bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome profiling of non-climacteric ‘yellow’ melon during ripening: insights on sugar metabolism
Authors: Schemberger Michelle Orane , Stroka Marília Aparecida , Reis Letícia , de Souza Los Kamila Karoline , de Araujo Gillize Aparecida Telles , Sfeir Michelle Zibetti Tadra , Galvão Carolina Weigert , Etto Rafael Mazer , Baptistão Amanda Regina Godoy , Ayub Ricardo Antonio 
Published: March 2020

Abstract
Background
The non-climacteric ‘Yellow’ melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers.

Results
The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric ‘Yellow’ melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that ‘hormone signal transduction’, ‘carbon metabolism’, ‘sucrose metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘spliceosome’ were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and 12 are down-regulated during fruit ripening.

Conclusions
The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric ‘Yellow’ melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 (CmINH3), trehalose phosphate phosphatase (CmTPP1) and trehalose phosphate synthases (CmTPS5, CmTPS7, CmTPS9). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.
Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase
Authors: Zou Xian , Lu Tingting , Zhao Zhifeng , Liu Guangbin , Lian Zhiquan , Guo Yongqing , Sun Baoli , Liu Dewu , Li Yaokun 
Published: March 2020

Abstract
Background
Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play critical roles in ovarian biological processes, the interaction between mRNAs and miRNAs in follicular development is not yet completely understood. In addition, less attention has been given to the study of single follicle (dominant or atretic follicle) in goats. This study aimed to identify mRNAs, miRNAs, and signaling pathways as well as their interaction networks in the ovarian follicles (large follicles and small follicles) of uniparous and multiple Chuanzhong black goats at estrus phase using RNA-sequencing (RNA-seq) technique.

Results
The results showed that there was a significant difference in the number of large follicles between uniparous and multiple goats (P < 0.05), but no difference in the number of small follicles was observed (P > 0.05). For the small follicles of uniparous and multiple goats at estrus phase, 289 differentially expressed mRNAs (DEmRNAs) and 16 DEmiRNAs were identified; and for the large follicles, 195 DEmRNAs and 7 DEmiRNAs were identified. The functional enrichment analysis showed that DE genes in small follicles were significantly enriched in ovarian steroidogenesis and steroid hormone biosynthesis, while in large follicles were significantly enriched in ABC transporters and steroid hormone biosynthesis. The results of quantitative real-time polymerase chain reaction were consistent with those of RNA-seq. Analysis of the mRNA-miRNA interaction network suggested that CD36 (miR-122, miR-200a, miR-141), TNFAIP6 (miR-141, miR-200a, miR-182), CYP11A1 (miR-122), SERPINA5 (miR-1, miR-206, miR-133a-3p, miR-133b), and PTGFR (miR-182, miR-122) might be related to fertility, but requires further research on follicular somatic cells.

Conclusions
This study was used for the first time to reveal the DEmRNAs and DEmiRNAs as well as their interaction in the follicles of uniparous and multiple goats at estrus phase using RNA-seq technology. Our findings provide new clues to uncover the molecular mechanisms and signaling networks of goat reproduction that could be potentially used to increase ovulation rate and kidding rate in goat.
De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
Authors: Bayega Anthony , Djambazian Haig , Tsoumani Konstantina T. , Gregoriou Maria-Eleni , Sagri Efthimia , Drosopoulou Eleni , Mavragani-Tsipidou Penelope , Giorda Kristina , Tsiamis George , Bourtzis Kostas , Oikonomopoulos Spyridon , Dewar Ken , Church Deanna M. , Papanicolaou Alexie , Mathiopoulos Kostas D. , Ragoussis Jiannis 
Published: March 2020

Abstract
Background
The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly’s biology and proposing alternative control methods to pesticide use.

Results
Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR.

Conclusions
The high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome’s organization, function and evolution and is poised to provide avenues for sterile insect technique approaches.
iMarmot: an integrative platform for comparative and functional genomics of marmots
Authors: Liu Baoning , Bai Liang , Yu Qingqing , Hu Fang , Wu Jing , Zhao Sihai , Wang Rong , Wang Weirong , Tao Yuanqing , Fan Jianglin , Liu Enqi 
Published: March 2020

Abstract
Background
Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integrative database is urgent needed.

Description
iMarmot is freely available on the web at http://www.marmotdb.org/ and currently contains the biological information of 14 marmots, genomic sequence of 6 marmots, syntenic relationship and orthologs among 3 marmots, and expression profiles of several hibernators and plague hosts. To assist with the genomic and transcriptomic analysis, we also integrated a set of analysis and visualization tools, such as KEGG or GO enrichment analysis, PCA, Blast, Muscle, GeneWise, Lastz, and JBrowse. Particularly, one DEGs (differentially expressed genes) module has been implemented in this database to visualize the gene expression changes in hibernators and plague hosts.

Conclusion
This database will provide comprehensive information and analysis platform for researchers interested in understanding the biological features of marmots.
Functional comparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs. Lymphoprep Tubes
Authors: Chen Han , Schürch Christian M. , Noble Kevin , Kim Kenneth , Krutzik Peter O. , O’Donnell Erika , Vander Tuig Jason , Nolan Garry P. , McIlwain David R. 
Published: March 2020

Abstract
Background
Cryopreserved human peripheral blood mononuclear cells (PBMCs) are a commonly used sample type for a variety of immunological assays. Many factors can affect the quality of PBMCs, and careful consideration and validation of an appropriate PBMC isolation and cryopreservation method is important for well-designed clinical studies. A major point of divergence in PBMC isolation protocols is the collection of blood, either directly into vacutainers pre-filled with density gradient medium or the use of conical tubes containing a porous barrier to separate the density gradient medium from blood. To address potential differences in sample outcome, we isolated, cryopreserved, and compared PBMCs using parallel protocols differing only in the use of one of two common tube types for isolation.

Methods
Whole blood was processed in parallel using both Cell Preparation Tubes™ (CPT, BD Biosciences) and Lymphoprep™ Tubes (Axis-Shield) and assessed for yield and viability prior to cryopreservation. After thawing, samples were further examined by flow cytometry for cell yield, cell viability, frequency of 10 cell subsets, and capacity for stimulation-dependent CD4+ and CD8+ T cell intracellular cytokine production.

Results
No significant differences in cell recovery, viability, frequency of immune cell subsets, or T cell functionality between PBMC samples isolated using CPT or Lymphoprep tubes were identified.

Conclusion
CPT and Lymphoprep tubes are effective and comparable methods for PBMC isolation for immunological studies.
Evolutionary analysis of gyrA gene from Neisseria meningitidis bacterial strains of clonal complex 4821 collected in China between 1978 and 2016
Authors: Zhao Pan , Xu Li , Zhang Aiyu , Zhu Bingqing , Shao Zhujun 
Published: March 2020

Abstract
Background
Neisseria meningitidis (N.meningitidis) bacteria belonging to clonal complex 4821 (CC4821) have been mainly reported in China and have been characterized by a high resistance rate to ciprofloxacin (CIP). The aim of this study was to assess the evolution of the DNA gyrase A (gyrA) gene from N.meningitidis CC4821 strains collected in China between 1978 and 2016. The complete sequence of gyrA gene from 77 strains are reported in this study and analyzed in the context of publicly available sequences from N. meningitidis of other CCs as well as other Neisseria species.

Results
The phylogenetic analysis of CC4821 gyrA gene reveals at least 5 distinct genetic clusters. These clusters are not CC4821-specific showing that gyrA evolution is independent of CC4821 evolution. Some clusters contain sequences from other Neisseria species. Recombination within N.meningitidis strains and between Neisseria species was identified in SimPlot analysis. Finally, amino acid substitutions within GyrA protein were analyzed. Only one position, 91 (83 in E.coli gyrA gene), was linked to CIP resistance. Thirty-one additional putative resistance markers were identified, as amino acid substitutions were only found in resistant strains.

Conclusions
The evolution of gyrA gene of CC4821 N.meningitidis strains is not dependent on CC4821 evolution or on CIP resistance phenotype. Only amino acid 91 is linked to CIP resistance phenotype. Finally, recombination inter- and intra-species is likely to result in the acquisition of various resistance markers, 31 of them being putatively mapped in the present study. Analyzing the evolution of gyrA gene within CC4821 strains is critical to monitor the CIP resistance phenotype and the acquisition of new resistance markers. Such studies are necessary for the control of the meningococcal disease and the development of new drugs targeting DNA gyrase.
Vibiro vulnificus hemolysin associates with gangliosides
Authors: Kashimoto Takashige , Sugiyama Hiroyuki , Kawamidori Keigo , Yamazaki Kohei , Kado Takehiro , Matsuda Kaho , Kodama Toshio , Mukai Takao , Ueno Shunji 
Published: March 2020

Abstract
Background
Vibrio vulnificus hemolysin (VVH) is a pore-forming toxin secreted by Vibrio vulnificus. Cellular cholesterol was believed to be the receptor for VVH, because cholesterol could bind to VVH and preincubation with cholesterol inhibited cytotoxicity. It has been reported that specific glycans such as N-acetyl-D-galactosamine and N-acetyl-D-lactosamine bind to VVH, however, it has not been known whether these glycans could inhibit the cytotoxicity of VVH without oligomer formation. Thus, to date, binding mechanisms of VVH to cellular membrane, including specific receptors have not been elucidated.

Results
We show here that VVH associates with ganglioside GM1a, Fucosyl-GM1, GD1a, GT1c, and GD1b by glycan array. Among them, GM1a could pulldown VVH. Moreover, the GD1a inhibited the cytotoxicity of VVH without the formation of oligomers.

Conclusion
This is the first report of a molecule able to inhibit the binding of VVH to target cells without oligomerization of VVH.
First evidence showing that Pepper vein yellows virus P4 protein is a movement protein
Authors: Li Sangsang , Su Xianyan , Luo Xiangwen , Zhang Yu , Zhang Deyong , Du Jiao , Zhang Zhanhong , OuYang Xian , Zhang Songbai , Liu Yong 
Published: March 2020

Abstract
Background
Plant viruses move through plasmodesmata (PD) to infect new cells. To overcome the PD barrier, plant viruses have developed specific protein(s) to guide their genomic RNAs or DNAs to path through the PD.

Results
In the present study, we analyzed the function of Pepper vein yellows virus P4 protein. Our bioinformatic analysis using five commonly used algorithms showed that the P4 protein contains an transmembrane domain, encompassing the amino acid residue 117–138. The subcellular localization of P4 protein was found to target PD and form small punctates near walls. The P4 deletion mutant or the substitution mutant constructed by overlap PCR lost their function to produce punctates near the walls inside the fluorescent loci. The P4-YFP fusion was found to move from cell to cell in infiltrated leaves, and P4 could complement Cucumber mosaic virus movement protein deficiency mutant to move between cells.

Conclusion
Taking together, we consider that the P4 protein is a movement protein of Pepper vein yellows virus.
Intravenous methylprednisolone or immunoglobulin for anti-glutamic acid decarboxylase 65 antibody autoimmune encephalitis: which is better?
Authors: Li Tao-Ran , Zhang Yu-Di , Wang Qun , Shao Xiao-Qiu , Li Zhi-Mei , Lv Rui-Juan 
Published: March 2020

Abstract
Background
Patients positive for anti-glutamic acid decarboxylase 65 (GAD65) antibodies have attracted increasing attention. Their clinical manifestations are highly heterogeneous and can be comorbid with tumors. Currently, there is no consensus on the therapeutic regimen for anti-GAD65-associated neurological diseases due to the clinical complexity, rarity and sporadic distribution. We reported six anti-GAD65 autoimmune encephalitis (AE) patients who received intravenous methylprednisolone (IVMP) or immunoglobulin (IVIG) or both. Then, we evaluated the therapeutic effect of both by summarizing results in previous anti-GAD65 AE patients from 70 published references.

Results
Our six patients all achieved clinical improvements in the short term. Unfortunately, there was no significant difference between IVMP and IVIG in terms of therapeutic response according to the previous references, and the effectiveness of IVMP and IVIG was 45.56% and 36.71%, respectively. We further divided the patients into different subgroups according to their prominent clinical manifestations. The response rates of IVMP and IVIG were 42.65% and 32.69%, respectively, in epilepsy patients; 60.00% and 77.78%, respectively, in patients with stiff-person syndrome; and 28.57% and 55.56%, respectively, in cerebellar ataxia patients. Among 29 anti-GAD65 AE patients with tumors, the response rates of IVMP and IVIG were 29.41% and 42.11%, respectively. There was no significant difference in effectiveness between the two regimens among the different subgroups.

Conclusion
Except for stiff-person syndrome, we found that this kind of AE generally has a poor response to IVMP or IVIG. Larger prospective studies enrolling large numbers of patients are required to identify the optimal therapeutic strategy in the future.
Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis
Authors: Li Xiaohua , Cao Minhui , Ma Weibo , Jia Caihua , Li Jinghuan , Zhang Mingxing , Liu Changchun , Cao Zhenzhen , Faruque Mohammad Omar , Hu Xuebo 
Published: March 2020

AbstractBackgroundLeaves of the medicinal plantAmpelopsis grossedentata, which is commonly known as vine tea, are used widely in the traditional Chinese beverage in southwest China. The leaves contain a large amount of dihydromyricetin, a compound with various biological activities. However, the transcript profiles involved in its biosynthetic pathway in this plant are unknown.ResultsWe conducted a transcriptome analysis of both young and old leaves of the vine tea plant using Illumina sequencing. Of the transcriptome datasets, a total of 52.47 million and 47.25 million clean reads were obtained from young and old leaves, respectively. Among 471,658 transcripts and 177,422 genes generated, 7768 differentially expressed genes were identified in leaves at these two stages of development. The phenylpropanoid biosynthetic pathway of vine tea was investigated according to the transcriptome profiling analysis. Most of the genes encoding phenylpropanoid biosynthesis enzymes were identified and found to be differentially expressed in different tissues and leaf stages of vine tea and also greatly contributed to the biosynthesis of dihydromyricetin in vine tea.ConclusionsTo the best of our knowledge, this is the first formal study to explore the transcriptome ofA. grossedentata.The study provides an insight into the expression patterns and differential distribution of genes related to dihydromyricetin biosynthesis in vine tea. The information may pave the way to metabolically engineering plants with higher flavonoid content.
Physicians’ abilities to obtain and interpret focused cardiac ultrasound images from critically ill patients after a 2-day training course
Authors: Zhang Hongmin , He Wei , Lian Hui , Chen Xiukai , Wang Xiaoting , Chao Yangong , Liu Dawei 
Published: March 2020

Abstract
Background
This study aimed to determine whether a focused 2-day cardiac ultrasound training course could enable physicians to obtain and interpret focused cardiac ultrasound (FCU) images from critically ill patients.

Methods
We retrospectively reviewed the FCU images submitted by the physicians who attended a 2-day FCU training courses. Three experienced trainers reviewed the images separately. They determined whether the images were assessable and scored the images on an 8-point scale. They also decided whether the physicians provided correct responses for visual estimations of the left ventricular ejection fraction (LVEF) and right ventricle (RV) dilatation and septal motion.

Results
Among the 327 physicians, 291 obtained images that were considered assessable (89%). The scores for parasternal short-axis view were lower than those obtained for other transthoracic echocardiographic views, p < 0.001. More physicians provided incorrect appraisals of LVEF than of RV dilatation and septal motion (19.9% vs. 3.1%, p < 0.001). The percentages of incorrect answers by LVEF category were as follows: 34.8% on images of LVEF < 30, 24.7% on images of LVEF 30–54, and 16.4% on images of LVEF ≥55%, p < 0.001. A logistic regression analysis showed that patients with abnormal LVEF were associated with physicians’ incorrect assessment of LVEF, with an odds ratio of 1.923 (95% confidence interval (CI):1.071–3.456, p = 0.029).

Conclusions
A large proportion of physicians could obtain and interpret FCU images from critically ill patients after a 2-day training course. However, they still scored low on the parasternal short-axis view and were more likely to make an incorrect assessment of LVEF in patients with abnormal left ventricular systolic function.
Capacity building for dementia care in community care services: a mixed methods approach
Authors: Chan Helen Y. L. , Ho Florence K. Y. , Chui Kenny C. M. , Hui Eunice Y. S. , Wong Bel , Chong Yuen-yu , Bowes Alison , Kwok Timothy C. Y. 
Published: March 2020

Abstract
Background
The prevalence of dementia is surging that results in huge service demand in the community care services. Dementia care competence of staff working in these settings is fundamental of the care quality. This project aims to examine the effects of staff training on their competence for the anticipated challenges in dementia care and explore how the training influence their care practices.

Methods
This study adopted a mixed methods triangulation design, including a prospective multi-center study with pre-test post-test evaluations and a narrative analysis of the participants’ reflective essays. Seventeen experienced health and social care professionals were trained as trainers at the Dementia Services Development Centre of the University of Stirling, UK. The trainers provided local facilitator training to staff members by using training materials that were culturally adapted to the local context. The facilitators were required to deliver 12 two-hour in-service training sessions for 6 months to their colleagues in a small group format in their respective workplace. Eventually a total of 1347 staff members from community care centers, day care centers, outreach teams and care homes of 70 non-government organizations in Hong Kong participated in the study between April 2017 and December 2018. Validated instruments were used to measure knowledge, attitude, sense of competence in dementia care and job satisfaction at the baseline and at 12-month follow-up. All participants were required to write a reflective essay to describe their experiences in dementia care by the end of the training.

Results
A total of 1264 participants, including 195 facilitators and 1069 learners, completed all assessment were included for analysis. Significant improvements were observed in all outcomes at the 12-month follow-up assessment (Ps ≤ .001). The magnitude of improvements in attitudes was the largest. The findings also showed that the effects of the training program significantly varied across different groups of learners in terms of age, occupation, work and training experience.

Conclusions
This community-wide large-scale project provided evidence that the train-the-trainer model and reflective learning are effective means to facilitate situated learning that promote awareness and understanding of dementia, and consequently enhance sustainability of changes in care practices.