bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syntenic quantitative trait loci and genomic divergence for Sclerotinia resistance and flowering time in Brassica napus
Authors: Zhang Fengqi , Huang Junyan , Tang Minqiang , Cheng Xiaohui , Liu Yueying , Tong Chaobo , Yu Jingyin , Sadia Tehrim , Dong Caihua , Liu Lingyan , Tang Baojun , Chen Jianguo , Liu Shengyi 
Published: December 2018

AbstractOilseed rape (Brassica napus) is an allotetraploid with two subgenomes descended from a common ancestor. Accordingly, its genome contains syntenic regions with many duplicate genes, some of which may have retained their original functions, whereas others may have diverged. Here, we mapped quantitative trait loci (QTL) for stem rot resistance (SRR), a disease caused by the fungus Sclerotinia sclerotiorum, and flowering time (FT) in a recombinant inbred line population. The population was genotyped using B. napus 60K single nucleotide polymorphism arrays and phenotyped in six (FT) and nine (SSR) experimental conditions or environments. In total, we detected 30 SRR QTL and 22 FT QTL and show that some of the major QTL associated with these two traits were co‐localized, suggesting a genetic linkage between them. Two SRR QTL on chromosome A2 and two on chromosome C2 were shown to be syntenic, suggesting the functional conservation of these regions. We used the syntenic properties of the genomic regions to exclude genes for selection candidates responsible for QTL‐associated traits. For example, 152 of the 185 genes could be excluded from a syntenic A2–C2 region. These findings will help to elucidate polyploid genomics in future studies, in addition to providing useful information for B. napus breeding programs.
OS1 functions in the allocation of nutrients between the endosperm and embryo in maize seeds
Authors: Song Weibin , Zhu Jinjie , Zhao Haiming , Li Yingnan , Liu Jiangtao , Zhang Xiangbo , Huang Liangliang , Lai Jinsheng 
Published: December 2018

AbstractUncovering the genetic basis of seed development will provide useful tools for improving both crop yield and nutritional value. However, the genetic regulatory networks of maize (Zea mays) seed development remain largely unknown. The maize opaque endosperm and small germ 1 (os1) mutant has opaque endosperm and a small embryo. Here, we cloned OS1 and show that it encodes a putative transcription factor containing an RWP‐RK domain. Transcriptional analysis indicated that OS1 expression is elevated in early endosperm development, especially in the basal endosperm transfer layer (BETL), conducting zone (CZ), and central starch endosperm (CSE) cells. RNA sequencing (RNA‐Seq) analysis of the os1 mutant revealed sharp downregulation of certain genes in specific cell types, including ZmMRP‐1 and Meg1 in BETL cells and a majority of zein‐ and starch‐related genes in CSE cells. Using a haploid induction system, we show that wild‐type endosperm could rescue the smaller size of os1 embryo, which suggests that nutrients are allocated by the wild‐type endosperm. Therefore, our data imply that the network regulated by OS1 accomplishes a key step in nutrient allocation between endosperm and embryo within maize seeds. Identification of this network will help uncover the mechanisms regulating the nutritional balance between endosperm and embryo.
The Efficacy of IV Tissue Plasminogen Activator for Restoring Cerebral Blood Flow in the Hours Immediately after Administration in Patients with Acute Stroke
Authors: Majidi Shahram , Simpkins Alexis N. , Leigh Richard ,   on behalf of the NIH Natural History of Stroke Investigators
Published: December 2018

ABSTRACTBACKGROUND AND PURPOSETimely restoration of tissue‐level cerebral blood flow is the goal of thrombolytic therapy in patients presenting with an acute ischemic stroke. We aimed to identify the incidence and predictors of reperfusion immediately following treatment with intravenous recombinant tissue plasminogen activator (IV rt‐PA).METHODSThis study included patients with acute ischemic stroke triaged using magnetic resonance imaging (MRI) with perfusion‐weighted imaging (PWI) and treated with IV rt‐PA who were subsequently enrolled in our natural history study and underwent repeat MRI with PWI approximately 2 hours posttreatment. Early reperfusion was defined as >80% decrease in the size of initial perfusion deficit on the 2 hours follow‐up MRI. Demographics, stroke risk factors, presenting National Institutes of Health Stroke Scale score, and location of the thrombosis were compared between patients with and without early reperfusion.RESULTSOf the 49 patients included in this study, 21 (43%) had early reperfusion. The mean age for patients with early reperfusion was significantly lower in comparison to the patients without early reperfusion (64 vs. 76, P = .01). The prevalence of hyperlipidemia was significantly lower among patients with early reperfusion (24% vs. 54%, P = .036). Patients with early reperfusion were less likely to have large‐vessel occlusion (LVO) (internal carotid artery terminus or proximal middle cerebral artery) (24% vs. 50%, P = .06). In a multivariate analysis, the presence of an LVO was an independent predictor of lack of early reperfusion (OR [95%Cl]: .13 [.019‐.89], P = .038).CONCLUSIONEarly reperfusion was found in a substantial percentage of the patients treated with IV rt‐PA. It was more common in patients without LVO.
The self and eating disorders
Authors: Bardone‐Cone Anna M. , Thompson Katherine A. , Miller Alexandra J. 
Published: December 2018

AbstractIn our review, we focus on self‐related constructs in the context of eating disorders with four aims. First, we examine a variety of self‐related constructs that have been theoretically and empirically linked to the development and course of eating disorders. In addition to the more well‐researched constructs of self‐esteem and self‐efficacy, we also report on findings related to selflessness, contingent self‐worth, self‐objectification, ego‐syntonicity, self‐concept clarity, self‐compassion, social comparison, self‐oriented perfectionism/self‐criticism, and narcissism. Second, we discuss self‐related constructs that may be especially relevant to comorbidities common among those with eating disorders. Third, we review intervention and prevention programs where self‐related constructs play a prominent role. Lastly, we share future research directions regarding self‐related constructs and eating disorders that we believe will advance a deeper understanding of the role of the self in the eating disorders.
Long‐Term Trends of Participation in Physical Activity During Adolescence With Educational Ambition and Attainment
Authors: Priesmeyer Jill , Fedewa Alicia L. , Toland Michael 
Published: December 2018

ABSTRACTBACKGROUNDInsufficient physical activity is a significant concern because a growing body of research demonstrates that physical activity during adolescence has numerous benefits on physical health, mental health, and educational achievement. A less‐studied area of physical activity research is how physical activity participation in adolescence relates to educational and career aspirations and attainment.METHODSUsing the Add Health dataset consisting of over 15,000 participants, this study addressed several research questions relating to the long‐term benefits of habitual physical activity in adolescence. Physical activity levels in adolescence and associations with activity participation in later adolescence and young adulthood were explored as were relationships with physical activity participation in adolescence and educational ambition and attainment in young adulthood. Moderator variables including adolescent sex, race, and age were also examined.RESULTSResults indicated several significant relationships between physical activity in adolescence and future physical activity and educational attainment outcomes.CONCLUSIONSGiven short‐ and long‐term benefits of physical activity, school personnel and parents should ensure children are meeting the required activity guidelines for children and find ways to keep children active as they approach adolescence.
Risk factors for positive urine cultures in cats with subcutaneous ureteral bypass and ureteral stents (2010‐2016)
Authors: Kopecny Lucy , Palm Carrie A. , Drobatz Kenneth J. , Balsa Ingrid M. , Culp William T. N. 
Published: December 2018

BackgroundUreteral stent and subcutaneous ureteral bypass (SUB) placement are commonly used for managing ureteral obstructions. Urinary tract infection (UTI) is a recognized complication.ObjectivesTo determine postoperative incidence of positive urine cultures in cats undergoing ureteral stent and SUB placement and to identify risk factors associated with positive urine cultures.DesignRetrospective study.AnimalsForty‐three cats that underwent 48 surgical events.ProceduresMedical records were reviewed. Cats were included if urine cultures were performed before and after surgery. Variables were compared to identify risk factors.ResultsUrine cultures were positive postoperatively pre‐discharge in 5/20 (25%) cats. Median duration of follow‐up post‐discharge was 209 days (range, 11‐2184 days), with a total of 143 urine cultures performed in cats post‐discharge. Of these, 16 (11%) were positive in 12/48 (25%) cats. Nine different bacteria were identified; Enterococcus spp. (n = 8) predominated as monomicrobic or mixed infections. In 14/16 instances of positive urine cultures, affected cats had lower urinary tract signs, signs of pyelonephritis or both. Cats that received antibiotics postoperatively were significantly less likely to have a positive urine culture compared to those that did not (odds ratio, 0.2, 95% confidence interval, 0.05, 0.8, P = 0.02). Chronic kidney disease, renal implant type and postoperative urinary catheterization were not associated with positive urine cultures.Conclusions and Clinical RelevancePostoperatively, occurrence of positive urine cultures was similar to previous reports. Subclinical bacteriuria was less common than UTI. Postoperative urinary catheterization has been speculated to increase risk of bacteriuria, but this was not the case in this cohort.
Pharmacokinetic profiles of florfenicol in spotted halibut, Verasper variegatus, at two water temperatures
Authors: Chang Zhiqiang , Chen Zhao , Gao Haiyu , Zhai Qianqian , Li Jian 
Published: December 2018

AbstractThe pharmacokinetic profiles of florfenicol in the spotted halibut (Verasper variegatus) were investigated at 15 and 20°C water temperatures, respectively. Florfenicol content in plasma samples was analyzed using an HPLC method. Drug concentration versus time data were best fitted to a three‐compartment model after a single intravenous administration (15 mg/kg BW), and fitted to a two‐compartment model after an oral administration (30 mg/kg BW) at 15 and 20°C. The florfenicol concentration in the blood increased slowly during the 12 hr following an oral administration at 15°C, with a peak concentration (Cmax) of 9.1 mg/L, and then declined gradually. The half‐lives of absorption, distribution, and elimination phase were 2.18, 5.66 and 14.25 hr, respectively. The bioavailability (F) was calculated to be 24.14%. After an oral administration at 20°C, shorter half‐lives of absorption (1.33 hr), distribution (2.51 hr) and elimination (9.71 hr), a higher Cmax (12.2 mg/L), and a similar F (23.98%) were found. Based on the pharmacokinetics and pharmacodynamics, an oral dose of 30 mg/kg BW was suggested to be efficacious for bacterial disease control in spotted halibut farming.
Population‐specific dynamics and selection patterns of transposable element insertions in European natural populations
Authors: Lerat Emmanuelle , Goubert Clément , Guirao‐Rico Sara , Merenciano Miriam , Dufour Anne‐Béatrice , Vieira Cristina , González Josefa 
Published: December 2018

AbstractTransposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome‐wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population‐specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents.
Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host
Authors: Ellison Silas , Knapp Roland A. , Sparagon Wesley , Swei Andrea , Vredenburg Vance T. 
Published: December 2018

AbstractThe fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow‐legged frog, Rana sierrae, using both culture‐dependent and culture‐independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such “persistent” populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture‐dependent Bd inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti‐Bd probiotic treatments.
Cotton fiber elongation requires the transcription factor GhMYB212 to regulate sucrose transportation into expanding fibers
Authors: Sun Wenjie , Gao Zhengyin , Wang Jun , Huang Yiqun , Chen Yun , Li Jianfu , Lv Mengli , Wang Jin , Luo Ming , Zuo Kaijing 
Published: December 2018

Summary

Cotton is white gold across the globe and composed of fiber cells derived from the outer integument of cotton ovules. Fiber elongation uses sucrose as a direct carbon source. The molecular mechanism transcriptionally controlling sucrose transport from ovules into the elongating fibers remains elusive.

In this study the involvement of GhMYB212 in the regulation of sucrose transportion into expanding fibers was investigated. GhMYB212 RNAi plants (GhMYB212i) accumulated less sucrose and glucose in developing fibers, and had shorter fibers and a lower lint index. RNA‐seq and protein−DNA binding assays revealed that GhMYB212 was closely linked to the pathways of sucrose and starch transportation and metabolism, directly controling the expression of a sucrose transporter gene GhSWEET12.

GhSWEET12 RNAi plants (GhSWEET12i) possessed similar fiber phenotypes to those of GhMYB212i. Exogenous sucrose supplementation in ovule cultures did not rescue the shorter fiber phenotype of GhMYB212i and GhSWEET12i. This finding supported the idea that the attenuated rate of sucrose transport from the outer seed coat into the fibers is responsible for the retardation of fiber elongation.

Current investigations support the idea that GhMYB212 functions as the main regulator of fiber elongation by controlling the expression of GhSWEET12, and therefore it is important to study cell expansion and sugar transportation during seed development.
NTN1 gene was risk to non‐syndromic cleft lip only among Han Chinese population
Authors: Jiang ShuYuan , Shi Jia‐Yu , Lin Yan‐Song , Duan Shi‐Jun , Chen Xieli , Jiao Jian‐Jun , Shen Wei , Jin Xiaoju , You Miao , Wang Moyao , Shi Bing , Jia Zhong‐Lin 
Published: December 2018

AbstractObjectiveGenome‐wide association studies (GWAS) found NTN1, NOG and the region between CREBBP and ADCY9 were risks to non‐syndromic cleft lip with or without cleft palate (NSCL/P). However, the association of single nucleotide polymorphisms (SNPs) in these genes with NSCL/P in Western China is unknown.Subjects and MethodsWe selected seven SNPs in NTN1, NOG and between CREBBP and ADCY9, and then performed transmission disequilibrium test (TDT), parent‐of‐origin effect and sliding window haplotype analysis to test the associations among 302 NSCL/P case–parent trios from Western Han Chinese.ResultsWe found allele G at rs4791774 in NTN1 was significantly overtransmitted among non‐syndromic cleft lip only (NSCLO) (p = 0.0067, OR = 1.79, 95% CI: 1.17–2.74); rs4791774 and rs9915089 tightly linked with each other among NSCL/P (D′ = 0.87, r2 = 0.67) and haplotypes carrying the risk allele G at rs4791774 were always found to be overtransmitted from parents to cases. Motif analysis indicated that allele G at rs4791774 could greatly alter the affinity of Myc_disc7, so allele G at rs4791774 in NTN1 might modulate C‐MYC transcription to participate in the aetiology of NSCLO.ConclusionsOur study suggested allele G at rs4791774 in NTN1 gene is risk of NSCLO, which could greatly increase the risk to have a baby with cleft.
Comparison of five different scoring methods in the evaluation of inflammatory infiltration (tumor‐infiltrating lymphocytes) in superficial spreading and nodular melanoma
Authors: Němejcová Kristýna , Tichá Ivana , Bártů Michaela , Kodet Ondřej , Důra Miroslav , Jakša Radek , Michálková Romana , Dundr Pavel 
Published: December 2018

AbstractThe objective of our study was to compare the five different scoring methods of tumor‐infiltrating lymphocytes (TILs) assessment in a group of 213 cases of superficial spreading and nodular melanoma. The scoring methods include (a) Clark scoring; (b) Melanoma Institute Australia system; (c) scoring system used in the study of Saldanha et al.; (d) scoring system used in the TCGA study and modified by Park et al.; and (e) the system recently proposed by the “International Immuno‐Oncology Biomarker Working Group” for TILs scoring in all solid tumors. Prediction of survival with three main outcomes—disease‐specific‐free survival, local recurrence‐free survival, and distant metastasis‐free survival—was evaluated. The prognostic value of TILs showed statistical significance in univariate analysis regarding all three of the outcomes only for three of the five evaluated methods; the Clark scoring, the Melanoma Institute Australia system, and the system proposed by the “International Immuno‐Oncology Biomarker Working Group”. However, in multivariate analysis with covariants including Breslow thickness, type of melanoma, location, sex, and age, we did not find TILs to be an independent prognostic factor.
The myelin protein PMP2 is regulated by SOX10 and drives melanoma cell invasion
Authors: Graf Saskia Anna , Heppt Markus Vincent , Wessely Anja , Krebs Stefan , Kammerbauer Claudia , Hornig Eva , Strieder Annamarie , Blum Helmut , Bosserhoff Anja‐Katrin , Berking Carola 
Published: December 2018

AbstractThe transcription factor sex determining region Y‐box 10 (SOX10) plays a key role in the development of melanocytes and glial cells from neural crest precursors. SOX10 is involved in melanoma initiation, proliferation, invasion, and survival. However, specific mediators which impart its oncogenic properties remain widely unknown. To identify target genes of SOX10, we performed RNA sequencing after ectopic expression of SOX10 in human melanoma cells. Among nine differentially regulated genes, peripheral myelin protein 2 (PMP2) was consistently upregulated in several cell lines. Direct regulation of PMP2 by SOX10 was shown by chromatin immunoprecipitation, electrophoretic mobility shift, and luciferase reporter assays. Moreover, a coregulation of PMP2 by SOX10 and early growth response 2 in melanoma cells was found. Phenotypical investigation demonstrated that PMP2 expression can increase melanoma cell invasion. As PMP2 protein was detected only in a subset of melanoma cell lines, it might contribute to melanoma heterogeneity.
Atypical presentation of necrobiosis lipoidica in a pediatric patient
Authors: Özkur Ezgi , Hasçiçek Seyhan Ö. , Altunay İlknur Kıvanç 
Published: December 2018

AbstractNecrobiosis lipoidica (NL) is a rare chronic granulomatous inflammatory skin disease characterized by brownish‐red papules and yellowish plaques with atrophic centers, which usually affect the legs, bilaterally. The average age of onset is 30‐40 years, and there are very few reported cases of necrobiosis lipoidica in children. A nondiabetic girl aged 14 years presented to our clinic with a history of an asymptomatic, 7 × 5‐cm single red plaque over her back in the interscapular area, which had started 5 years ago. Her laboratory tests were normal. A histopathologic evaluation confirmed the diagnosis of NL, and local treatment with clobetasol propionate twice daily was administrated. The patient will be followed up to monitor plasma glucose levels and evaluation of the lesion. Herein, we report a pediatric patient without diabetes mellitus who had NL in an atypical location and review the literature in view of the clinical features, complications, and treatment regimens for NL in children.
New insight into the diversity of exon and intron 5 regions of Oncorhynchus mykiss growth hormone (GH) gene: sexual dimorphism in the GH gene
Authors: Akbarialmajough Tahereh , Manaffar Ramin , Najdegerami Ebrahim H. , Bossier Peter 
Published: December 2018

AbstractThe growth in vertebrates is controlled by growth hormone (GH) gene which is a member of the somatotropin/prolactin family. In salmonids, a series of gene duplications is thought to have occurred in GH gene. In this family, the diversity in intron and exon regions of the GH gene is assumed to be not only in charge of a different growth rate but also in sex maturation. Due to the sex determination importance in salmonids, especially during early stages of development, in present study, an easy and accurate molecular marker was investigated for sex determination of Oncorhynchus mykiss fish using the diversity of the exon and intron 5 of GH gene. A pseudogene (GH‐ψ) copy of growth hormone gene was found on the Y chromosome which is in homology with type‐2 GH genes that can be used for sexual dimorphism of this species. This pseudogene was detected using a specific primer pairs combination using polymerase chain reaction (PCR) to select monosex female population. As recent findings suggest new functions of pseudogenes in the regulation of gene expression, it is believed that the putative gene could have an impact on GH expression in this species.