bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and Fine Mapping of a New Dwarf Mutant in Brassica Napus
Authors: Li Xin , Xiang Fujiang , Zhang Wei , Yan Jindong , Li Xinmei , Zhong Ming , Yang Piao , Chen Caiyan , Liu Xuanming , Mao Donghai , Zhao Xiaoying 
Published: September 2020

Abstract
Background: Plant height is an important plant architecture character closely related to yield performance of many crops. Reasonable reduction of plant height of crops is beneficial for enhancing lodging resistance and improving yield. Results: In the present study, we described a Brassica napus dwarf mutant bnd2 induced by ethyl methanesulfonate (EMS) mutagenesis. Compared to wild type, bnd2 showed shorter stature, shorter hypocotyl, as well as shorter petiole leaves. We crossed the bnd2 mutant with its wild type and found that the ratio of the mutant to the wild type in the F2 population was close to 1:3, indicating that bnd2 is a recessive mutation of a single locus. Following bulked segregant analysis (BSA) by resequencing, BND2 was located into the 13.77 Mb-18.08 Mb interval of chromosome A08, with a length of 4.31 Mb. After fine mapping with SNP and InDel markers, the gene was narrowed to a 140-Kb interval ranging from 15.62 Mb to 15.76 Mb. According to reference genome annotation, there are 27 genes in the interval, and one of them BnaA08g20960D has a SNP type variation in the intron between the mutant and its parent, which may be the candidate gene conferring to BND2. The hybrid line derived from a cross between the mutant bnd2 and a commercial cultivar L329 has similar plant height but higher grain yield than the commercial cultivar, suggesting that the allele bnd2 is benefit for hybrid breeding of lodging resistance and high yield in rapeseed.Conclusion: In this study, we found a fresh resource and a new locus for dwarf in rapeseed, which may be benefit for functional analysis of genetic mechanism of plant architecture and grain yield in rapeseed.
Congenital muscular dystrophy-associated inflammatory chemokines provide axes for effective recruitment of therapeutic adult stem cell into muscles
Authors: Alexeev Vitali , Olavarria Jacquelyn , Bonaldo Paolo , Merlini Luciano , Igoucheva Olga 
Published: September 2020

Abstract
Background: Congenital muscular dystrophies (CMD) are a clinically and genetically heterogeneous group of neuromuscular disorders characterized by muscle weakness. The two most prevalent forms of CMD, collagen VI-related myopathies (COL6RM) and laminin a2 deficient CMD type 1A (MDC1A), are both caused by deficiency or dysfunction of extracellular matrix proteins. Previously, we showed that an intramuscular transplantation of human adipose-derived stem cells (ADSC) into the muscle of the Col6a1-/- mice results in efficient stem cell engraftment, migration, long-term survival, and continuous production of the collagen VI protein, suggesting the feasibility of the systemic cellular therapy for COL6RM. In order for this therapeutic approach to work however, stem cells must be efficiently targeted to the entire body musculature. Thus, the main goal of this study is to test whether muscle homing of systemically transplanted ADSC can be enhanced by employing muscle-specific chemotactic signals originating from CMD-affected muscle tissue. Methods: Proteomic screens of chemotactic molecules were conducted in the skeletal muscles of COL6RM- and MDC1A-affected patients and CMD mouse models to define the inflammatory and immune activities, thus, providing potential markers of disease activity or treatment effect. Also using a pre-clinical animal model, recapitulating mild Ullrich congenital muscular dystrophy (UCMD), the therapeutic relevance of identified chemotactic pathways was investigated in vivo, providing a basis for future clinical investigations.Results: Comprehensive proteomic screens evaluating relevant human and mouse skeletal muscle biopsies offered chemotactic axes to enhance directional migration of systemically transplanted cells into CMD-affected muscles, including CCL5-CCR1/3/5, CCL2-CCR2, CXCL1/2-CXCR1,2 and CXCL7-CXCR2. Also, the specific populations of ADSC selected with an affinity for the chemokines being released by damaged muscle showed efficient migration to injured site and presented their therapeutic effect.Conclusions: Collectively, identified molecules provided insight into the mechanisms governing directional migration and intra-muscular trafficking of systemically infused stem cells, thus, permitting broad and effective application of the therapeutic adult stem cells for CMD treatment.
iDPGK: Characterization and Identification of Lysine Phosphoglycerylation Sites Based on Sequence-Based Features
Authors: Huang Kai-Yao , Hung Fang-Yu , Kao Hui-Ju , Lau Hui-Hsuan , Weng Shun-Long 
Published: September 2020

Abstract
Background:Protein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine (pgK), is a reversible and non-enzymatic post-translational modification (PTM) and plays a regulatory role in glucose metabolism and glycolytic process. As the number of experimentally verified phosphoglycerylated sites has increased significantly, statistical or machine learning methods are imperative for investigating the characteristics of phosphoglycerylation sites. Currently, research into phosphoglycerylation is very limited, and only a few resources are available for the computational identification of phosphoglycerylation sites. Result: We present a bioinformatics investigation of phosphoglycerylation sites based on sequence-based features. The TwoSampleLogo analysis reveals that the regions surrounding the phosphoglycerylation sites contain a high relatively of positively charged amino acids, especially in the upstream flanking region. Additionally, the non-polar and aliphatic amino acids are more abundant surrounding phosphoglycerylated lysine following the results of PTM-Logo, which may play a functional role in discriminating between phosphoglycerylation and non- phosphoglycerylation sites. Many types of features were adopted to build the prediction model on the training dataset, including amino acid composition, amino acid pair composition, positional weighted matrix and position-specific scoring matrix. Further, to improve the predictive power, numerous top features ranked by F-score were considered as the final combination for classification, and thus the predictive models were trained using DT, RF and SVM classifiers. Evaluation by five-fold cross-validation showed that the selected features was most effective in discriminating between phosphoglycerylated and non- phosphoglycerylated sites.Conclusion: The SVM model trained with the selected sequence-based features performed well, with a sensitivity of 77.5%, a specificity of 73.6%, an accuracy of 74.9%, and a Matthews Correlation Coefficient value of 0.49. Furthermore, the model also consistently provides the effective performance in independent testing set, yielding sensitivity of 75.7% and specificity of 64.9%. Finally, the model has been implemented as a web-based system, namely iDPGK, which is now freely available at http://mer.hc.mmh.org.tw/iDPGK/.
Host-adaptation of Rare Enterocytozoon bieneusi genotype CHN4 in Coypus (Myocastor coypus) in China
Authors: Yu Fuchang , Cao Yangwenna , Wang Haiyan , Liu Qiang , Zhao Aiyun , Qi Meng , Zhang Longxian 
Published: September 2020

Abstract
Background: Enterocytozoon bieneusi is a zoonotic gastrointestinal pathogen and can infect both humans and animals. Coypus (Myocastor coypus) are semi-aquatic rodents, in which few E. bieneusi infections have been reported and the distribution of genotypes and zoonotic potential remains unknown.Methods: A total of 308 fresh fecal samples were collected from seven coypu farms in China to determine the infection rate and the distribution of genotypes of E. bieneusi from coypus using nested-PCR amplification of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene.Results: E. bieneusi was detected with an infection rate of 41.2% (n = 127). Four genotypes were identified, including three known genotypes: CHN4 (n = 111), EbpC (n = 8) and EbpA (n = 7) and a novel genotype named CNCP1 (n = 1). Conclusions: The rare genotype CHN4 was the most common one in the present study, and the transmission dynamics of E. bieneusi in coypus were different from other rodents. This is the first report of E. bieneusi infections in coypus in China. Our study reveals that E. bieneusi in coypus may be potential infection source to humans.
Maxillary and mandibular dental arch forms in a Jordanian population with normal occlusion
Authors: Aljayousi Mohammed , Al-Khateeb Suzan Nadeem , Badran Serene , Alhaija Elham SJ Abu 
Published: September 2020

Abstract
BackgroundEthnic background had been claimed to affect arch form. The purpose of this study was to describe the maxillary and mandibular arch forms in Jordanian population and to develop a classification of these forms which could be used to construct orthodontic archwires accordingly.MethodsThe sample comprised the study casts of five hundred and twenty subjects (231 males and 289 females with mean age 15.4 ± 1.02 years). All subjects had permanent dentition with normal occlusion. A mathematical method associated with a polynomial function of 6th degree was used to evaluate the dental arch forms. The resulting arch forms were organized into 5 groups for both the maxilla and the mandible utilizing computer software with special code designed for this study. Each group was subdivided into 3 subgroups: small, medium, and large sizes.ResultsCatenary arch form was found in 47% and 41.2% (P˂0.01) in maxilla and mandible, respectively. Form 2 (between half ellipse and U-shaped arch form) was found in 27.7% and 26.7%. Medium size arch form was found in 55.4% in the maxilla and 65.6% in the mandible.ConclusionsCatenary arch form was the most common arch form, followed by wide elliptical form. The other forms; tudor arch, tapered equilateral and quadroangular forms were less frequent. With respect to size, the medium size was the most common one in the studied sample.
The Effect of the Underlying Malignancy on Short- and Medium-Term Survival of Critically Ill Patients Admitted to the Intensive Care Unit : A Retrospective Analysis Based on Propensity Score Matching
Authors: Yuan Zhennan , Wang Haijun , Gao Yong , Qu Shining , Huang Chulin , Wang Hao , Zhang Hao , Yang Quanhui , Xing Xuezhong 
Published: September 2020

Abstract
Background Advances in oncology led to a substantial increase in the number of patients requiring admission to the ICU. It is significant to confirm which cancer critical patients can benefit from the ICU care service like noncancer patients. Methods An observational retrospective cohort study using intensive care unit (ICU) admissions of Medical Information Mart for Intensive Care III from the Beth Israel Deaconess Medical Center in Boston, MA, USA between 2001 and 2012 was conducted. Propensity score matching was used to reduce the imbalance between two matched cohorts. ICU patients with cancer were compared with those without cancer in terms of patients’ characteristics and survival. Results There were 38,508 adult patients admitted to ICUs during the period. The median age was 65 years (IQR, 52-77) and 8,308 (21.8%) had an underlying malignancy diagnosis. The noncancer group had a significant survive advantage at the point of 28-day, 90-day, 365-day and 1095-day after ICU admission compared with cancer group (P < 0.001 for all) after PSM. Subgroup analysis showed that the diagnosis of malignancy didn’t decrease 28-day and 90-day survive when patients’ age ≥65-year, patients in surgical intensive care unit or cardiac surgery recovery unit or traumatic surgical intensive care unit, elective admission, patients with renal replacement therapy or vasopressor support (P > 0.05 for all). Conclusions Malignancy is a common diagnosis among ICU patients. Patients without cancer have a survive advantage compared with patients with cancer in the short- and medium-term. However, in selected groups, cancer critical patients can benefit from the ICU care service like noncancer patients in the short-term.
Root Morphology and Secretion of two subtropical tree species to NH4+-N and NO3–-N Deposition
Authors: Zhang Rui , Wang Yi , Zhou Zhichun 
Published: September 2020

Abstract
Background: Both NH4+ and NO3– are capable of greatly influencing plants’ growth and biomass. However, the belowground responses of subtropical trees to either NH4+ or NO3– deposition remain poorly understood. Here, we discuss how these two forms of N deposition can affect root development, and experimentally analyzed how they could impact nitrogen and phosphorus absorption in two types (broadleaved with a fibrous root system vs. conifer with a tap root system) of subtropical tree species. Results: In a greenhouse in southern China, 1-year-old S. superba and P. massoniana seedlings grown on P-limited and P-normal soil were treated with NaNO3 and NH4Cl solutions of 0, 80, and 200 kg N ha–1 year–1, corresponding to the control, N80, and N200 groups, respectively. Root phenotype characteristics and metabolism ability were measured after 8 months of growth. The results showed that the root morphology and physiology variables differed significantly between the two species under different N and P treatments. Although S. superba had a larger quantity of roots than P. massoniana, both its root growth rate and root absorption were respectively lower and weaker. N addition differentially affected root growth and activity as follows: (1) NO3–-N80 and NH4+-N80 increased root growth and activity of the two species, but NH4+-N80 led to thicker roots in S. superba; (2) NO3–-N200 and NH4+-N200 had inhibitory effects on the roots of P. massoniana, for which NH4+-N200 led to thinner and longer roots and even the death of some roots; and (3) NH4+-N could promote metabolic activity in thicker roots (> 1.5 mm) and the NO3–-N was found to stimulate activity in thinner roots (0.5–1.5 mm) in the fibrous root system having a larger quantity of roots, namely S. superba. By contrast, NO3–-N and NH4+-N had an opposite influence upon functioning in the tap root system with a slender root, namely P. massoniana. Conclusion: We conclude P. massoniana has a much higher root absorption efficiency; however, nitrogen deposition is more beneficial to the root growth of S. superba.
Transcriptome Profiling Revealed Early Vascular Smooth Muscle Cell Gene Activation Following Focal Ischemic Stroke in Female Rats – Comparisons with Males
Authors: Rehnström Mimmi , Frederiksen Simona Denise , Edvinsson Lars 
Published: September 2020

Abstract
Background. Women account for 60% of all stroke deaths and are more often permanently disabled than men, despite their higher observed stroke incidence. Considering the clinical population affected by stroke, an obvious drawback is that many pre-clinical and clinical studies only investigate young males. To improve therapeutic translation from bench to bedside, we believe that it is advantageous to include both sexes in experimental models of stroke. The aims of this study were to identify early cerebral vascular responses to ischemic stroke in females, compare the differential gene expression patterns with those seen in males, and identify potential new therapeutic targets.Results. Transient middle cerebral artery occlusion (tMCAO) was used to induce stroke in both female and male rats, the middle cerebral arteries (MCAs) were isolated 3 hours post reperfusion and RNA was extracted. Affymetrix whole transcriptome expression profiling was performed on female MCAs to reveal differentially expressed genes. In total, 1076 genes had an increased expression and 879 genes a decreased expression in the occluded MCA as compared to the non-stroke control arteries from female rats. An enrichment of genes related to apoptosis, regulation of transcription, protein autophosphorylation, inflammation, oxidative stress, and tissue repair and recovery were seen in the occluded MCA. The high expression genes chosen for qPCR verification (Adamts4, Olr1, JunB, Fosl1, Serpine1, S1pr3, Ccl2 and Socs3) were all shown to be upregulated in the same manner in both females and males after tMCAO (p < 0.05). When comparing the differentially expressed genes in female MCAs (occluded and non-occluded) with our previous findings in males after tMCAO, a total of 297 genes overlapped (all groups had 32 genes in common).Conclusions. The cascades of processes initiated in the vasculature following reperfusion are complex. Dynamic gene expression alterations were observed in the occluded MCA, and to a less pronounced degree in the non-occluded MCA. Dysregulation of inflammation and blood-brain barrier breakdown are possible pharmacological targets. The sample of genes (<1% of the differentially expressed genes) validated for this microarray did not reveal any sex differences. However, sex differences might be observed for other gene targets.
Construction of A High-Density SNP Genetic Map by Genotyping-By-Sequencing and Location of Seed Quality traits in Flax (Linum usitatisimum L.)
Authors: Zhao Li , Zhao Wei , Wang Limin , Wang Bin , Dang Zhao , Li Wenjuan 
Published: September 2020

Abstract
Background

Oil and five main fatty acid content(especially linolenic acid content (LNA) )are six main quality traits in flax, and also the important target traits in flax breeding. However, the reports on genetic map construction and QTL mapping of linolenic acid content in flax are limited, which results in low accuracy and efficiency of quality breeding in oil flax. Construction the genetic linkage map and location the QTLs to discover the stable genetic QTLs sites related to oil content and fatty acid content, so as to provide targeted targets for breeders and improve breeding efficiency.
Results

In this study, a final integrated map consisting of 2,239 single nucleotide polymorphism (SNP) markers on 15 linkage groups (LGs) with an average distance of 0.46 cM between adjacent markers was generated using genotyping-by-sequencing (GBS) technique. A total of 21 quantitative trait loci (QTL)s for the six traits, i.e., palmitic acid content (PAL), stearic acid content (STE), oleic acid content (OLE), linoleic acid content (LIN), linolenic acid content (LNA), and oil content (OIL) in the RIL population under three environments. One QTL cluster harbored two QTLs for LIN and LNA trait, respectively was also identified. Especially, QTL qLIN-Group12-2 for LIN and QTL qLNA-Group12-2 for LNA on chromosome 12 were detected in multi-environments.
Conclusions

A high-density SNP genetic map with total 2239 markers was constructed with GBS technique, The total genetic distance of the SNP map was 1032.90 cM, with the average genetic distance of 0.46 cM per marker. A total of 21 quantitative trait loci (QTL)s for the six traits under three environments were determined. One QTL cluster harbored two QTLs for LIN and LNA trait, respectively was also identified. QTL qLIN-Group12-2 for LIN and QTL qLNA-Group12-2 for LNA on chromosome 12 were detected in multi-environments. These results provide more information for determining the seed quality related candidate genes and contribute to the marker-assisted selection in flax breeding.
Assessing Uptake and Utilization of Modern Contraceptive Method Amongst Young People in Tertiary Institutions of Lilongwe University of Agriculture and Natural Resources (LUANAR)) and Kamuzu College of Nursing (KCN)) in Lilongwe: A Cross-sectional Exploratory Study
Authors: Phiri Yewo Kayira , Chimwaza Wanangwa Manda , Chipeta Effie 
Published: September 2020

Abstract
Background: Modern contraceptive uptake and utilization still remains a significant global health issue among young people. Despite a number of interventions on modern contraceptive services targeting young people in primary and out of schools, evidence on Modern contraceptive use in Malawi tertiary institutions is limited. Hence, an assessment on uptake and utilisation of modern contraceptives among tertiary institutions of Lilongwe University of Agriculture and Natural Resources and Kamuzu College of Nursing was carried out in Lilongwe between 2017 and 2019.Methods: A cross sectional exploratory study which used a mixed methods approach to assess uptake and utilisation of modern contraceptive methods among young people in tertiary institutions of LUANAR and KCN in Lilongwe. 8 focus groups were conducted, 6 key informants were interviewed and 220 females and male students were interviewed using self-administered questionnaires from the two institutions which were purposively selected.Results: Modern contraceptives uptake was higher among young people of LUANAR and KCN while utilisation was lower. On comparative basis, utilisation and knowledge of modern contraceptives was higher among students at KCN than LUANAR. Male condoms and emergency contraceptive services were frequently accessed. The type of tertiary institution was statistically significant to utilization of modern contraceptives. The odds of utilizing modern contraceptives was almost 2 times higher for students at KCN than LUANAR students. Barriers to access modern contraceptives were noted and included: provider attitudes, privacy and confidentiality, shortage of some modern contraceptives and long waiting time at the clinics.Conclusion: Access to modern contraceptives among young people in tertiary institutions is influenced by individual, health system related and environmental factors. Tertiary institutions students need information on modern contraceptives to reduce sexual and reproductive health problems. Providing young people with access to modern contraceptives in tertiary institutions can reduce teenage pregnancies, abortions and maternal deaths.
Application of Deep Learning as a Noninvasive Tool to Determine Pathological Diagnosis of Enlarged Cervical Lymph Nodes with PET/CT
Authors: Yang Yuhan , Zheng Bo , Wang Yixi , Ma Xuelei 
Published: September 2020

Abstract
Objective: To construct a deep-learning convolution neural network (DL-CNN) system for pathological diagnosis of cervical lymph nodes by using computed tomography (CT), fluorine-18 fluorodeoxyglucose (18F-FDG) positron emission tomography (PET), and fused PET/CT images.Materials and methods: A total of 1020 cross-sectional images for each imaging modality was obtained from 211 patients (153 patients with lymphomas and 116 patients with metastases) with enlarged cervical lymph nodes from January 2014 to June 2018. All eligible images were distributed randomly into the training, validation, and testing cohorts with ratios of 70%, 15%, and 15%. We applied eight DL-CNN algorithms with pretrained bases from ImageNet dataset on CT, PET, and fused PET/CT imaging datasets to differentiate lymphomatous nodes from metastatic nodes, respectively. Attention heatmaps of PET and fused PET/CT images generated by class activation mapping (CAM) were used in visualization of class specific regions recognized by the prediction model with best performance. Results: The accuracy of eight deep learning algorithms with pretrained base ranged from 0.650 to 0.981 on PET testing cohort, and from 0.738 to 0.981 on fused PET/CT testing cohort. The VGG16 model on PET images and DenseNet121 model on fused PET/CT images had the best diagnostic performance among all eight algorithms with sensitivity and specificity of 1.000 and 0.963. Class-specific discriminative subregions were highlighted by attention maps for clinical review.Conclusion: A DL-CNN system was developed for classifying metastatic and lymphomatous involvement with favorable diagnostic performance on PET and PET/CT images in patients with enlarged cervical lymph nodes. The further clinical practice of this system may improve quality of the following therapeutic interventions and optimize patients’ outcomes.