bluuebunny/crossref_metadata_2025_split huggingface dataset:
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research
Authors:   as members of the Sustainability and Outreach Work Package of the H3ABioNet Consortium, Kumuthini Judit , Zass Lyndon , Panji Sumir , Salifu Samson P. , Kayondo Jonathan K. , Nembaware Victoria , Mbiyavanga Mamana , Olabode Ajayi , Kishk Ali , Wells Gordon , Mulder Nicola J. 
Published: December 2019

Abstract
Background
Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)‘s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation.

Results
The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD.

Conclusion
To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.
Molecular differentiation of the Murraya paniculata Complex (Rutaceae: Aurantioideae: Aurantieae)
Authors: Nguyen Chung Huy , Beattie G. Andrew C. , Haigh Anthony M. , Astuti Inggit Puji , Mabberley David J. , Weston Peter H. , Holford Paul 
Published: December 2019

AbstractBackgroundOrange jasmine has a complex nomenclatural history and is now known asMurraya paniculata(L.) Jack. Our interest in this common ornamental stemmed from the need to resolve its identity and the identities of closely related taxa as hosts of the pathogen ‘CandidatusLiberibacter asiaticus’ and its vectorDiaphorina citri. Understanding these microbe-vector-plant relationships has been hampered by taxonomic confusion surroundingMurrayaat both the generic and specific levels.ResultsTo resolve the taxonomic uncertainty, six regions of the maternally-inherited chloroplastal genome and part of the nuclear-encoded ITS region were amplified from 85 accessions ofMurrayaandMerrilliausing the polymerase chain reaction (PCR). Clustering used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI). Chronograms were produced for molecular dating, and to test the monophyly ofMurrayarigorously, using selected accessions ofMurrayaand 26 accessions of the Rutaceae and Simarubaceae. Sequence data from the ITS and chloroplastal regions suggest thatMurraya paniculata(sensu (Swingle WT and Reece CR, The Citrus Industry, p. 190–430, 1967)) can be separated into four distinct but morphologically somewhat cryptic taxa:Murraya paniculata(sensu (Mabberley DJ, Taxon 65:366–371, 2016)),M. elongata,M. sumatranaandM. lucida. In addition,Murraya omphalocarpawas identified as a putative hybrid ofM. paniculataandM. lucidawith two geographically isolated nothovarieties representing reciprocal crosses.Murrayais monophyletic, and molecular dating suggests that it diverged fromMerrilliaduring the Miocene (23–5 Ma) with thisMurrayagroup speciating and dispersing during the Middle Miocene onwards.ConclusionsThe accessions from Asia and Australasia used in this study grouped into biogeographical regions that match herbarium specimen records for the taxa that suggest natural allopatric distributions with limited overlap and hybridity.Murraya paniculatahas been distributed around the world as an ornamental plant. The division of theMurraya paniculatacomplex into four species with a rare hybrid also confirms morphological studies.
Effects of cage and floor rearing system on the factors of antioxidant defense and inflammatory injury in laying ducks
Authors: Zhang Yang , Gu Tiantian , Tian Yong , Chen Li , Li Guoqin , Zhou Wei , Liu Guofa , Wu Xinsheng , Zeng Tao , Xu Qi , Chen Guohong , Lu Lizhi 
Published: December 2019

Abstract
Background
Cage-rearing in laying ducks, as a novel rearing system, not only fundamentally solves the pollution problem of the duck industry and improve bio-safety and product quality but also exhibits more benefits by implementing standardized production compared with the floor-rearing. Of course, this system also brings some welfare problems and stress injuries to layers due to lack of water environment and limited activities in the cages. However, the effects on the factors of antioxidant defense and inflammatory injury in the early cage stage are not well-understood.

Results
In this study, eighty Shaoxing layers were reared on floor and in cages from 12 weeks of age. The ducks were caged 1, 2, 4, 7, and 10 days, the factors of antioxidant defense and inflammatory injury were investigated. The results showed that the caged ducks suffered liver injury to a certain extent when the ducks were just put into the cages. Analysis of antioxidant enzyme activities indicated that the different rearing system could not affect the change of antioxidant capacities, while the liver malondialdehyde (MDA) level was significant higher in the 2-d, 7-d, and 10-d ducks compared with the 1-d ducks during the change of days, while catalase (CAT) activity showed the opposite results. Additionally, quantitative real-time PCR (qRT-RCR) revealed that the relative mRNA levels of endoplasmic reticulum (ER) stress-related gene (CHOP and GRP78) were significantly upregulated in cage rearing ducks compared to that of the floor rearing ducks. Moreover, the mRNA levels of inflammatory cytokines including cycloxygenase-2 (COX-2), nitric oxide synthase (iNOS), Interleukin 1 beta (IL-1β), Interleukin 2 (IL-2) and Interleukin 6 (IL-6), were also increased significantly in caged layers.

Conclusions
Taken together, although antioxidant defense has no obvious effect on cage stress, the stress levels of laying ducks vary greatly in the early cage stage, which not only caused liver tissue damage to some extent, but also resulted in increases in the expression of the factors of inflammatory injury. Therefore, we recommend that anti-stress agents should be added in the feed to alleviate the stress in the early cage stage.
Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms
Authors: Lindblad Kelsi A. , Pathmanathan Jananan S. , Moreira Sandrine , Bracht John R. , Sebra Robert P. , Hutton Elizabeth R. , Landweber Laura F. 
Published: December 2019

AbstractBackgroundWhole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even “third generation” sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliateOxytricha trifallaxhas a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly.ResultsWe used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the publishedOxytricha trifallaxJRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall.ConclusionsThis assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)
Authors: Bai Jian-fang , Wang Yu-kun , Guo Li-ping , Guo Xiao-ming , Guo Hao-yu , Yuan Shao-hua , Duan Wen-jing , Liu Zihan , Zhao Chang-ping , Zhang Feng-ting , Zhang Li-ping 
Published: December 2019

Abstract
Background
MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the crosstalk between Jasmonic acid regulatory pathway and light signaling in Arabidopsis, but such kinds of studies are rare in wheat, especially in photo-thermo-sensitive genic male sterile (PTGMS) wheat line.

Results
27 non-redundant MYC gene copies, which belonged to 11 TaMYC genes, were identified in the whole genome of wheat (Chinese Spring). These gene copies were distributed on 13 different chromosomes, respectively. Based on the results of phylogenetic analysis, 27 TaMYC gene copies were clustered into group I, group III, and group IV. The identified TaMYC genes copies contained different numbers of light, stress, and hormone-responsive regulatory elements in their 1500 base pair promoter regions. Besides, we found that TaMYC3 was expressed highly in stem, TaMYC5 and TaMYC9 were expressed specially in glume, and the rest of TaMYC genes were expressed in all tissues (root, stem, leaf, pistil, stamen, and glume) of the PTGMS line BS366. Moreover, we found that TaMYC3, TaMYC7, TaMYC9, and TaMYC10 were highly sensitive to methyl jasmonate (MeJA), and other TaMYC genes responded at different levels. Furthermore, we confirmed the expression profiles of TaMYC family members under different light quality and plant hormone stimuli, and abiotic stresses. Finally, we predicted the wheat microRNAs that could interact with TaMYC family members, and built up a network to show their integrative relationships.

Conclusions
This study analyzed the size and composition of the MYC gene family in wheat, and investigated stress-responsive and light quality induced expression profiles of each TaMYC gene in the PTGMS wheat line BS366. In conclusion, we obtained lots of important information of TaMYC family, and the results of this study was supposed to contribute novel insights and gene and microRNA resources for wheat breeding, especially for the improvement of PTGMS wheat lines.
Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
Authors: Jehl F. , Désert C. , Klopp C. , Brenet M. , Rau A. , Leroux S. , Boutin M. , Lagoutte L. , Muret K. , Blum Y. , Esquerré D. , Gourichon D. , Burlot T. , Collin A. , Pitel F. , Benani A. , Zerjal T. , Lagarrigue S. 
Published: December 2019

AbstractBackgroundProduction conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to better understand the long-term effects of a 15%-energy depleted diet on egg-production, energy homeostasis and metabolism via a multi-tissue transcriptomic analysis. Study was designed to compare effects of the nutritional intervention in two layer chicken lines divergently selected for residual feed intake.ResultsChicken adapted to the diet in terms of production by significantly increasing their feed intake and decreasing their body weight and body fat composition, while their egg production was unchanged. No significant interaction was observed between diet and line for the production traits. The low energy diet had no effect on adipose tissue and liver transcriptomes. By contrast, the nutritional challenge affected the blood transcriptome and, more severely, the hypothalamus transcriptome which displayed 2700 differentially expressed genes. In this tissue, the low-energy diet lead to an over-expression of genes related to endocannabinoid signaling (CN1R,NAPE-PLD) and to the complement system, a part of the immune system, both known to regulate feed intake. Both mechanisms are associated to genes related polyunsaturated fatty acids synthesis (FADS1,ELOVL5andFADS2), like the arachidonic acid, a precursor of anandamide, a key endocannabinoid, and of prostaglandins, that mediate the regulatory effects of the complement system. A possible regulatory role ofNR1H3(aliasLXRα) has been associated to these transcriptional changes. The low-energy diet further affected brain plasticity-related genes involved in the cholesterol synthesis and in the synaptic activity, revealing a link between nutrition and brain plasticity. It upregulated genes related to protein synthesis, mitochondrial oxidative phosphorylation and fatty acid oxidation in the hypothalamus, suggesting reorganization in nutrient utilization and biological synthesis in this brain area.ConclusionsWe observed a complex transcriptome modulation in the hypothalamus of chicken in response to low-energy diet suggesting numerous changes in synaptic plasticity, endocannabinoid regulation, neurotransmission, lipid metabolism, mitochondrial activity and protein synthesis. This global transcriptomic reprogramming could explain the adaptive behavioral response (i.e. increase of feed intake) of the animals to the low-energy content of the diet.
The transcriptomic signature of low aggression in honey bees resembles a response to infection
Authors: Rittschof Clare C. , Rubin Benjamin E. R. , Palmer Joseph H. 
Published: December 2019

AbstractBackgroundBehavior reflects an organism’s health status. Many organisms display a generalized suite of behaviors that indicate infection or predict infection susceptibility. We apply this concept to honey bee aggression, a behavior that has been associated with positive health outcomes in previous studies. We sequenced the transcriptomes of the brain, fat body, and midgut of adult sibling worker bees who developed as pre-adults in relatively high versus low aggression colonies. Previous studies showed that this pre-adult experience impacts both aggressive behavior and resilience to pesticides. We performed enrichment analyses on differentially expressed genes to determine whether variation in aggression resembles the molecular response to infection. We further assessed whether the transcriptomic signature of aggression in the brain is similar to the neuromolecular response to acute predator threat, exposure to a high-aggression environment as an adult, or adult behavioral maturation.ResultsAcross all three tissues assessed, genes that are differentially expressed as a function of aggression significantly overlap with genes whose expression is modulated by a variety of pathogens and parasitic feeding. In the fat body, and to some degree the midgut, our data specifically support the hypothesis that low aggression resembles a diseased or parasitized state. However, we find little evidence of active infection in individuals from the low aggression group. We also find little evidence that the brain molecular signature of aggression is enriched for genes modulated by social cues that induce aggression in adults. However, we do find evidence that genes associated with adult behavioral maturation are enriched in our brain samples.ConclusionsResults support the hypothesis that low aggression resembles a molecular state of infection. This pattern is most robust in the peripheral fat body, an immune responsive tissue in the honey bee. We find no evidence of acute infection in bees from the low aggression group, suggesting the physiological state characterizing low aggression may instead predispose bees to negative health outcomes when they are exposed to additional stressors. The similarity of molecular signatures associated with the seemingly disparate traits of aggression and disease suggests that these characteristics may, in fact, be intimately tied.
Efficacy and safety of prophylactic use of ketamine for prevention of postanesthetic shivering: a systematic review and meta analysis
Authors: Zhou Yang , Mannan Abdul , Han Yuan , Liu He , Guan Hui-Lian , Gao Xing , Dai Ming-Sheng , Cao Jun-Li 
Published: December 2019

AbstractBackgroundPostanesthetic shivering is a common complication of anesthesia, which accounts for much discomfort in postoperative patients and may increase postoperative complications in high-risk patients. Due to the lack of high-quality evidence, it is difficult to draw a conclusion about optimal anti-shivering medication. The main purpose of this meta-analysis was to analyze and evaluate the efficacy and safety of prophylactic use of ketamine for preventing postanesthetic shivering.MethodsWe searched the following databases: Medline, Embase, and the Cochrane Central Register of Controlled Trails for randomized controlled trials. The primary outcome observed was the difference of the incidence rate of postanesthetic shivering between ketamine group and placebo group. The secondary outcomes were the sedation score and incidence of the side effects caused by ketamine and any other drugs utilized in the studies.ResultsIn this meta-analysis, we analyzed a total of 16 trials including 1485 patients. Ketamine reduced the incidence rate of postanesthetic shivering compared to a placebo (odds ratio [OR]: 0.13, 95% confidence interval [CI]: 0.06 to 0.26, P<0.01). Regarding side effects, there was no evident variability of the incidence of nausea and vomiting. Usage of ketamine was associated with a lower rate of hypotension and bradycardia when compared to a placebo. Hallucinations were more frequently observed in patients who received higher doses of ketamine. No significant difference was found in the incidence of postanesthetic shivering with ketamine versus other pharmacological interventions.ConclusionsKetamine can prevent postanesthetic shivering without severe side effects. However, ketamine shows no advantage over other anti-shivering drugs.
Costs and effects of interventions targeting frequent presenters to the emergency department: a systematic and narrative review
Authors: Korczak Viola , Shanthosh Janani , Jan Stephen , Dinh Michael , Lung Thomas 
Published: December 2019

Abstract
Background
Previous systematic reviews have examined the effectiveness of interventions for frequent presenters to the Emergency Department (ED) but not the costs and cost-effectiveness of such interventions.

Method
A systematic literature review was conducted which screened the following databases: Pubmed, Medline, Embase, Cochrane and Econlit. An inclusion and exclusion criteria were developed following PRISMA guidelines. A narrative review methodology was adopted due to the heterogeneity of the reporting of the costs across the studies.

Results
One thousand three hundred eighty-nine papers were found and 16 were included in the review. All of the interventions were variations of a case management approach. Apart from one study which had mixed results, all of the papers reported a decrease in ED use and costs. There were no cost effectiveness studies.

Conclusion
The majority of interventions for frequent presenters to the ED were found to decrease ED use and cost. Future research should be undertaken to examine the cost effectiveness of these interventions.
Microscopic features of small bowel mucosa of patients with Crohn’s disease
Authors: Cui Yun , Lu Shi-yuan , Xu Jie , Peng Yan-shen , Miao Qi , Wang Xiao-qing , Chen Xiao-yu , Ran Zhi-hua 
Published: December 2019

AbstractBackgroundDouble-balloon enteroscopy enables performing numerous small bowel biopsies for pathologic analysis. However, most histopathological characteristics of Crohn’s disease are non-specific characteristics. We aimed to explore the small bowel mucosal histopathologic characters of Crohn’s disease and identify some disease-specific changes.MethodsWe included 253 patients without tumors and grouped them into Crohn’s disease, suspected Crohn’s disease, and non-Crohn’s disease groups. These patients underwent double-balloon endoscopy examination and small bowel biopsy at Renji Hospital, Shanghai. All histopathological sections were reviewed, and > 20 histopathological parameters were assessed. Immunohistochemistry was conducted when necessary.ResultsThere were different forms of granulomatous lymphangitis on the small bowel mucosa in Crohn’s disease. They showed as various macrophages or epithelioid cells in the lumina of lymphatics or in the center of the villi with or without evident obstruction. These features were only observed in Crohn’s disease patients. Furthermore, they were correlated with granuloma and lymphangiectasia. Additionally, 15 other features showed significant differences among the three groups, and Crohn’s disease patients showed an average of almost seven histopathological characteristics.ConclusionsWe described the detailed morphologies of granulomatous lymphangitis on the small bowel mucosa and recommend it as a useful histopathological feature for the diagnosis of Crohn’s disease. In terms of specificity and sensitivity, it was superior to non-caseating epithelioid granuloma.
Bacteriuria and vitamin D deficiency: a cross sectional study of 385 nursing home residents
Authors: Arnljots Rebeka , Snaebjörnsson Arnljots Egill , Thorn Jörgen , Elm Marie , Moore Michael , Sundvall Pär-Daniel 
Published: December 2019

AbstractBackgroundUp to half of elderly people at nursing homes have asymptomatic bacteriuria, and concentrations of 25-hydroxyvitamin D (25OHD) are generally low. Vitamin D is a modulator of the immune system and involved in protection of the epithelium in the urinary tract as well. The objective was to determine a possible association between bacteriuria and vitamin D deficiency among elderly people at nursing homes.MethodsCross-sectional study: Voided urine specimens and blood samples for cultivation and analysis of 25OHD were collected from elderly people at nursing homes in Sweden. Exclusion criteria were: urinary catheter, ongoing antibiotic treatment, incontinence or dementia too severe to provide a voided urine specimen or leave a blood sample, unwillingness to participate or terminal illness. Urine cultures and serum 25OHD concentrations were outcome measures and the association of bacteriuria with vitamin D deficiency was determined by logistic regression.ResultsTwenty-two nursing homes participated and 385 of 901elderly people provided voided urine specimens and blood samples. The mean age was 87 (SD 6.7), 69% women, 19% received vitamin D supplement, 13% had diabetes mellitus, and 54% were diagnosed with dementia. There was significant growth of potentially pathogenic bacteria in 32% (123/385) of voided urine specimens.Escherichia coliwere present in 83% of positive urine cultures. The mean concentration of 25OHD in serum was 35 nmol/L (SD 21). Thirty-seven per cent (143/385) had 25OHD < 25 nmol/L, and 3.1% (12/385) 25OHD < 12.5 nmol/L. No association between bacteriuria and 25OHD < 25 nmol/L, OR 1.4 (0.86–2.3;p = 0.18) adjusted for age, gender, diabetes mellitus and dementia was found. However, if using 25OHD < 12.5 nmol/L as a cut-off for vitamin D deficiency the adjusted odds-ratio was 4.4 (1.1–17;p = 0.031).ConclusionsBacteriuria and vitamin D deficiency was common. No association between bacteriuria and 25OHD < 25 nmol/L was found. If using 25OHD < 12.5 nmol/L as cut-off for vitamin D deficiency there was an association. However, this has to be interpreted with caution as causality cannot be evaluated as well as only few residents had 25OHD < 12.5 nmol/L.