bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Avena sativa L.)
Authors: Yang Zheng , Wang Kai , Aziz Usman , Zhao Cuizhu , Zhang Meng 
Published: July 2020

Abstract
Background: Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids.Results: In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for “all samples”, “shoots and roots of seedlings”, “developing seeds” and “developing endosperms” were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets.Conclusions: Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
Perspectives and practices of health workers around diagnosis of paediatric tuberculosis in hospitals in a resource-poor setting – modern diagnostics meet age-old challenges
Authors: Oliwa Jacquie Narotso , Odero Sabina Adhiambo , Nzinga Jacinta , Hensbroek Michaël Boele van , Jones Caroline , English Mike , Hoog Anja van't 
Published: July 2020

Abstract
Background Detection of tuberculosis (TB) in children in Kenya is sub-optimal. Xpert MTB/RIF® assay (Xpert®) has the potential to improve speed of TB diagnosis due to its sensitivity and fast turnaround for results. Significant effort and resources have been put into making the machines widely available in Kenya, but use remains low, especially in children. We set out to explore the reasons for the under-detection of TB and underuse of Xpert® in children, identifying challenges that may be relevant to other newer diagnostics in similar settings.Methods This was an exploratory qualitative study with an embedded case study approach. Data collection involved semi-structured interviews; small-group discussions; key informant interviews; observations of TB trainings, sensitisation meetings, policy meetings, hospital practices; desk review of guidelines, job aides and policy documents. The Capability, Opportunity and Motivation (COM-B) framework was used to interpret emerging themes. Results At individual level, knowledge, skill, competence and experience, as well as beliefs and fears impacted on capability (physical & psychological) as well as motivation (reflective) to diagnose TB in children and use diagnostic tests. Hospital level influencers included hospital norms, processes, patient flows and resources which affected how individual health workers attempted to diagnose TB in children by impacting on their capability (physical & psychological), motivation (reflective & automatic) and opportunity (physical & social). At the wider system level, community practices and beliefs, and implementation of TB programme directives impacted some of the decisions that health workers made through capability (psychological), motivation (reflective & automatic) and opportunity (physical). Conclusion We used comprehensive approaches to identify influencers of TB case detection and use of TB diagnostic tests in children in Kenya. These results are being used to design a contextually-appropriate intervention to improve TB diagnosis, which may be relevant to similar low-resource, high TB burden countries and can be feasibly implemented by the National TB programme.
Antibiotics prescription for febrile outpatients: a health facility-based secondary data analysis for the Greater Accra region of Ghana
Authors: Opoku Michael Mireku , Bonful Harriet Affran , Koram Kwadwo A. 
Published: July 2020

Abstract
Background: Misguided prescription of antibiotics is an important contributor towards the emergence and spread of antibiotic resistance. The absence of effective interventions to control antibiotic use leads to increased consumption beyond the needed requirements. Antibiotic stewardship interventions must be appropriately targeted and assessed to enhance the controlled use of antibiotics. The objective of this study was to determine the factors associated with antibiotic prescription to febrile outpatients who seek care in health facilities within the Greater Accra region of Ghana.Methods: Secondary data obtained from the medical records of 2,519 febrile outpatients, consecutively sampled at the outpatient department of 6 health facilities in 3 municipalities during the baseline survey of a quasi-experiment in 2016 was used. The primary outcome was prescription of any antibiotic. Independent variables included patients’ demographics, symptoms, laboratory investigations (blood film microscopy, malaria rapid diagnostic test, full blood count, urine and stool routine examinations), diagnoses, and prescribers’ demographics. Crude and adjusted logistic regression analyses were used to determine the factors associated with antibiotic prescription. Results: The prevalence of antibiotic prescription was 70.1% (95% CI: 67.7-72.4). Prescribers with more years of practice (>5years) were more likely to prescribe antibiotics compared to those with less than 3 years of practice (p < 0.001). Integrated Management of Neonatal and Childhood Illnesses (IMNCI) training was associated with a 2.3 (95% CI: 1.54, 3.53, p < 0.001) folds odds of antibiotic prescribing. Patients aged 5 years or more were 60% less likely to receive antibiotics compared with those under 5 years (AOR=0.40, 95% CI: 0.32, 0.51; p<0.001). Patients referred for laboratory investigations were 29% less likely to be prescribed for antibiotics than those not referred. The presence of cough as a presenting symptom was associated with a 3.5 (95% CI: 2.54, 4.92) fold odds of antibiotic prescription. Conclusion: Prescription of antibiotics to febrile outpatients was high. Promoting laboratory testing can potentially reduce irrational antibiotics prescribing. Prescribing antibiotics for children under five and the prescribing practices of prescribers with longer years of practice should be targeted with interventions to reduce high use of antibiotics.
An outbreak of intestinal schistosomiasis, alongside increasing urogenital schistosomiasis prevalence, in primary school children on the shoreline of Lake Malawi, Mangochi District, Malawi
Authors: Kayuni Sekeleghe , O’Ferrall Angus M. , Baxter Hamish , Hesketh Josie , Mainga Bright , Lally David , Al-Harbi Mohammad H. , LaCourse E. James , Juziwelo Lazarus , Musaya Janelisa , Makaula Peter , Stothard John Russell 
Published: July 2020

Abstract
Background: Intestinal schistosomiasis was not considered endemic in Lake Malawi until November 2017 when populations of Biomphalaria pfeifferi were first reported; in May 2018, emergence of intestinal schistosomiasis was confirmed. This emergence was in spite of ongoing control of urogenital schistosomiasis by preventive chemotherapy. Our current study sought to ascertain whether intestinal schistosomiasis is transitioning from emergence to outbreak, to judge if stepped-up control interventions are needed.Methods: During late-May 2019, three cross-sectional surveys of primary school children for schistosomiasis were conducted using a combination of rapid diagnostic tests, parasitological examinations and applied morbidity-markers; 1) schistosomiasis dynamics were assessed at Samama (n = 80) and Mchoka (n = 80) schools, where Schistosoma mansoni was first reported, 2) occurrence of S. mansoni was investigated at two non-sampled schools, Mangochi Orphan Education and Training (MOET) (n = 60) and Koche (n = 60) schools, where B. pfeifferi was nearby, and 3) rapid mapping of schistosomiasis, and B. pfeifferi, conducted across a further 8 shoreline schools (n = 240). After data collection, univariate analyses and Chi-square testing were performed, followed by binary logistic regression using generalized linear models, to investigate epidemiological associations.Results: In total, 520 children from 12 lakeshore primary schools were examined, mean prevalence of S. mansoni by ‘positive’ urine circulating cathodic antigen (CCA)-dipsticks was 31.5% (95% Confidence Interval (CI): 27.5–35.5). Upon comparisons of infection prevalence in May 2018, significant increases at Samama (Relative Risk (RR) = 1.7, 95% CI: 1.4–2.2) and Mchoka (RR = 2.7, 95% CI: 1.7–4.3) schools were observed. Intestinal schistosomiasis was confirmed at MOET (18.3%) and Koche (35.0%) schools, and in all rapid mapping schools, ranging from 10.0% to 56.7%. Several populations of B. pfeifferi were confirmed, with two new eastern shoreline locations noted. Mean prevalence of urogenital schistosomiasis was 24.0% (95% CI: 20.3–27.7). Conclusions: We notify that intestinal schistosomiasis, once considered non-endemic in Lake Malawi, is now transitioning from emergence to outbreak. Once control interventions can resume after coronavirus disease 2019 (COVID-19) suspensions, we recommend stepped-up preventive chemotherapy, with increased community-access to treatments, alongside renewed efforts in appropriate environmental control.
Concurrent ipsilateral Tillaux fracture and medial malleolar fracture in adolescents: management and outcome
Authors: yuan quanwen , Guo Zhixiong , Wang Xiaodong , Dai Jin , Zhang Fuyong , Fang Jianfeng , Yin Chunhua , Yu Wentao , Zhen Yunfang 
Published: July 2020

Abstract
Background: The concurrent ipsilateral Tillaux fracture with medial malleolar fracture in adolescents commonly suffer from high-energy injury, making treatment more difficult. The aim of this study was to discuss the mechanism on injury, diagnosis and treatment of this complex fracture pattern. Methods: The charts and radiographs of six patients were reviewed. The function was assessed by the American Orthopedic Foot and Ankle Society ankle-hindfoot scores. Results: The mean age at operation was 12.8 years. The mean interval from injury to operation was 7.7 days. Five Tillaux fractures and all medial malleolar fractures were shown on AP plain radiographs. One Tillaux fracture and two cases with avulsion of posterolateral tibial aspect were confirmed in axial computerized tomography. Talar subluxation laterally with medial space widening in three, and syndesmotic disruption in one. There were five patients sustaining ipsilateral distal fibular fractures. All fractures, except nonunion in two medial malleolar fractures and in one Tillaux fracture, healed within 6-8 weeks. There was one case of osteoarthritis of ankle joint. The average AOFAS score was 88.7. Conclusions: Computerized tomography is helpful in identifying the fracture pattern. Anatomic reduction and internal fixation of Tillaux and medial malleolar fracture was recommended to restore the articular surface congruity and ankle stability.
Deficiency in Aim2 affects viability and calcification of vascular smooth muscle cells from murine aortas and Angiotensin-II induced aortic aneurysms
Authors: Wortmann Markus , Arshad Muhammad , Hakimi Maani , Böckler Dittmar , Dihlmann Susanne 
Published: July 2020

Abstract
Background: Phenotypic transformation of vascular smooth muscle cells is a key element in vascular remodeling and aortic aneurysm growth. Previously, deletion of several inflammasome components decreased formation of aortic aneurysm (AA) in the Angiotensin II (AngII) -induced mouse model. We hypothesized that the inflammasome sensor Absent in melanoma 2 (Aim2) might affect the phenotype of vascular smooth muscle cells (VSMC), thereby reducing AA formation.

Methods : Aim2-/- mice and wild-type (WT) C57Bl/6J mice were used as an animal model. VSMC were isolated from 6 months old mice and grown in vitro . Young (passage 3-5) and senescent (passage 7-12) cells were analyzed in vitro for calcification in mineralization medium by Alizarin Red S staining. Expression of calcification and inflammatory markers were studied by real-time RT-PCR and Western blotting, release of cytokines was determined by ELISA. To induce AA, osmotic mini-pumps loaded with AngII (1500 ng/kg bodyweight/min) were implanted for 28 days in male mice at 6 months of age.

Results : Compared with VSMC from WT mice, VSMC isolated from Aim2-/- mice were larger, less viable, and underwent stronger calcification in mineralization medium, along with induction of Bmp4 and repression of Tnfsf11/Rankl gene expression. In addition, Aim2 deficiency was associated with reduced inflammasome gene expression and release of Interleukin-6. Using the mouse model of AngII induced AA, Aim2 deficiency reduced AA incidence to 48.4% (15/31) in Aim2-/- mice versus 76.5% (13/17) in WT mice. In contrast to Aim2-/- mice, AA from WT mice expressed significantly increased levels of alpha-smooth muscle actin/ Acta2 , indicating tissue remodeling. Reduced cell proliferation in Aim2-/- mice was indicated by significantly increased p16ink4a/ Cdkn2a expression in untreated and AngII-infused aortas, and by significantly lower amounts of proliferating (Ki67 positive) VSMC in AngII-infused Aim2-/- mice.

Conclusions: Our results suggest a role for Aim2 in regulating VSMC proliferation and transition to an osteoblast-like or osteoclast-like phenotype, thereby modulating the response of VSMC in aortic remodeling and AA Formation.
Fermented Astragalus in diet improved laying performance, egg quality, antioxidant and immunological status and intestinal microbiota in laying hens
Authors: Shi Hongtao , Wang Baiyu , Bian Chuanzhou , Han Yingqian , Qiao Hongxing 
Published: July 2020

Abstract
In the era of increased antibiotic resistance and ever-stricter control on antibiotic use, it is urgent to develop green, safe, and non-residue alternatives to antibiotics applied to the poultry industry. To this end, we supplied the potential Lactobacillus Plantarum (L. Plantarum) fermented Astragalus in the diet of laying hens, with a final addition of 3‰. Its effects have been assessed on laying performance, egg quality, antioxidant and immunological status, and intestinal microbiota, and are compared to the control group, to the Astragalus group containing 3‰ unfermented Astragalus, and to the L. Plantarum group containing 2% L. Plantarum (5×108 colony-forming unit (CFU) per milliliter (mL)). During the second half of the experimental period (15 to 28 days), the egg production rate was considerably higher in the fermented Astragalus group than that in the other groups, with the fermented Astragalus group having the lowest feed conversion ratio. No significant difference (P>0.05) was noted among treatments on egg quality. Fermented Astragalus-treated hens exhibited significantly increased catalase (CAT), glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) in serum, and reduced malondialdehyde (MDA) in serum. Furthermore, fermented Astragalus supplementation resulted in a significant increase in ileal microbiota abundance relative to control. In conclusion, feeding laying hens with L. Plantarum fermented Astragalus has beneficial effects on production, antioxidant potential, immunity, and ileal microbiota. L. Plantarum fermented Astragalus is expected to be a novel feed additive used in poultry production.
Operative invasiveness does not affect the prognosis of patients with non-small cell lung cancer
Authors: Motono Nozomu , Iwai Shun , Iijima Yoshihito , Usuda katsuo , Uramoto Hidetaka 
Published: July 2020

Abstract
Background: The relationship between operative invasiveness and the prognosis in non-small cell lung cancer (NSCLC) patients who have undergone surgery has been controversial.Methods: Clinical data were analyzed for 463 NSCLC patients. Operative invasiveness was defined by wound length, operation time, and the postoperative C-reactive protein (postCRP) level. The operative approach was divided into video-assisted thoracic surgery (VATS) and thoracotomy.Results: The wound length and operation time were significantly correlated with the postCRP level (correlation coefficient (CC) = 0.39, p<0.01; CC = 0.54, p<0.01, respectively). The postCRP level in the VATS group was significantly lower than that in the thoracotomy group (12.2 mg/dl vs 20.58 mg/dl, p<0.01). The relapse-free survival differed significantly based on wound length (p<0.01), operation time (p=0.01), CRP level (p<0.01), and operative approach (p<0.01). The carcinoembryonic antigen level (hazard ratio [HR], 1.58; p = 0.02), pathological stage (pStage) (HR, 2.57; p < 0.01), vascular invasion (HR, 1.95; p = 0.01), and preoperative CRP level (preCRP) (HR, 1.91; p < 0.01) were identified as significant prognostic factors for relapse-free survival in a multivariate analysis. Furthermore, the multivariate analysis showed that smoking history (HR, 2.36; p = 0.03), pStage (HR, 3.26; p < 0.01), and preCRP level were significant prognostic factors for overall survival.Conclusion: Preoperative CRP level was associated with poor prognosis. Although the VATS approach might be less invasive procedure for NSCLC patients, operative invasiveness does not affect the prognosis. Trial registrationThe Institutional Review Boards of Kanazawa Medical University approved the protocol (approval number: I392), and written informed consent was obtained from all of the patients.
Pelvic injury prognosis is more closely related to vascular injury severity than anatomical fracture complexity: The WSES classification for pelvic trauma makes sense
Authors: Wu Yu-Tung , Cheng Chi-Tung , Tee Yu-San , Fu Chih-Yuan , Liao Chien-Hung , Hsieh Chi-Hsun 
Published: July 2020

Abstract
Background: The most common cause of death in cases of pelvic trauma is exsanguination caused by associated injuries, not the pelvic injury itself. For patients with relatively isolated pelvic trauma, the impact of vascular injury severity on outcome remains unclear. We hypothesized that the severity of the pelvic vascular injury plays a more decisive role in outcome than fracture pattern complexity. Methods: Medical records of patients with pelvic fracture at a single center between Jan 2016 and Dec 2017 were retrospectively reviewed. Those with an abbreviated injury scale (AIS) score ≥3 in areas other than the pelvis were excluded. Lateral compression (LC) type 1 fractures and anteroposterior compression (APC) type 1 fractures according to the Young-Burgess classification and ischial fractures were defined as simple pelvic fractures, while other fracture types were considered complicated pelvic fractures. Based on CT, vascular injury severity was defined as minor (fracture with or without hematoma) or severe (hematoma with contrast pooling/extravasation). Patient demographics, clinical parameters, and outcome measures were compared between the groups.Results: Severe vascular injuries occurred in 26 of the 155 patients and were associated with poorer hemodynamics, a higher injury severity score (ISS), more blood transfusions, and a longer ICU stay (3.81 vs. 0.86 days, p=0.000) and total hospital stay (20.7 vs. 10.1 days, p=0.002) compared with minor vascular injuries. By contrast, those with complicated pelvic fractures (LC II/III, APC II/III, vertical shear and combined type fracture) required a similar number of transfusions and had a similar length of ICU stay as those with simple pelvic fractures (LC I, APC I and ischium fracture) but had a longer total hospital stay (13.6 vs. 10.3 days, p=0.034). These findings were similar even if only patients with ISS >=16 were considered.Conclusions: Our results indicate that even in patients with relatively isolated pelvic injuries, vascular injury severity is more closely correlated to outcome than the type of anatomical fracture. Therefore, a more balanced classification of pelvic injury that takes both the fracture pattern and hemodynamic status into consideration, such as the WSES classification, seems to have better utility for clinical practice.Trial registration: This is a retrospective review study, not a clinical trial.
Bioinformatic Analysis Revealing Mitotic Spindle Assembly regulated NDC80 and MAD2L1 as Prognostic Biomarkers in Non-Small Cell Lung Cancer Development
Authors: Wei Rong , Wang Ziyue , Zhang Yaping , Wang Bin , Shen Ningning , E Li , Li Xin , Shang Lifang , Shang Yangwei , Yan Wenpeng , Zhang Xiaoqin , Ma Wenxia , Wang Chen 
Published: July 2020

Abstract
Background Lung cancer has been the leading cause of tumor related death, and 80%~85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the treatment is still challenging. The study is to identify credible responsible genes during the development of NSCLC using bioinformatic analysis, developing new prognostic biomarkers and potential gene targets to the disease. Methods Firstly, three genes expression profiles GSE44077, GSE18842 and GSE33532 were picked from Gene Expression Omnibus (GEO) to analyze the genes with different expression level (GDEs) between NSCLC and normal lung samples, and the cellular location, molecular function and the biology pathways the GDEs enriched in were analyzed. Then, gene function modules of GDEs were explored based on the protein-protein interaction network (PPI), and the top module which contains most genes was identified, followed by containing genes annotation and survival analysis. Moreover, multivariate cox regression analysis was performed in addition to the Kaplan meier survival to narrow down the key genes scale. Further, the clinical pathological features of the picked key genes were explored using TCGA data. Results Three GEO profiles shared a total of 664 GDEs, including 232 up-regulated and 432 down-regulated genes. Based on the GDEs PPI network, the top function module containing a total of 69 genes was identified, and 31 of 69 genes were mitotic cell cycle regulation related. And survival analysis of the 31 genes revealed that 17/31 genes statistical significantly related to NSCLC overall survival, including 4 spindle assembly checkpoints, namely NDC80, BUB1B, MAD2L1 and AURKA. Further, multivariate cox regression analysis identified NDC80 and MAD2L1 as independent prognostic indicators in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively. Interestingly, pearson correlation analysis indicated strong connection between the four genes NDC80, BUB1B, MAD2L1 and AURKA, and their clinical pathological features were addressed. Conclusions Using bioinformatic analysis of GEO combined with TCGA data, we revealed two independent prognostic indicators in LUAD and LUSC respectively and analyzed their clinical features. However, more detailed experiments and clinical trials are needed to verify their drug targets role in clinical medical use.