bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification the ferroptosis-related gene signature in Gastric cancer based on weighted gene co-expression network analysis (WGCNA)
Authors: Wang Feng , Chen Cheng , Chen Wei-Peng , Li Zu-Ling , Cheng Hui
Published: May 2021

Background

Ferroptosis is a mode of regulated cell death that depends on iron, plays pivotal roles in regulating various biological process in human cancers. However, the role of ferroptosis in Gastric cancer (GC) remains unclear.
Methods

A total of 2721 differentially expressed genes (DEGs) were filtered base on The Cancer Genome Atlas (TCGA) (n = 375) dataset. Gene modules were identified based on co-expression network analysis (WGCNA). Functional analysis was performed to explore the biological function. Lasso-penalized and univariate Cox regression (UCR) analysis, survival genes were screened out to construct a prognostic model, which validated by the GSE43292 dataset. Gene set enrichment analysis (GSEA) for prognostic index was performed. Finally, the correlations of ferroptosis and immune cells were assessed through the TIMER database.
Results

Compared to normal specimens, 1063 highly upregulated and 1658 downregulated genes respectively and their normal counterparts in GC specimens were screened. WGCNA analysis was used and identified 7 modules, of which, blue module with the most significant enrichment result was selected. By taking intersections of blue module and differentially expressed ferroptosis-related genes (DEFRGs), we got 23 common genes. Functional analysis was performed to explore the biological function of the interested genes, and with the consequences Lasso-penalized and univariate Cox regression (UCR) analysis, survival genes were screened out to construct a prognostic model based on 3 genes (SLC1A5, ANGPTL4, and CGAS), which could play a role in predicting the survival of GC patients. UCR and multivariate Cox regression (MCR) analysis revealed that the prognostic index could be used as independent prognostic indicators and validated using another GSE84437 dataset. Notably, patients in high-risk groups had higher levels of higher mutation frequencies such as TTN and TP53.Mechanistically. Gene set enrichment analysis (GSEA) unveiled several significant and pathways involved in GC. TIMER analysis demonstrated that risk score strongly correlated with Macrophage and CD4 + T cells infiltration. In addition, high- and low-risk group illustrated different distributions in different immune status.
Conclusions

In this study, a novel FRGs signature was built. It could accurately predict GC prognosis and pave the new way for diagnosis and therapy strategy. May reflect the status of tumor immune microenvironment.
Community Knowledge, Perceptions, And Practices Regarding Malaria and Its Control In Jabi Tehnan District, Amhara Region, Northwest Ethiopia
Authors: Asale Abebe , Abro Zewdu , Enchalew Bayu , Tesager Alayu , Belay Aklilu , Kassie Menale , Mutero Clifford
Published: May 2021

Background: Key program components of malaria control in Ethiopia include community empowerment and mobilization, vector control using long-lasting insecticidal nets (LLINs), indoor residual spraying (IRS), prompt diagnosis and treatment, and disease surveillance. However, the effectiveness of these interventions is often undermined by various challenges, including insecticide and drug resistance, the plasticity of malaria vectors feeding and biting behavior, and certain household factors that lead to misuse and poor utilization of LLINs. The primary objective of this study was to document households’ perceptions towards malaria and assess the prevalence of the disease and the constraints related to the ongoing interventions in Ethiopia (LLINs, IRS, community mobilization house screening). Method: The study was conducted in Jabi Tehnan district, Northwestern Ethiopi,a from November 2019 to March 2020. A total of 3,010 households distributed over 38 kebeles (villages) were randomly selected for socio-economic and demographic survey. Focus group discussions (FGDs) were conducted in 11 different health clusters taking into account agro-ecological differences. A total of 1,256 children under 10 years of age were screened for malaria parasites using microscopy in order to determine malaria prevalence. Furthermore, five-year malaria trend analysis was undertaken based on data obtained from the district health office to understand the disease dynamics.Result: Malaria knowledge in the area was high as all FGD participants correctly identified mosquito bites during the night as sources of malaria transmission. Delayed health seeking behavior remains a key behavioral challenge in malaria control as it took patients on average 4 days before reporting the case at the nearby health facility. On average households lost 2.53 working days per person-per malaria episode and theey spent US$ 18 per person perepisode. Out of the 1,256 randomly selected under 10 children tested for malaria parasites, 11 (0.89%) were found to be positive. Malaria disproportionately affected the adult segment of the population more, 50% of the total cases reported from households whose age was 15 and beyond. The second most affected group was the age group between 5 and 14 years followed by children under 10, with 31% and 14% burden,respectively.Conclusion: Despite the achievement of universal coverage in terms of LLINs access, utilization of vector control interventions in the area remained low.Using bed nets for unintended purposes remained a major challenge. Therefore, continued community education and communication work should be prioritised in the study area to bring about the desired behavioral changes.
Saccharomyces Cerevisiae as an untapped source of fungal chitosan for antimicrobial action
Authors: Afroz Md Masirul , Kashem Md Nayeem Hasan , Piash KM Prottoy Shariar , Islam Nafisa
Published: May 2021

Despite being widely available, Saccharomyces cerevisiae has not been widely explored for direct extraction of chitosan biopolymer for antimicrobial applications. In our study, S. cerevisiae from Baker’s yeast and Aspergillus niger from moldy onion extracts are studied as alternative sources of chitosan; and S cerevisiae chitosan tested for antimicrobial efficacy. The properties of S. cerevisiae chitosan are compared with moldy onion chitosan and shrimp chitosan extracted from shrimp shells. Chitosan extracted from S. cerevisiae is tested for antimicrobial efficacy against Staphylococcus Aureus. The maximum yields of fungal chitosan are 20.85 ± 0.35 mg/g dry S. cerevisiae biomass at 4th day using a culture broth containing sodium acetate, and 16.15 ± 0.95 mg/g dry A. niger biomass at 12th day. The degree of deacetylation (DD%) of the extracted fungal chitosan samples from S. cerevisiae and A. niger are found to be 63.4%, and 61.2% respectively, using Fourier Transform Infrared Spectroscopy. At a concentration of 2 g/L, S. cerevisiae chitosan shows the maximum inhibition zone diameter of 15.48 ± 0.07 mm. Baker’s yeast S cerevisiae biomass and A. niger from moldy onions has not been previously explored as a source of extractible fungal chitosan. This study gives insight that S. cerevisiae and A. niger from agricultural or industrial wastes could be a potential biomass source for production of the chitosan biopolymer. The S. cerevisiae chitosan displayed effective antimicrobial properties against S aureus , indicating the viablitiy of S cerevisae as a resource for extraction of high-quality chitosan.
Developing global vulnerabilities and conservation priorities for cave-dwelling bats
Authors: Tanalgo Krizler , Oliveira Hernani , Hughes Alice
Published: May 2021

Research and conservation interventions are disproportionately focused on taxa perceived as charismatic, while other systems with high levels of endemism, and often under-protected such as caves and subterranean ecosystems remain neglected. Bats are keystone to cave ecosystems making them ideal surrogates to understand diversity patterns and assay conservation priorities. Using a novel framework, we assessed and mapped the global bat cave vulnerabilities and priorities at the biome and site level. Almost half (N = 678, 48%) of bat species across the world regularly use caves, with 32% endemic to a single country, and 15% currently threatened with extinction. Tropical realms and small-ranged species faced the highest levels of risk. Our analyses consistently showed that most caves with lower threat levels show higher cave biotic potential (i.e., evolutionary distinctiveness and endemism), though this may be due to the loss of species from more disturbed caves. We estimate that 3% to 28% are high-priority caves for conservation in broad-scale (biome level) and fine-scale (site-dependent) analyses respectively. Amongst regions, the highest concentration of conservation priority areas are in the Palearctic and tropical regions (except Afrotropical), which requires more intensive data sampling. Our results further highlight the importance of prioritising bat caves at local scales but show that broader scale analysis is possible if robust cave data is present and effective parameters are included (i.e., appropriate landscape features and threats). Developing priorities for these systems requires more systematic approaches as a standard measure to develop the priorities needed to maintain cave diversity.
Validation of Fatty Liver Index as a Marker for Metabolic Dysfunction-associated Fatty Liver Disease
Authors: Han A lum , Kim Youngjon
Published: May 2021

Background: Metabolic dysfunction-associated fatty liver disease (MAFLD) is a new nomenclature for non-alcoholic fatty liver. Fatty liver associated with metabolic dysfunction is increasing with obesity and has become a serious socioeconomic problem. Non-invasive testing to confirm MAFLD, such as the fatty liver index (FLI), can be used as an alternative method for diagnosing steatosis when imaging modalities are not available. To date, few studies have examined the effectiveness and validity of FLI for diagnosing MAFLD. Therefore, this study analyzed the effectiveness and validity of FLI for diagnosing MAFLD.Methods: The medical records of men and women aged 19 years or older who underwent abdominal computed tomography (CT) examination at the University Hospital Health Promotion Center from March 2012 to October 2019 were reviewed retrospectively. A comparative analysis between non-continuous variables was performed using the chi-squared test. The area under receiver operating characteristic (AUROC) curve was used to verify the effectiveness of FLI as a predictive index for MAFLD. Results: Analysis of the association between MAFLD and abdominal CT revealed that the sensitivity and specificity of FLI for diagnosing MAFLD were 0.712 and 0.713, respectively. The AUROC of FLI for the prediction of MAFLD was 0.776. Conclusion: Our study verified the accuracy of FLI for predicting MAFLD using CT. Additionally, FLI can be used as a simple and cost-effective tool for screening MAFLD in clinical settings.
Multifaceted Empathy Differences in Children and Adults with Autism
Authors: Quinde-Zlibut Jennifer M. , Williams Zachary J. , Gerdes Madison , Mash Lisa E. , Heflin Brynna H. , Cascio Carissa
Published: May 2021

Although empathy impairments have been reported in autistic individuals, there is no clear consensus on how emotional valence influences this multidimensional process. In this study, we use the Multifaceted Empathy Test for juveniles (MET-J) to interrogate emotional and cognitive empathy in 184 participants (ages 8–59 years, 83 autistic) under the robust Bayesian inference framework. Group comparisons demonstrate previously unreported interaction effects between: (1) valence and autism diagnosis in predictions of emotional resonance, and (2) valence and age group in predictions of arousal to images portraying positive and negative facial expressions. These results extend previous studies using the MET by examining differential effects of emotional valence in a large sample of autistic children and adults with average or above-average intelligence. We report impaired cognitive empathy in autism, and subtle differences in emotional empathy characterized by less distinction between emotional resonance to positive vs. negative facial expressions in autism compared to neurotypicals. Reduced emotional differentiation between positive and negative affect in others could be a mechanism for diminished social reciprocity that poses a universal challenge for people with autism. These component- and valence- specific findings are of clinical relevance for the development and implementation of target-specific social interventions in autism.
Fetal MRI Mediastinal Shift Angle, Respiratory and Cardiovascular Pharmacological Support in Newborns With Congenital Diaphragmatic Hernia
Authors: Amodeo Ilaria , Borzani Irene , Corsani Giulia , Pesenti Nicola , Raffaeli Genny , Macchini Francesco , Condò Valentina , Persico Nicola , Ghirardello Stefano , Colnaghi Mariarosa , Mosca Fabio , Cavallaro Giacomo
Published: May 2021

Introduction. In newborns with congenital diaphragmatic hernia (CDH), the mediastinal shift caused by the herniated organs negatively affects lung development. Assessment of the fetal magnetic resonance imaging (MRI) mediastinal shift angle (MSA) was shown to have an inverse correlation with the total fetal lung volume (TFLV), being associated with neonatal survival. However, a possible association with postnatal morbidity has never been investigated. We hypothesize that the degree of the mediastinal shift could be associated with higher respiratory and cardiocirculatory impairment, requiring intensive treatments and extended hospitalization in survivors.Method. We retrospectively consider a cohort of isolated, left-sided CDH, for whom we calculated the MSA and the observed/expected (O/E) TFLV at fetal MRI. We performed a data collection regarding inotropic or vasoactive support, treatment with pulmonary vasodilators, mechanical ventilation, and length of stay. General linear models were performed. Results. The MSA and O/E TFLV were inversely correlated (Pearson’s coefficient -0.65, p < 0.001) and deceased patients showed higher MSA values then survivors (p = 0.011). Among survivors, an increase in MSA was associated with longer pharmacological treatments (dobutamine: p = 0.016; dopamine: p = 0.049; hydrocortisone: p = 0.003; nitric oxide: p = 0.002; sildenafil: p = 0.039; milrinone: p = 0.039; oxygen: p = 0.066), and mechanical ventilation (p = 0.005), with an increasing trend in the length of hospitalization (p = 0.089). Conclusions. The MSA indirectly reflects lung hypoplasia and is associated with the higher neonatal intensity of cares. Further studies are needed to consolidate the results. Clinical Trial Registration: The study is an exploratory post-hoc analysis of the registered NeoAPACHE protocol at ClinicalTrials.gov with the identifier NCT04396028
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

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

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

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

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

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

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

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

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

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

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

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

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.
Comparison of Early F-18 Florbetaben PET/CT to Tc-99m ECD SPECT Using Voxel, Regional, and Network Analysis
Authors: Kwon Soo Jin , Ha Seunggyun , Yoo Sang-Won , Shin Na-Young , O Joo Hyun , Yoo Ie Ryung , Kim Joong-Seok
Published: May 2021

This study aimed to validate early-phase F-18 Florbetaben positron emission tomography (eFBB PET) as a brain perfusion test and determine the optimal reference region. A total of 27 patients with early Parkinson’s disease with ethyl cysteinate dimer single positron emission tomography (ECD SPECT) and FBB PET were included. Six reference regions, including whole brain (GN), pons, central white matter (CWM), whole cerebellum (WC), WC with brain stem (WC + B), and cerebellar gray matter (CG), were applied to obtain SUVR. Correlations of SUVRs between eFBB PET and ECD SPECT were calculated for each normalization method. Voxel-wise comparison of the two imaging studies was done with paired t-test. Pearson’s r for SUVRs were 0.791 for GN (p < 0.001), 0.422 for pons (p = 0.028), -0.005 for CWM (p = 0.982), 0.886 for WC (p < 0.001), 0.897 for WC + B (p < 0.001), and 0.904 for CG (p < 0.001), respectively. Early phase FBB PET had significantly higher voxel-wise SUVR in cerebral cortices, striatum, midbrain regions, and lower voxel-wise SUVR in white matter, concordantly in both GN and CG normalization method (FDR adjusted-p < 0.05). Our findings suggest that eFBB PET is a reliable perfusion test based on a high correlation of SUVR with ECD SPECT. High gray-to-white matter contrast would be another advantage of eFBB PET for clinical use.
Accelerated Life Reliability Evaluation of Grating Ruler for CNC Machine Tools Based on Competing Risk Model and Incomplete Data
Authors: Yang Haiji , Li Guofa , He Jialong , Ma Yupeng , Wang Liding , Zhang Wei
Published: May 2021

Grating ruler is the high-precision linear displacement sensor used in the servo control system of CNC machine tools. It is one of the key components affecting the machining accuracy of CNC machine tools. Due to the long life-time of grating ruler, and it will cost a lot of time and resources to evaluate its reliability level by traditional life test. At the same time, there are some incomplete data in the failure data, which will cause inaccurate evaluation results. In this paper, an accelerated life reliability evaluation method of grating ruler based on competing risk model and incomplete data is proposed. Firstly, according to the characteristics of grating ruler, the life distribution model based on competitive risk is established, and the representation method and conversion method of failure data considering incomplete data are proposed. Secondly, the accelerated life test system which can apply temperature and humidity accelerated stress is built, and the reliability level of JFT series closed absolute grating ruler is evaluated by the proposed method. Finally, the proposed method is compared with the single life distribution model to verify the effectiveness.
Learning dynamics by computational integration of single cell genomic and lineage information
Authors: Wang Shou-Wen , Klein Allon
Published: May 2021

A goal of single cell genome-wide profiling is to reconstruct dynamic transitions during cell differentiation, disease onset, and drug response. Single cell assays have recently been integrated with lineage tracing, a set of methods that identify cells of common ancestry to establish bona fide dynamic relationships between cell states. These integrated methods have revealed unappreciated cell dynamics, but their analysis faces recurrent challenges arising from noisy, dispersed lineage data. Here, we develop coherent, sparse optimization (CoSpar) as a robust computational approach to infer cell dynamics from single-cell genomics integrated with lineage tracing. CoSpar is robust to severe down-sampling and dispersion of lineage data, which enables simpler, lower-cost experimental designs and requires less calibration. In datasets representing hematopoiesis, reprogramming, and directed differentiation, CoSpar identifies fate biases not previously detected, predicting transcription factors and receptors implicated in fate choice. Documentation and detailed examples for common experimental designs are available at https://cospar.readthedocs.io/.
Short-term effect of PM 2.5 and O3 on non-accidental mortality and respiratory mortality in Lishui District , China
Authors: Chen Yuqi , Jiao Zhigang , Chen Ping , Fan Lijun , Zhou XuDan , Pu Yuepu , Du Wei , Yin Lihong
Published: May 2021

Background

In recent years, air pollution has become an imminent problem in China. Few studies have investigated the impact of air pollution on the mortality of middle-aged and elderly people. Therefore, this study aims to evaluate the impact of PM2.5 and O3 on non-accidental mortality and respiratory mortality of the middle-aged and elderly in Lishui district of China and provide the scientific basis for the prevention and control measures of air pollution.
Method:

Using daily mortality and atmospheric monitoring data from 2015 to 2019, we applied a generalized additive model with time-series analysis to study the association of PM2.5 and O3 exposure with daily non-accidental mortality and respiratory mortality in Lishui district of China. Using attributable risk to estimate the death burden attributable to short-term exposure to O3 and PM2.5。
Result

PM2.5 and O3 were associated with non-accidental and respiratory mortality. For every 10µg/m3 increased in PM2.5, non-accidental mortality increased 0.94% (95%CI: 0.05%-1.83%), and PM2.5 had a more significant impact on women. For every 10µg/m3 increased in O3, respiratory mortality increased 1.35% (95%CI: 0.05%-2.66%). and O3 had a more significant impact on men. Compared with single pollutant model, the impact of the two-pollutant model on non-accidental mortality and respiratory mortality slightly decreased. Besides, in summer and winter, O3 had a more obvious impact on non-accidental mortality. The Population Attributable Fractions of non-accidental mortality were 0.839% (95%CI:0.004–1.626%) for PM2.5 and the PAF of respiratory mortality were 0.135% (95%CI:0.005–0.263%) for O3.
Conclusion

PM2.5 and O3 could significantly increase the risk of non-accidental and respiratory mortality in middle-aged and elderly people in Lishui district, China. Exposing to air pollutants, men were more susceptible to O3 damage, and women were more susceptible to PM2.5 damage.
CircTUBGCP3 facilitates the tumorigenesis of lung adenocarcinoma by sponging miR-885-3p
Authors: Yang Yang , Fan Xin , Nie Yunfei , Liu Donglei , Zhu Dengyan , Wu Kai , Zhang Yuan , Li Wenhua , Tian Xiangyu , Wang Huaqi , Fan Yuxia
Published: May 2021

Background: Circular RNAs (circRNAs) act pivotal roles in the progression of multiple malignancies. However, the underlying mechanisms by which hsa_circ_0007031 (circTUBGCP3) contributes to lung adenocarcinoma (LAC) remain largely unknown.Methods: The association of circTUBGCP3 expression with clinicopathological characteristics and prognosis in patients with LAC was determined by RT-qPCR and fluorescence in situ hybridization. The in vitro functional experiments as well as a subcutaneous tumorigenesis model were executed to estimate the role of circTUBGCP3 in LAC cells. The interaction between circTUBGCP3 and miR-885-3p was confirmed by RNA immunoprecipitation, luciferase gene report and RT-qPCR assays. The effects of circTUBGCP3 on miR-885-3p-mediated Wnt10b/β-catenin signaling were evaluated by Western blot. Results: The upregulation of circTUBGCP3 or downregulation of miR-885-3p was associated with the pathological stage and poor survival in patients with LAC. Restored expression of circTUBGCP3 facilitated the growth and invasion of LAC cells, but knockdown of circTUBGCP3 harbored the opposite effects. In mechanism, circTUBGCP3 could act as a sponge of miR-885-3p, which suppressed the cell proliferation and colony formation and attenuated the tumor-promoting effects of circTUBGCP3. Wnt10b as a target of miR-885-3p could be upregulated be circTUBGCP3 and indicate poor survival in patient with LAC. Conclusions: Our findings demonstrated that circTUBGCP3 promoted LAC progression by sponging miR-885-3p, and might represent a prognostic factor for LAC.
Shaping Ability of Three Nickel-Titanium Rotary Instruments in Simulated L-Shaped Canals: Oneshape, Hero Shaper, and Revo-S
Authors: Vakili-Gilani Pooyan , Tavanafar Saeid , Saleh Abdulrahman Mohammad
Published: May 2021

Background
This study aimed to compare the shaping ability of OneShape, Hero Shaper, and Revo-S instruments in simulated L-shaped canals.
Methods
forty-eight simulated L-shaped canals were prepared to an apical size of 25 using OneShape, Hero Shaper, and Revo-S (all from Micro-Mega SA, Besançon, France), (n = 16 canals/group) systems. The amount of resin removed after each canal's preparation was measured and compared after producing a composite image made from the superimposition of pre and post-instrumented canals. Canal aberrations and the preparation time were also recorded. The data were statistically analyzed by using ANOVA, Tukey, and Chi-square tests.
Results
One file fractured during instrumentation in Revo-S group. A significant difference was found at the apical end of the prepared simulated canal between the groups, with Revo-S showing the least amount of resin removal from the inner side of the canals and Hero Shaper showing the highest amount of resin removal from the outer side (P < 0.05). Regarding the total width of the canals after preparation, a significant difference was found between the groups at the apical end and the straight portion of the canals, and Revo-S removed the least amount of resin at the straight portion of the canals (P < 0.05). No statistically significant differences were found between the different instruments regarding canal aberrations' incidence (P > 0.05).
Conclusions
all of the files showed a tendency to straighten the canals, whereas OneShape files maintained the original canal curvatures well.