to account for missing entries per participant and week. Generalized estimating equations with an inverse time predictor were then used to calculate point-estimates of drinks per week at follow-up, the confidence intervals of which were compared to that from the measurement at follow-up. Next, calendar data form the first half of the intervention were retained and summary functions used to create 18 predictors for random forest machine learning models, the classification accuracies of which were ultimately estimated using nested cross-validation.

Results
While the raw calendar data substantially underestimated drinks reported at follow-up, the confidence interval of the trajectory-derived point-estimate from the adjusted data overlapped with the confidence interval of drinks reported at follow-up. Machine learning models achieved prediction accuracies of 64% (predicting non-hazardous drinking) and 48% (predicting AUD severity decrease), in both cases with higher sensitivity than specificity.

Conclusions
Data from a non-mandatory alcohol consumption diary, adjusted for missing entries, approximates follow-up data at a group level, suggesting that such data can be used to reveal trajectories and processes during treatment and possibly be used to impute missing follow-up data. At an individual level, however, calendar data from the first half of the intervention did not have high predictive accuracy, presumable due to a high rate of missing data and unclear missing mechanisms.
Reduced mean platelet volume levels predict shorter survival in patients with resectable pancreatic ductal adenocarcinoma and type 2 diabetes
Authors: Yin Ji-bin , Li Na , Cui Ming-ming , Wang Xin , Wang Rui-tao 
Published: May 2020

Abstract
Background
Type 2 diabetes mellitus (T2DM) increased the risk of developing pancreatic cancer. Pancreatic ductal adenocarcinoma (PDAC) is the most common neoplastic disease originating from the pancreas. Increasing evidence indicates that platelets activation plays a prominent role in tumor and T2DM. Mean platelet volume (MPV) is an indicator of activated platelets and is altered in several cancers. The current study aimed to evaluate the prognostic role of MPV in resectable PDAC patients with T2DM.

Methods
Eight hundred and three patients with PDAC were included in this retrospective study. We determined the optimal cutoff value of MPV for 5-year overall survival (OS) using the receiver operating characteristic (ROC) method. The associations between MPV levels and clinical characteristics were analyzed. Kaplan-Meier survival analysis and Cox’s proportional hazard regression model were used to evaluate the prognostic value of MPV for OS.

Results
Compared to the PDAC patients without T2DM, MPV levels were significantly higher in the PDAC patients with T2DM. Moreover, MPV was significantly associated with the differentiation between T2DM and non-T2DM. In addition, Kaplan-Meier analysis found that patients with low MPV levels had a poorer 5-year OS than patients with high MPV levels in diabetic patients. Multivariate analyses revealed that MPV was an independent prognostic factor for OS in patients with T2DM. However, the independent prognostic role of MPV was not observed in patients without T2DM.

Conclusion
MPV independently predicts poor survival in PDAC patients with T2DM. Prospective studies are required to confirm the role of MPV in PDAC.
Production of ERCP training model using a 3D printing technique (with video)
Authors: Kwon Chang-Il , Shin Yeonsun , Hong Jaeok , Im Minje , Kim Guk Bae , Koh Dong Hee , Song Tae Jun , Park Won Suk , Hyun Jong Jin , Jeong Seok 
Published: May 2020

Abstract
Background
ERCP training models are very different in terms of anatomical differences, ethical issues, storage problems, realistic tactile sensation, durability and portability. There is no easy way to select an optimized model for ERCP training. If the ERCP training model could be made as a soft silicone model using 3D printing technique, it would have numerous advantages over the models presented so far. The purpose of this study was to develop an optimized ERCP training model using a 3D printing technique and to try to find ways for implementing various practical techniques.

Methods
All organ parts of this model were fabricated using silicone molding techniques with 3D printing. Especially, various anatomy of the ampulla of Vater and common bile duct (CBD) were creatively designed for different diagnostic and therapeutic procedures. In order to manufacture each of the designed organ parts with silicone, a negative part had to be newly designed to produce the molder. The negative molders were 3D printed and then injection molding was applied to obtain organ parts in silicone material. The eight different types of ampulla and CBD were repeatedly utilized and replaced to the main system as a module-type.

Results
ERCP training silicone model using 3D technique was semi-permanently used to repeat various ERCP procedures. All ERCP procedures using this model could be observed by real-time fluoroscopic examination as well as endoscopic examination simultaneously. Using different ampulla and CBD modules, basic biliary cannulation, difficult cannulation, stone extraction, mechanical lithotripsy, metal stent insertion, plastic stent insertion, and balloon dilation were successfully and repeatedly achieved. Endoscopic sphincterotomy was also performed on a specialized ampulla using a Vienna sausage. After repeat procedures and trainings, all parts of organs including the ampulla and CBD modules were not markedly damaged or deformed.

Conclusions
We made a specialized ERCP training silicon model with 3D printing technique. This model is durable, relatively cheap and easy to make, and thus allows the users to perform various specialized ERCP techniques, which increases its chances of being a good ERCP training model.
Molecular identification and antifungal susceptibility profile of yeast from vulvovaginal candidiasis
Authors: Shi Yu , Zhu Yuxia , Fan Shangrong , Liu Xiaoping , Liang Yiheng , Shan Yingying 
Published: May 2020

Abstract
Background
Accurate identification Candida is important for successful therapy and epidemiology study. The aim of research is to study API 20C yeast identification system identification rate by using molecular identification as gold standard and tested the antifungal susceptibility of Candida from patients with vulvovaginal candidiasis (VVC).

Methods
In total, 3574 yeast isolates were obtained from patients with VVC. API 20C yeast identification, molecular identification and in vitro antifungal susceptibility were performed.

Results
C. albicans was the predominant Candida species [2748 isolates, 76.9%] in VVC. The isolates from vaginal samples represented 22 species based on molecular identification. The API 20C system identifies only 11 of the species encountered during the study period. Based on the API 20C system, 3273 (91.58%) isolates were correctly identified to the species level. The correct identification rate of the API 20C system for rare yeast was 15.29% (26/170 isolates). Antifungal susceptibility was tested in a total of 1844 isolates of Candida from patients with VVC. C. albicans was susceptible to most of the tested antifungals. The MICs of azoles for C. glabrata were higher than those for C. albicans. The MICs of echinocandins for C. parapsilosis were higher than those for C. albicans.

Conclusions
The API 20C yeast identification system can be used to reliably identify the most common Candida species while molecular methods are necessary for the identification of closely related, emerging, and rare yeast species. The results from this study suggest that much of the previous studies on the epidemiology of VVC should be re-thought. C. albicans was susceptible to most of the tested antifungals.
Anopheles gambiae s.l (Diptera: Culicidae) seasonal abundance, abdominal status and parity rates in Metema-Armachiho lowland, Northwest Ethiopia
Authors: Aschale Yibeltal , Ayehu Animen , Worku Ligabaw , Addisu Ayenew , Zeleke Ayalew Jejaw , Bayih Abebe Genetu , Lemma Wossenseged 
Published: May 2020

Abstract
Background
Malaria is a life threating vector borne disease caused by different Plasmodium parasites. Metema and Armachiho are two of the top five malaria endemic areas among the districts of Amhara region in Ethiopia. Transmission pattern is seasonal and migrant laborers who visit these areas for employment in mechanized agriculture are highly affected. The aim of this study was to investigate seasonal abundance, abdominal status and parity rate of An.gambiae s.l in Metema-Armachiho lowlands, Northwest Ethiopia.

Method
A 1 year longitudinal entomological study was conducted in Metema-Armachiho lowlands from June 2016–May 2017. Mosquitoes were collected using CDC-light traps in indoor and outdoor sites for four consecutive days in each month. A total of eight standard battery operated CDC-light traps were used to collect mosquitoes. Female mosquitoes were classed as unfed, fed or gravid under a dissecting microscope. The ovaries of all unfed An.gambiae s.l mosquitoes were examined for evidence of parity. Data were entered and analyzed using SPSS-20 software. Chi-square test was applied to show significant difference between variables. P-value< 0.05 was taken as statistically significant.

Results
Of the total 1253 mosquitoes collected, 713 (552 female, 161 male) were culex and 540 (501 female, 39 male) were An.gambiae s.l. About 50.9% were collected in June–August 2016, 21.7% in September–November 2016, 12.0% in December 2016–February 2017 and 15.4% in March to May 2017. Of the total, 57.2 and 42.8% of the An.gambiae s.l were collected from indoor and outdoor sites respectively. Of the total females collected, 76.8% were unfed; of which 69.4% were parous. Significantly higher number of female An.gambiae s.l were collected in indoor and there was significant difference in abdominal status of An.gambiae s.l mosquitoes collected in different season (P < 0.05).

Conclusions
Highest number of An.gambiae s.l was observed from June–August followed by September–November. The parity rate of An.gambiae s.l was high and there was significant difference in abdominal status of An.gambiae s.l collected in different season.
Recurrent secondary genomic alterations in desmoplastic small round cell tumors
Authors: Chow Warren A. , Yee Jiing-Kuan , Tsark Walter , Wu Xiwei , Qin Hanjun , Guan Min , Ross Jeffrey S. , Ali Siraj M. , Millis Sherri Z. 
Published: May 2020

Abstract
Background
Desmoplastic small round cell tumor (DSRCT) is a rare, highly aggressive, translocation-associated soft-tissue sarcoma that primarily affects children, adolescents, and young adults, with a striking male predominance. It is characterized by t(11;22) generating a novel EWSR1-WT1 fusion gene. Secondary genomic alterations are rarely described.

Methods
Tumor tissue from 83 DSRCT patients was assayed by hybrid-capture based comprehensive genomic profiling, FoundationOne® Heme next generation sequencing analysis of 406 genes and RNA sequencing of 265 genes. Tumor mutation burden was calculated from a minimum of 1.4 Mb sequenced DNA. Microsatellite instability status was determined by a novel algorithm analyzing 114 specific loci.

Results
Comprehensive genomic profiling identified several genomically-defined DSRCT subgroups. Recurrent genomic alterations were most frequently detected in FGFR4, ARID1A, TP53, MSH3, and MLL3 genes. With the exception of FGFR4, where the genomic alterations predicted activation, most of the alterations in the remaining genes predicted gene inactivation. No DSRCT were TMB or MSI high.

Conclusions
In summary, recurrent secondary somatic alterations in FGFR4, ARID1A, TP53, MSH3, and MLL3 were detected in 82% of DSRCT, which is significantly greater than previously reported. These alterations may have both prognostic and therapeutic implications.
Three intellectual disability-associated de novo mutations in MECP2 identified by trio-WES analysis
Authors: Gu Yi , Xiang Bingwu , Zhu Lina , Ma Xiuwei , Chen Xiang , Cai Tao 
Published: May 2020

Abstract
Background
To date, at least 746 genes have been identified to cause intellectual disability (ID). Among them, mutations in the Methyl CpG binding protein 2 (MECP2) gene are the leading cause of Rett syndrome and associated ID.

Methods
Considering the large number of ID-associated genes, we applied trio-based whole-exome sequencing (trio-WES) and in silico analysis for genetic diagnosis of 294 children with ID.

Results
Three de novo heterozygous mutations [NM_004992.3: c.502C > T, p.(Arg168*), c.916C > T, p.(Arg306Cys), and c.879C > G, p.(Ile293Met)] in MECP2 were identified in three unrelated girls. The first two mutations were detected in two patients who were diagnosed as typical Rett syndrome, X-linked ID and psychomotor retardation. The third mutation (c.879C > G), a previously unreported, was found in a 6-year-old girl with ID, microcephaly, severe underweight and psychomotor retardation. Particularly, this extremely rare de novo mutation (DNM) is located in the transcriptional repression domain (TRD) of MECP2, where at least 62 different causal mutations are identified.

Conclusions
We identified three DNMs in MECP2 in a cohort of 294 individuals with ID. The novel c.879C > G mutation, as a likely pathogenic allele, may become a risk factor associated with X-linked ID, microcephaly and psychomotor retardation.