bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate
Authors: Kim Eiseul , Yang Seung-Min , Lim Bora , Park Si Hong , Rackerby Bryna , Kim Hae-Yeong 
Published: April 2020

Abstract
Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.
Molecular identification of severe fever with thrombocytopenia syndrome viruses from tick and bitten patient in Southeast China
Authors: Tong Yongxi , wang qiujing , Fu Yongfeng , Li Shibo , Zhang Zhao , Zhang Zheen , Yu Xuewen 
Published: April 2020

Abstract
Background Severe fever and thrombocytopenia bunyavirus (SFTSV) infection causes severe fever and thrombocytopenia syndrome with high mortality. It is extremely rare that a transmitting tick can be directly captured in bite wounds, and that SFTSV can be isolated from both the captured tick and patient’s serum to establish a solid pathogen diagnosis.Case presentation We report a case infected with severe fever and thrombocytopenia bunyavirus. The 69-year-old male patient presented fever and tenderness on two lymph nodes in right groin. A visible tick bite mark appeared on right upper quadrant of the patient’s abdomen, and an live tick was captured in the bite wound upon physical examination. The virus was detected in both the blood of the patient and in the tick that stayed in the bite wound for seven days. The phylogenetic analysis indicated that the SFTSV isolated from the tick and the patient’s serum sample belonged to type B, in which the L/S segment of these two isolates shared 100% homology, while the M segment had 99.9% homology. The bitten patient was given various supportive care, but eventually died of multiple organ failure. Conclusion The present case provides the direct evidence of SFTSV transmission from H. longicornis to humans, and suggests that direct cross-species transmission can occur without additional intermediate hosts.
Lay therapist delivered low intensity psychosocial intervention for refugees and asylum seekers (PROSPER): protocol for a pilot randomised controlled trial.
Authors: Rawlinson Rebecca , Aslam Rabeea’h , Burnside Girvan , Chiumento Anna , Eriksson-Lee Malena , Humphreys Amy , Khan Naila , Lawrence Daniel , McCluskey Rachel , Mackinnon Annette , Orton Lois , Rahman Atif , Roberts Ewan , Rosala-Hallas Anna , Tudor-Edwards Rhiannon , Uwamaliya Philomene , White Ross , Winrow Eira , Dowrick Christopher 
Published: April 2020

Abstract
Background Asylum seekers and refugees (AS&Rs) experience impaired mental health and wellbeing, related to stresses in their country of origin, experiences in transit and reception on arrival, including significant barriers to accessing mainstream services. Their contact with healthcare is often crisis-driven and mediated through non-governmental organisations (NGOs). Problem Management Plus (PM+) is a psychosocial intervention recommended by the World Health Organization to address distress experienced by adults affected by humanitarian crises. We are investigating its application for the first time in a high income country. Methods In a pilot randomised controlled trial, PM+ will be delivered to AS&Rs in contact with NGOs in Liverpool City Region, UK, by lay therapists who have lived experience of forced migration. Following systematic review and stakeholder engagement, PM+ has been adapted to the local context, and lay therapists have been trained in its delivery. We will assess the feasibility of conducting a three-arm RCT of five 90-minute sessions of PM+, delivered individually or in groups by lay therapists to AS&Rs experiencing emotional distress and functional impairment, compared with each other and with usual support offered by local NGOs. Distress and impairment at baseline will be measured by Hospital Anxiety and Depression Scale (HADS) and WHO Disability Assessment Schedule (WHO-DAS). We aim to recruit 105 participants, 35 per arm. Primary health outcomes are anxiety and depressive symptoms at 3 months, measured by HADS. Secondary outcomes include subjective wellbeing, functional status, progress on identified problems, post-traumatic stress disorder, depressive disorder and service usage. Longer term impact will be assessed at 6-months post baseline, on the same parameters. We will assess the feasibility of conducting a full RCT in relation to the following elements: recruitment and retention of lay therapists and study participants; fidelity of delivery of PM+; and suitability of the study measures, including any linguistic or cultural barriers. Discussion We will use these findings to specify the parameters for a full randomised controlled trial to test the effectiveness and cost effectiveness of PM+ in reducing emotional distress and health inequalities, and improving functional ability and wellbeing, amongst asylum seekers and refugees.
A network pharmacology-based study on Alzheimer disease prevention and treatment of Qiong Yu Gao
Authors: You Jieshu , Li Chen-yue , Chen Wei , Wu Xia-lin , Huang Li-jie , Li Ren-kai , Gao Fei , zhang Ming-yue , Liu Huan-lan , Qu Wei-ling 
Published: April 2020

Abstract
Background and objective: As the pathological mechanisms of AD are complex, increasing evidence have demonstrated Chinese Medicine with multi-ingredients and multi-targets may be more suitable for the treatment of diseases with complex pathogenesis. Therefore, the study was to preliminarily decipher the bioactive compounds and potential mechanisms of Qiong Yu Gao (QYG) for AD prevention and treatment by an integrated network pharmacology approach. Methods: Putative ingredients of QYG and significant genes of AD were retrieved from public database after screening. Then QYG ingredients target proteins/genes were obtained by target fishing. Compound-target-disease network was constructed using Cytoscape to decipher the mechanism of QYG for AD. KEGG pathway and GO enrichment analysis were performed to investigate the molecular mechanisms and pathways related to QYG for AD treatments. Results: Finally, 70 compounds and 511 relative drug targets were collected. In which, 17 representative direct targets were found. Gene ontology enrichment analysis revealed that the adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway was the key biological processes and were regulated simultaneously by the 17 direct targets. The KEGG pathway enrichment analysis found that three signaling pathways were closely related to AD prevention and treatment by QYG, including PI3K-Akt signaling pathway, regulation of actin cytoskeleton pathway and insulin resistance pathway. Conclusion: This study demonstrated that QYG exerted the effect of preventing and treating AD by regulating multi-targets with multi-components. Furthermore, the study demonstrated that a network pharmacology-based approach was useful for elucidation of the interrelationship between complex diseases and interventions of Chinese herbal medicines.
Bone ongrowth and mechanical fixation of implants in cortical and cancellous bone
Authors: Walsh William Robert , Pelletier Matthew Henry , Bertollo Nicky , Lovric Vedran , Wang Tian , Morberg Per , Parr William Chase Harington , Bergadano Dario 
Published: April 2020

Abstract
Background What is the right surface for an implant to achieve biological fixation? Surface technologies can play important roles in encouraging interactions between the implant surface and the host bone to achieve osseointegration. Pre-clinical animal models provide important insight into in-vivo performance related to bone ongrowth and implant fixation.Methods A large animal model was used to compare the in vivo response of HA and plasma sprayed titanium coatings in a well reported adult ovine model to evaluate bone ongrowth in terms of mechanical properties in cortical sites, histology and histomorphometry in cortical and cancellous sites at 4 and 12 weeks. Results Titanium plasma sprayed surfaces outperformed the HA coated samples in push-out testing in cortical sites while both surfaces supported new bone ongrowth and remodeling in cortical and cancellous sites. Conclusions While both HA and Ti plasma provided an osteoconductive surface for bone ongrowth, the Ti plasma provided a more robust bone-implant interface that ideally would be required for load transfer and implant stability in the longer term.
Determinants of Diabetic Retinopathy in Southwest Ethiopia: A facility-based case-control study
Authors: Garoma Dugasa , Merga Hailu , Hiko Desta 
Published: April 2020

Abstract
Background: Diabetic Retinopathy is one of the serious complications patients’ diabetic patients suffer from. Little is known about which risk factors are associated with this complication. The aim of this study was therefore to identify determinants of Diabetic Retinopathy in Jimma University Medical Center. Methods: A facility-based case-control study was conducted. Cases were Diabetic patients with diabetic retinopathy and who were on follow up at the Jimma University Medical Center while controls were Diabetic patients but free of diabetic retinopathy and who were on follow up at the Jimma University Medical Center. Cases and controls were identified and 311 of them were recruited using systematic random sampling. Data were entered into the Epi-Data version 4.1 and analyzed using SPSS Version 20. Binary Logistic regression analysis was conducted to identify determinants of diabetic retinopathy. Result: A total of 106 cases and 205 controls diabetic participated in the study. Being ≥60 years of age (AOR=5.04,95%CI: 1.83,13.87),being illiterate (AOR=7.17, 95% CI: 2.61,19.7), poor adherence to medication (AOR =3: 95% CI: 1.29,6.95),having high systolic blood pressure (AOR=3.38:95% CI: 1.26,9.05), having family history of Diabetes Mellitus (AOR=3.95: 95% CI: 1.64,9.54), having other micro vascular complications (AOR=3.76,95% CI: 1.33,10.66), poor glycemic control (AOR=9.08, 95%CI: 3.7,22.29), poor cholesterol control (AOR= 0.21, 95%CI: 0.08,0.51) and being anaemic (AOR= 2.8, 95%CI: 1.05,7.47) were the independent determinants of diabetic retinopathy. Conclusion: This study found that poor adherence to medication, being at the age of 60 years and above, being illiterate patients, having high systolic blood pressure, having a family history of Diabetes Mellitus, having other micro vascular complication, poor glycemic control, poor cholesterol control and being anemic patient were the independent determinants of diabetic retinopathy. Therefore, more attention should be given to older age and illiterate patients. Giving more emphasis for patients poorly adhered to anti-diabetic medications and giving advice for diabetic patients with high systolic blood pressure to follow their blood pressure regularly are also vital. Diabetic patients should also control their Blood sugar and blood cholesterol levels to prevent diabetic retinopathy or reduce its further complications.
Development of In Vitro resistance to fluoroquinolones in Pseudomonas aeruginosa
Authors: Zhao Lei , Wang Shiqi , Li Xiaobing , He Xiaojing , Jian Lingyan 
Published: April 2020

Abstract
Background: The objectives of this study were to investigate the dynamics of different resistant mechanisms in P.aeruginosa populations that have evolved under fluoroquinolone pressure, and any interactions between these mechanisms in the evolutionary trajectories. Methods: In this study, bacteria of the strain ATCC27853 were selected under different concentrations of levofloxacin and ciprofloxacin for six parallel lineages. The four target genes in the quinolone-resistance determining region were amplified and then Sanger sequencing was used to find the mutations. The expression of four efflux pump proteins were evaluated by real-time PCR, using the relative quantitation method, and the ATCC27853 was selected as a control. Results: we found that the P.aeruginosa was killed by ciprofloxacin earlier than levofloxacin. We found five different mutations in three subunits of QRDRs in our study; gyrA was the main mutated gene for conferring resistance to fluoroquinolone. A greater number of mutations appeared at 4mg/L for levofloxacin and at 2mg/L for ciprofloxacin. The main efflux pump that was expressed was MexCD-OprJ, and the first over expressed was evident at 0.5mg/L for levofloxacin and 0.25mg/L for ciprofloxacin. Conclusions: The mutation of gyrA83 and overexpression of MexCD-OprJ were the main mechanisms that conferred resistance of P.aeruginosa to levofloxacin and ciprofloxacin. Ciprofloxacin had a stronger ability to kill the bacteria, while may render bacteria more susceptible to resistance.
Jejunal Microbiome and Bile Acids Induced by Diets in Angus Beef Cattle
Authors: Liu Jianan , Liu Fang , Cai Wentao , Jia Cunling , Bai Ying , He Yanghua , Zhu Weiyun , Li Robert W. , Song Jiuzhou 
Published: April 2020

Abstract
Background: The small intestine, while serving as the main absorption organ, also possesses a unique microbiome environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able to regulate microbiome structure and promote the growth of bacteria that convert primary bile acids to secondary bile acids. However, in beef cattle, few studies have explored the microbiome compositions of the jejunum and its relationships with bile acids. Therefore, the hypothesis is that microbiome compositions in the intestine are influenced by diet style and also related to bile acids.Results: We demonstrated that the influences of diets on the intestinal microbiome could be observed in young beef cattle after weaning. A significantly higher level of microbial diversity was evidenced in feces of grass-fed animals comparing to grain-fed cattle. Top 20 essential genera were obtained with random forest analysis on the fecal microbiome to identify candidate microbial biomarkers. Moreover, the jejunal microbiome of adult Angus beef cattle exhibited significant differences in microbial composition and metabolic potential under different diets. Global balances and microbiome signatures of bile acids were identified. Conclusions: The findings from this study provided deep insights into microbiome compositions in fecal and jejunal and identified relationships between jejunal microbiome and bile acids with diets in Angus beef cattle. Our results should help us better understand grass-fed beef in production practice and potential health benefits.
Genome-wide characterization and expression analysis of geranyl geranyl diphosphate synthase genes of cotton (Gossypium spp.) in plant development and abiotic stresses
Authors: Ali Faiza , Qanmber Ghulam , Wei Zhenzhen , Yu Daoqian , Li Yonghui , Gan Lei , Li Fuguang , Wang Zhi 
Published: April 2020

Abstract
Background: GGPP (geranyl geranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has not been performed in any plant species except Arabidiosis thaliana. Here, we performed a complete computational and bioinformatics analysis of GGPPS and detected their transcription expression pattern in Gossypium hirsutum for the first time in order to explore their evolutionary relationship and potential functions. We unravel evolutionary relationship, conserved sequence logos, gene duplication and potential involvement in plant development and abiotic stresses tolerance of GGPPS genes in G. hirsutum.Results: A total of 134 GGPPS genes from 17 plant species were identified. Evolutionary analysis divided GGPPS genes into five groups and indicated their divergence from a common ancestor. Further, GGPPS family genes were conserved during evolution and underwent segmental duplication. 25 GhGGPPS genes identified showed diverse expression pattern particularly in ovule and fiber development indicating their vital and divers roles in the fiber development. Additionally, GhGGPPS genes exhibited wide range of responses when subjected to abiotic (heat, cold, NaCl and PEG) and hormonal (BL, GA, IAA, SA and MeJA) stresses. Conclusions: Collectively, GGPPS genes are evolutionary conserved, may are involved in different development stages and stress signaling pathways, some potential key genes (e.g. GhGGPP4, GhGGPP9, GhGGPP15) were suggested and provide valuable source for cotton breeding in fiber quality and resistant to various stresses.
Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)
Authors: Hall Nathan Daniel , Patel Jinesh D , McElroy Joseph Scott , Goertzen Leslie Richard 
Published: April 2020

Abstract
Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs.Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes supports A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of expression within the ciradian rhythm pathway suggests A subgenomic preference.Co﻿nclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.
Development, validation and implementation of a program to detect malnutrition with NRS-2002 screening tool in patients of the oncology and hematology service
Authors: Pérez Marta , Soriano José M , Merino-Torres J Francisco 
Published: April 2020

Abstract
Background: Hospital malnutrition is an increasingly prevalent situation, which involves both an increase in health costs, a decrease in the life quality of those who suffer from it, and greater morbimortality. Nutritional screening is essential to detect malnutrition early and avoid these complications.Methods: NRS-2002 was performed on all patients admitted to the oncohaematology service, followed by the complete nutritional assessment (VN) to check its validity, which is repeated weekly to determine the degree of malnutrition during the hospital stay. Data were summarized using mean (standard deviation) and median (1st, 3rd quartile) for numerical variables, and absolute frequency (relative) for qualitative variables. To measure agreement between the two diagnoses, Cohen's Kappa was calculated for each visit. The level of association between the variables was measured using the Goodman and Kruskal measure.Results: 573 patients were admitted to the oncohaematology service, of which: 34.4% malnutrition, 44.7% risk of malnutrition and 20.9% good nutritional condition, on admission to hospital according to the NRS-2002. In patients admitted for more than a week, NRS-2002 was performed weekly and found that, upon discharge, they suffered: 34.4% malnutrition, 50.8% risk of malnutrition and 14.76% good nutritional status; also 12.3% worsen their nutritional status, 68.9% maintain it and only 18.9% improve it. 78.8% of patients with longer admissions require a VN.Conclusions: Our results suggest that the NRS-2002 is a simple and effective method for early malnutrition detection. It's important a nutritional monitoring during the hospitalization period, because the patients are susceptible to worsening of their nutritional status.
Plasma transfusion promoted reprogramming CD4+ T lymphocytes immune response in severe sepsis mice model through modulating the exosome protein Galectin 9
Authors: Zhang Lei , Zhang Jian-Ping , Liu Yang , Wang Huan , Cheng Yong , Wang Jin-Huo , Zhang Wen-Jie , Li Zhen-Zhou , Guo Jian-rong 
Published: April 2020

Abstract
Sepsis is a life-threatening disease resulting in excessive stimulation of the host’s immune cells. In the study, the purpose is to investigate the roles of fresh frozen plasma (FFP) transfusion in shaping the CD4+ T lymphocytes immune response through modulating the secreted exosome protein Galectin 9 in mice with severe sepsis. We firstly identified the protein Galectin 9 highly accumulated in the blood plasma of severe sepsis mice with western blot, then with transmission electron microscopy (TEM) and protein analysis, we found protein Galectin 9 was a secreted exosome protein in sepsis mice. Thereafter, we treated the severe sepsis mice with antibiotic-Cefuroxime Axetil, meanwhile, one group mice received FFP transfusion, the other one group mice received normal saline. Surprisingly, the FFP transfusion reduced the secretion of exosome protein Galectin 9 and there was crosstalking between the exosome protein Galectin 9 and CD4+ T lymphocytes in mice with severe sepsis. Results showed that the proliferation of Th1, Th17 were promoted and obiviously inhibited Treg cells maintenance in the sepsis mice receiving FFP transfusion. Correspondingly, this immune reprogrammed activity shaped the inflammatory cytokines secretion with increase of IL-1β, IL-6 and IFN-γ, whilst, decrease of IL-10. Taken together, it was suggested that FFP transfusion promoted reprogramming CD4+ T lymphocytes immune response through inhibiting the secretion of exosome protein Galectin 9 in mice with severe sepsis to relieve immunosuppression.