bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep
Authors: Paz Erwin A. , Chua Eng Guan , Greeff Johan C. , Hassan Shamshad Ul , Palmer Dieter G. , Liu Shimin , Lamichhane Binit , Sepúlveda Néstor , Liu Chunhua , Tay Chin Yen , Martin Graeme B. 
Published: May 2021

Abstract
Background
Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. It has been the subject of decades of research, but little attention has been paid to the role of the gut microbiota in the responses to infection. The present study characterized the microbiome along the gastro-intestinal tract (GIT) of sheep and tested whether it had been affected by three decades of breeding for resistance to helminth infection. Australian Sheep Breeding Values (ASBVs) for faecal egg count (FEC) were used to select the 10 most worm-susceptible (High-FEC) and 10 most worm-resistant (Low-FEC) animals. DNA was extracted and sequenced for 16S rRNA gene from faeces and from the lumen of the rumen, abomasum, duodenum, jejunum, ileum, caecum, and colon.
Results
The most frequent genera identified along the GIT were Eubacterium, Oscillibacter, and Ruminococcus. Intersectoral-specialization zones were identified along the GIT, with the duodenum revealing major differences between the High-FEC (helminth-susceptible) and Low-FEC (helminth-resistant) animals in values for Alpha and Beta diversity. The High-FEC and Low-FEC sheep differed significantly for three phyla (Firmicutes, Elusimicrobia, Chloroflexi) and 11 genera. At other GIT sites, Firmicutes was the most abundant phylum followed by Bacteroidetes, and Proteobacteria presenting no major differences between High-FEC and Low-FEC.
Conclusions
The gastro-intestinal microbial profile varies widely between helminth-resistant and helminth-susceptible sheep. Each GIT section appears to supports a particular bacterial composition leading to inter-sectoral differences among the various microbial communities. The animal’s duodenum creates the right environment which results in a more diverse and richness microbial population in the helminth-resistant sheep and suggests that this population favours bacterial genera that generally ferment carbohydrates. The energy metabolism of sheep is largely based on the production of volatile fatty acids (acetate, butyrate, propionate) in the rumen, raising the possibility that butyrate-producing bacteria in the duodenum of helminth-resistant sheep, modulate the host’s metabolism and assist in the regulation of the parasite burden.
Field Efficacy of Priming Agents to Enhance Physiological Parameters of Sunflower Under Stress From Charcoal Rot (M. Phaseolina)
Authors: Ghazanfar Muhammad Usman , Qamar Misbah Iqbal Iqbal , Habib Amer , Abbas Muhammad Fahim 
Published: May 2021

Abstract
Charcoal rot (Macrophomina phaseolina (Tassi) Goid.) can cause significant yield losses in sunflower (Helianthus annuus L.) throughout the world. Fungicide treatments are often used to manage this pathogen, but due to costs and environmental impacts, alternative methods need to be explored. Priming is an adaptive strategy which enables plant defense systems to react more effectively to pathogen attack. The priming phase in plants can be achieved by stimuli from chemicals, beneficial microbes, arthropods, and abiotic stress which can induce defense systems in plants. The present study was conducted to evaluate the effect of different priming agents such as salicylic acid (SA), abscisic acid (AA), gibberellic acid (GA), and jasmonic acid (JA), as either seed or foliar treatments, on charcoal rot on the sunflower. The experiments were conducted under field conditions in two consecutive years (2017-2018). Ten seed of one susceptible (17577) and two moderately resistant (HA-259 and B-224) sunflower cultivars were treated with 2, 4 and 6 mM concentrations of the individual priming agents.. The plants were artificially inoculated with M. phaseolina before sowing by infesting soil, and sixty days after sowing. A number of yield parameters were quantified [head diameter (cm), 100-seed weight (g), achene per head (number), plant height (cm), stem girth (cm), shoot weight (g), root wet and dry weight (g) and chlorophyll content (mg/g)]. Among the priming agents evaluated, AA exhibited a significant impact on all yield parameters at a higher concentration (6 mM) in both susceptible and moderately resistant cultivars, followed by SA, GA, and JA. The results also revealed that seed treatment priming was more effective than foliar priming. There were statistical differences in yield parameters between both years of the study. The AA seed priming treatment showed the most promise for managing charcoal rot of sunflower. The outcome of this study will help to explore an environmentally sound and economically feasible approach for the management of charcoal rot to get sustainability in edible oil production.
Retrospective analysis of pediatric hepatoblastoma with tumor rupture: experience from a single center
Authors: Zhang Yu-Tong , Zhao Yu-fei , Yang Dian-fei , Chang Jian 
Published: May 2021

Abstract
Background Hepatoblastoma (HB) tumor rupture is currently considered as a high-risk factor in some risk-stratification systems. This study aimed to investigate the value of HB tumor rupture in predicting the poor prognosis of child patients. Methods The clinical data from children with high-risk HB or HB tumor rupture at our institution from October 2008 to October 2017 were retrospectively reviewed and analyzed. Results Altogether 34 children with high-risk HB or HB tumor rupture were retrospected, including 25 in the high-risk group and 9 in tumor rupture group. The 3-year overall survival (OS) rate in tumor rupture group was significantly higher than that in high-risk group (100% vs 60%, p=0.035). In tumor rupture group, 7 (77.8%) out of 9 patients had the hemoglobin level ≤ 8 g/L and 3 (33.3%) had that ≤ 6 g/L at the time of diagnosis. Peritoneal perfusion with normal saline and interleukin-2 was implemented for each patient until the free fluid was under normal level. At the end of the treatment, 7 (77.8%) of 9 patients achieved complete response (CR). No patient died at the last follow-up. Conclusions Tumor rupture is not predictive of poor prognosis with the risk of peritoneal dissemination/relapse.
Computational Prediction and Experimental Validation of the Unique Molecular Mode of Action of Scoulerine
Authors: Moshari M. , Wang Q. , Michalak M. , Klobukowski M. , Tuszynski J. A. 
Published: May 2021

Abstract

Scoulerine is a natural compound that is known to bind to tubulin and has anti-mitotic properties demonstrated in various cancer cells. Its molecular mode of action has not been precisely known. In this work we perform computational prediction and experimental validation of the mode of action of scoulerine. Based on the existing data in the Protein Data Bank (PDB) and using homology modeling we create human tubulin structures corresponding to both free tubulin dimers and tubulin in a microtubule. We then perform docking of the optimized structure of scoulerine and find the highest affinity binding sites located in both the free tubulin and in a microtubule. We conclude that binding in the vicinity of the colchicine binding site and near the laulimalide binding site are the most likely locations for scoulerine interacting with tubulin. Thermophoresis assays using scoulerine and tubulin in both free and polymerized form confirm these computational predictions. We conclude that scoulerine exhibits a unique property of a dual mode of action with both microtubule stabilization and tubulin polymerization inhibition, both of which have similar affinity values.
Downregulation of SNX5 By KLF9 Leads to Clear Cell Renal Cell Carcinoma Progression By Inducing CD44 Internalization and Suppressing Epithelial-to-Mesenchymal Transition
Authors: Zhou Qingqing , Li Jiajun , Ge Chao , Chen Jinsi , Tian Wei , Tian Hua 
Published: May 2021

Abstract
Background: Aberrant expression of SNX5 can contribute to tumourigenesis, invasion, and metastasis of several human cancers. However, the clinicopathological and biological significance of SNX5 in clear cell renal cell carcinoma (ccRCC) remain unclear. The aim of this study was to examine the role of SNX5 in the progression of ccRCC.Methods: Immunohistochemical (IHC), Western blot, qRT-PCR, western blot, flow cytometry and immunofluorescence were used to detect the expression of indicated molecules. The biological role of SNX5 in ccRCC cells was evaluated by CCK8, colony formation, transwell assay, subcutaneous tumor formation as well as veil tail injection. ChIP assay and luciferase reporter assay were used to determine the direct binding of KLF9 to the promoter of the SNX5 gene.Results: SNX5 expression was downregulated in human ccRCC tissues. SNX5 expression was negatively correlated with tumor size, AJCC stage, tumor thrombus of inferior vena cava (IVC) and poor prognosis of ccRCC. Ectopic expression of SNX5 inhibited ccRCC cell proliferation and metastasis whereas knockdown of SNX5 increase these activities both in vitro and in vivo. Mechanistically, overexpression of SNX5 blocked internalization and intracellular trafficking of CD44 in ccRCC cells. Exogenous expression of CD44 partially rescued the inhibitory effects of SNX5 on the proliferation and invasion activity of ccRCC cells. Knockdown of SNX5 in ccRCC cells was associated with epithelial mesenchymal transition (EMT), including the down-regulation of E-cadherin, ZO-1 and Claudin-1 and the concomitant up-regulation of Snail and N-cadherin. In addition, SNX5 inhibited TGF-β-induced migration, invasion and EMT in ccRCC cells. Moreover, we observed a significant correlation between SNX5 expression and E-cadherin levels in ccRCC patients. In addition, KLF9 directly bound to the SNX5 promoter and increased SNX5 transcription. SNX5 expression was closely correlated with KLF9 expression in ccRCC. Moreover, we found that the combination of SNX5 and CD44 or E-cadherin or KLF9 was a more powerful predictor of poor prognosis than either parameter alone.Conclusion: Collectively, our data reveal a mechanism that KLF9-mediated SNX5 expression was associated with poor prognosis via trafficking of CD44 and promoting EMT in ccRCC. SNX5 may be a potential prognostic biomarker and therapeutic target for patients with ccRCC.
AGR2 – a Novel Predictor of Neoadjuvant Chemoradiotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Lin Chih-Hung , Chuang Han-Ni , Hsiao Tzu-Hung , Kumar V. Bharath , Hsu Chiung-Hung , Huang Chih-Yang , Lee Li-Wen , Mao Chien-Lin , Ko Jiunn-Liang , Hsu Chung-Ping 
Published: May 2021

Abstract
BackgroundEsophageal squamous cell carcinoma (ESCC) still has a poor prognosis despite the use of multidisciplinary therapy. In the locally advanced stage, neoadjuvant chemoradiotherapy (nCRT) followed by surgery might provide survival benefits to some patients. MethodsIn this study, we aimed to identify biomarker to predict tumor response against neoadjuvant chemoradiotherapy (nCRT) by next-generation sequencing (NGS).ResultsOur data showed that 464 genes was differentially expressed ESCC specimens, in which AGR2 was 2.8 fold up-regulated in the patients with Non-complete response before nCRT than complete response group. In vitro study showed that, AGR2 was significantly reduced in AGR2 knockdown CE146T/VGH, TE2, and CE48T/VGH cells. MTT assay indicated that cell viability of AGR2-knockdown TE-2 cell line significantly decreased following 2.5µM cisplatin and 3µM 5-FU treatment. Furthermore, 6µM cisplatin and 20 µM 5-FU treatment greatly decreased AGR2-knockdown-CE48T/VGH, CE146T/VGH and TE-2 cells compared to control group. We also found in AGR2-knockdown cells, that protein level of p21 was increased in comparison with the control group. ConclusionsThis study suggest that AGR-2 as a promising and potential prediction gene marker dataset for response to neoadjuvant chemoradiation in ESCC.
Exploration to Identify Radiosensitive Genes in PD-L1 Expression and PD-1 check Point Pathway in Cancer
Authors: Shen Junjie , Liu Jingfang , Li Huijun , Bai Lu , Geng Ruirui , Cao Jianping , Sun Peng , Tang Zaixiang 
Published: May 2021

Abstract
PurposeTo identify radiosensitive genes in PD-L1 expression and PD-1 check point pathway in cancer.Methods and MaterialsGene expression datasets and information were downloaded from TCGA. Stepwise multivariate Cox regression based on AIC was performed using stacking multiple interpolation data to identify radiosensitive (RS) genes.ResultsAmong the 74 PD-1/PD-L1 pathway genes, we identified 10 RS genes in BRCA dataset, 11 RS genes in STAD dataset and 13 RS genes in HNSC dataset. These genes could be thought as independent factors and biomarkers to identify the sensitivity of cancer patients to radiotherapy. Gene CD274 was the common RS gene in the three tumor datasets. And gene ZAP70 was verified as a RS gene in the external validation. There were moderate co-expression relationships and interactions in these genes. Functional enrichment analysis showed that most of these genes were related to T cells. ConclusionsOur study identified potential radiosensitive biomarkers of several main cancer types in an important tumor immune checkpoint pathway. New types of RS genes were identified based on the expanded definition to radiosensitive genes. Different types of tumors may share same RS genes due to the common carcinogenic mechanisms.
Genetic Findings of Sanger and Nanopore Single-Molecule Sequencing in Patients with X-Linked Hearing Loss and Incomplete Partition Type III
Authors: Chen Ying , Qiu Jiajun , Wu Yingwei , Jia Huan , Jiang Yi , Jiang Mengda , Wang Zhili , Sheng Hai-Bin , Hu Lingxiang , Zhang Zhihua , Wang Zhaoyan , Li Yun , Huang Zhiwu , Wu Hao 
Published: May 2021

Abstract
BackgroundPOU3F4 is the causative gene for X-linked deafness-2 (DFNX2), characterized by incomplete partition type III (IP-III) malformation of the inner ear. The aim of this study was to investigate the clinical characteristics and molecular findings by Sanger or Nanopore single-molecule sequencing in IP-III patients. MethodsDiagnosis of IP-III was mainly based on clinical characteristics including radiological and audiological findings. Sanger sequencing of POU3F4 were carried out for these IP-III patients. For those patients with negative results for POU3F4 Sanger sequencing, Nanopore long-read single-molecule sequencing was used to identify the possible pathogenic variants. Hearing intervention outcomes of hearing aids fitting and cochlear implantation were also analyzed. Grouped by different locations of POU3F4 variants, aided PTA was further compared between patients in whom the variants located in the exon region or in the upstream region.ResultsIn total, 18 male patients from 14 unrelated families were diagnosed with IP-III. 10 variants were identified in POU3F4 by Sanger sequencing and 9 of these were novel (p.Val321Gly, p.Gln181*, p.Cys233*, p.Val215Gly, p.Arg282Gln, p.Trp57*, p.Gln316*, c.903_912 delins TGCCA and p.Arg205del). Four different deletions (DELs) that varied from 80 to 486 kb were identified 876-1503 kb upstream of POU3F4 by Nanopore long-read single-molecule sequencing. Of them, de novo genetic mutations occurred in 21.4% (3/14) of patients with POU3F4 mutations. Of these 18 patients, 7 had bilateral hearing aids (HAs) and 10 patients received unilateral cochlear implantation (CI). The mean aided pure tone average (PTA) for HAs and CI users were 41.1±5.18 and 40.3±7.59 dB HL respectively. The mean PTAs for whom the variants located in the exon and upstream regions were 39.6±6.31 vs 43.0±7.10 dB HL, which presented no significant difference (p=0.342).ConclusionsAmong IP-III patients, 28.6% (4/14) had no definite mutation in exon region of POU3F4, however, possible pathogenic deletions were identified in upstream region of this gen. De novo genetic mutations occurred in 21.4% (3/14) of patients with POU3F4 mutation. Hearing intervention outcomes of IP-III patients presented no difference regardless of the variants locations on exon or upstream regions.
Strategies to implement SARS-CoV-2 point-of-care testing into primary care settings: A qualitative secondary analysis guided by the Behaviour Change Wheel
Authors: Kierkegaard Patrick , Hicks Timothy , Allen A. Joy , Yang Yaling , Hayward Gail , Glogowska Margaret , Nicholson Brian D. , Buckle Peter , Committee CONDOR Steering 
Published: May 2021

Abstract
Background
There is little empirical evidence to inform implementation strategies for introducing SARS-CoV-2 point of care (POC) testing into primary care settings. The purpose of this study is to develop a theory-driven understanding of the behavioural determinants underpinning the implementation of SARS-CoV-2 POC testing in primary care. This will allow identification of potential intervention strategies that could encourage successful implementation of testing into routine practice and facilitate face-to-face consultations.
Methods
We used a secondary qualitative analysis approach to re-analyse data from a qualitative study that involved interviewing 22 primary care physicians from 21 primary care practices across three regions in England. We followed the three-step method based on the Behaviour Change Wheel to identify barriers/enablers to the implementation of SARS-CoV-2 POC testing and identified behaviour change techniques to inform intervention strategies that targeted the barriers/enablers.
Results
We identified 10 barriers and enablers to POC implementation under eight Theoretical Domains Framework (TDF): (1) knowledge; (2) behavioural regulation; (3) reinforcement; (4) skills; (5) environmental context and resources; (6) social influence; (7) professional role and identity; and (8) belief about consequences. Linkages with the Behaviour Change Techniques (BCT) taxonomy enabled the identification of intervention strategies to address the social and contextual factors influencing primary care physician’s willingness and capacity to adopt POC testing.
Conclusions
A theory-informed approach identified barriers to the adoption of POC tests in primary care as well as guiding implementation strategies to address these challenges.
Increased Plasma YKL-40 Level and Chitotriosidase Activity in Cystic Fibrosis Patients
Authors: Topcu Dilara Bal , Tugcu Gökcen , Er Berrin , Polat Sanem Eryilmaz , Hizal Mina , Yalcin Ebru Elmas , Ersoz Deniz Dogru , Coplu Lutfi , Ozcelik Ugur , Kiper Nural , Lay Incilay , Oztas Yesim 
Published: May 2021

Abstract
Background
We investigated plasma YKL-40 levels and chitotriosidase (CHIT1) activity in patients with cystic fibrosis (CF) lung disease and evaluated clinically relevant factors that may affect their levels.
Methods
Plasma samples were obtained from pediatric (n = 19) and adult patients (n = 15) during exacerbation, discharge and stable period of the disease. YKL-40 levels and chitotriosidase activity were measured by enzyme-linked immunosorbent assay and fluorometric assay, respectively. Data were compared with healthy children and adults of similar age.
Results
YKL-40 levels of pediatric and adult CF patients at all periods were significantly higher than controls (p < 0.001 and p < 0.05). CHIT1 activities of adult patients at all periods were significantly higher compared to controls (p < 0.05). On the other hand, CHIT1 activities of pediatric CF patients were similar with controls. YKL-40 levels of exacerbation period of adult CF patients were negatively correlated with % FVC (r= -0.800, p = 0.014) and % FEV1 (r= -0.735, p = 0.008). YKL-40 levels in the exacerbation period of pediatric CF patients were negatively correlated with % FVC (r= -0.697, p = 0.0082) and % FEV1 (r= -0.720, p = 0.006).
Conclusions
CHIT1 activity may be a valuable marker of chronic inflammation in adult CF patients who suffer from CF for a longer period of time compared to pediatric patients. Increased YKL-40 levels in both pediatric and adult patients compared to controls may point to a role in between CF pathology. Furthermore, as YKL-40 levels are correlated with FEV1 and FVC in patients, it may be useful for the monitoring of pulmonary function in CF patient.
A Perspective View of Cotton Leaf Image Classification Using Machine Learning Algorithms Using WEKA
Authors: Patil Bhagya , Barkpalli Vishwanath 
Published: May 2021

Abstract
Cotton is one of the major crops in India where 23% of cotton gets exported to other countries. Hence, the cotton yield depends on the crop growth, and it gets affected because of diseases. In this paper, cotton disease classification is performed using different machine learning algorithms. For this research, the cotton database was created by capturing images in the field under controlled conditions. The same database is used for segmenting the images using modified factorization-based active contour. The color and texture features are extracted from segmented images and later its fed to the machine learning algorithms like Multilayer perceptron, Support vector machine, Naïve Bayes, Random forest, Ada Boost, K nearest neighbor. The performance of the classifiers is better when color features are extracted than texture features extraction. The color features are enough to classify the healthy and unhealthy cotton leaf images. Among the different classifiers, Multilayer perceptron gives nearly 96.69% which is greater than other classifiers.
Improving Administration of Fascia-iliaca Blocks for Patients With a Fractured Neck of Femur by Clinical Audit
Authors: Okereke Isaac , Sampalli Sridhar Rao 
Published: May 2021

Abstract
BackgroundHip fracture is the most common serious injury in older people. It is also the most common reason for older people to need emergency anaesthesia and surgery, and the commonest cause of death following an accident. A FICB is the injection of anaesthetic agents into the fascia- iliaca compartment with the effect of blocking the lumbar plexus via an anterior approach. FICB is clinically safe and efficient and provides consistent analgesic effects irrespective of the performing doctor's experience of frailty fractures of the proximal femur.Methods Data from the National Hip Fracture Database (NHFD) for all patients admitted with a neck of femur fracture between October 2018 and May 2019 was interrogated and audited. Results of this audit were discussed in the department of Trauma & Orthopaedics' and the Trust's mortality review meetings. Teaching sessions were held for doctors and filling out of the neck of femur fracture proforma to detail administration or not of FICB and a valid reason when the later occurred was encouraged. A re-audit was carried out in May 2020 where a retrospective study of patients admitted with a neck of femur fracture over six months from October 2019 to April 2020 was done to assess improvement in compliance rates of administration of fascia iliaca blocks.Results We noted a statistically significant increase in the number of patients who got a fascia iliaca block on presentation with a fractured neck of the femur from after our second audit (p<0.00001). There were no complications associated with the administration of FICB to patients with neck of femur fractures. ConclusionThis study showed that clinical processes could be improved through audits, staff education and by employing the use of proformas to ensure compliance.