bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Overall Survival for Early-stage Non-small Cell Lung Cancer via a Novel 7-gene Prognostic Signature and Allele Frequency Deviation (AFD)
Authors: AL-Dherasi Aisha , Liao Yuwei , Huang Qi-Tian , Wang Yichen , Hua Rulin , Mosiab Sultan AL , Zhang Jingkai , Yu Ying , Zhang Yu , Zhang Xuehong , Huang Chao , Sufiyan Sufiyan , Ge Dongcen , Bai Wanting , Liu Ruimei , Shao Yanyan , Li Yulong , Mousa Haithm , Shi Leming , Lv Dekang , Li Zhiguang , Liu Quentin 
Published: September 2020

Abstract
Background Due to the late and poor prognosis of non-small lung cancer(NSCLC), the mortality of patients is high, underlines the need to identify a credible prognostic marker for NSCLC patients. The aim of our study is to examine the association of allele frequency deviation (AFD) with the patient's survival, as well as identification and validation of a new prognostic signature to predict NSCLC overall survival(OS).Methods First, we developed a new algorithm to calculate AFD from whole-exome sequencing(WES) data, then we compared the predictability of the patient's survival between AFD, tumor mutation burden (TMB) and change of variants allele frequency (dVAF). Second, we overlapped the differentially expressed genes (DEGs) from our data with the genes associated with the survival of The Cancer Genome Atlas (TCGA) database to confirm all genes significantly related to the survival of lung cancer. We identified 149 genes, 31 of which are new genes and have not been reported for lung cancer, that was used to develop a new prognostic model. Lung cancer adenocarcinoma (LUAD) data from the TCGA database was used to validate the gene-signature model. The prognostic model relating to the genes was established and validated in training and LUAD validation groups.Results There was a significant association found between the high AFD value and poor survival among non-small cell lung cancer (NSCLC) patients. A novel seven genes (UCN2, RIMS2, CAVIN2, GRIA1, PKHD1L1, PGM5, CLIC6) were obtained through multivariate Cox regression analysis and significantly associated with NSCLC patients survival. Cox regression analysis confirmed that AFD and 7-gene signature are an independent prognostic marker in NSCLC patients. The AUC for 5-year survival in AFD and the AUC for 3-year survival in both training and validation groups were greater than 0.7.Conclusion As a result, AFD and 7-gene signatures were identified as new independent predictive factors used for predicting the survival among NSCLC patients.
Phages from Ganges River curtail in vitro biofilms and planktonic growth of drug resistant Klebsiella pneumoniae in a zebrafish infection model
Authors: Sundaramoor Niranjana Sri , Thothathri Subramanian , Bhaskaran Muthu Meenakshi , GaneshPrasad ArunKumar , Nagarajan Saisubramanian 
Published: September 2020

Abstract
Bacteriophages are a promising alternative for curtailing infections caused by multi drug resistant (MDR) bacteria. The objective of the present study is to evaluate phage populations from water bodies to inhibit planktonic and biofilm mode of growth of drug resistant Klebsiella pneumoniae in vitro and curtail planktonic growth in vivo in a zebrafish model. Phage specific to K. pneumoniae (MTCC 432) was isolated from Ganges river (designated as KpG). One-step growth curve, in vitro time kill curve study and in vivo infection model were performed to evaluate the efficacy of phage against planktonic growth. Crystal violet assay and colony biofilm assay was done to determine the action of phages on biofilms. KpG phages had a greater burst size, better bactericidal potential and enhanced inhibitory effect against biofilms formed at liquid air and solid air interfaces. In vivo injection of KpG phages revealed that it did not pose any toxicity to zebrafish as evidenced by liver/brain enzyme profiles and by histopathological analysis. In vitro time kill assay showed a 3 log decline and a 6 log decline in K. pneumoniae colony counts, when phages were administered individually and in combination with streptomycin, respectively. The muscle tissue of zebrafish, infected with K. pneumoniae and treated with KpG phages showed a significant 2 log decline in bacterial counts relative to untreated control. Our study reveals that KpG phages has the potential to curtail plantonic and biofilm mode of growth in vivo in higher animal models.
Cost-effectiveness analysis of initial nonoperative management versus emergency laparoscopic appendectomy for acute complicated appendicitis
Authors: Sugiura Kiyoaki , Suzuki Keiichi , Umeyama Tomoshige , Omagari Kenshi , Hashimoto Takeo , Tamura Akihiko 
Published: September 2020

Abstract
Background
Although evidence regarding the safety and efficacy of nonoperative management is growing, the best treatment strategy for acute complicated appendicitis remains controversial. We aimed to evaluate the cost-effectiveness of treatment strategies in complicated appendicitis patients. This study sought to determine the most cost-effectiveness strategy from the health care-payer's perspective
Methods
The primary outcome was an incremental cost effectiveness ratio (ICER) using nonoperative management with or without interval laparoscopic appendectomy (ILA) as the intervention compared with operative management with emergency laparoscopic appendectomy (ELA) alone as the control. Model variables were abstracted from a literature review, and from data from the hospital records of Tochigi Medical Center. Cost-effectiveness was evaluated using an ICER. We constructed a Markov model to compare treatment strategies for complicated appendicitis in otherwise-healthy adults, over a time horizon of a single year. Uncertainty surrounding model parameters was assessed via one-way- and probabilistic-sensitivity analyses. Threshold analysis was performed using the willingness-to-pay threshold set at the World Health Organization's criterion of $107,690.
Results
Three meta-analysis were included in our analysis. Operative management cost $6,075 per patient. Nonoperative management with interval laparoscopic appendectomy (ILA) cost $984 more than operative management and produced only 0.005 more QALYs, resulting in an ICER of $182,587. Nonoperative management without ILA cost $235 more than operative management, and also yielded only 0.005 additional QALYs resulting in an ICER of $45,123 per QALY. Probabilistic sensitivity analysis with 1,000 draws resulted in average ICER of $172,992 in nonoperative management with ILA and $462,843 in Nonoperative management without ILA. The threshold analysis demonstrated that regardless of willingness-to-pay, nonoperative management without ILA would not be most cost-effective strategy
Conclusions
Nonoperative management with ILA and Nonoperative management without ILA were not cost-effective strategies compared with operative management to treat complicated appendicitis. Based on our findings, operative management remains the standard of care and nonoperative management would be reconsidered as a treatment option in complicated appendicitis from economic perspective.
Low-Grade Endometrial Stromal Sarcoma with Intravenous and Intracardiac Extension: A Case Report
Authors: Chai Xiaoshan , Ding Hui , Zhou Peng , Mei Xilong , Li XiaoXue , Tao Guangshi 
Published: September 2020

Abstract
Background: Low-grade endometrial stromal sarcoma (ESS) is rare mesenchymal neoplasm, which has an indolent history with late recurrences. ESS usually spread through the lymph nodes and venous system but very seldom involve large vessels or the heart.Case presentation: A 38-year-old Chinese woman was admitted to our department due to pelvic mass found on physical examination. The superior and inferior vena cava CT angiography (CTA) showed an enlarged uterine as well as low density image in the left internal iliac vein, the left common iliac vein, the inferior vena cava, the left renal vein adjacent to the heart and the right atrium, with a range of 110*16mm. The filling defect of right atrium was about 30*14mm. The three-dimensional computed tomography reconstruction showed that the mass originated from the uterine and invaded into the reproductive vein, subsequently extended along the inferior vena cava to the right atrium. Needle biopsy of the pelvic mass was performed and the tissue indicates smooth muscle. The preoperative diagnosis was intravascular leiomyomatosis and the patient underwent radical resection: thrombectomy and total hysterectomy with bilateral salpingo-oophorectomy. Postoperative histopathology revealed low grade endometrial stromal sarcoma. Microscopically, the tumors in both original uterine lesions and intravascular and intracardiac metastases shared morphologic features characterized by neoplastic cells similar to proliferative-phase endometrial stromal cells, in which small spiral artery differentiation was recognized and tumor tissue showed invasive growth pattern by inserting into the surrounding smooth muscle. Immunohistochemistry showed tumor cells were reactive to Estrogen Receptor, Progesterone Receptor,CD10. Primary uterine foci showed cyclin D1(5%+) and Ki-67(20%+),whereas metastatic lesions of the intracardiac and the intravascular component identified cyclin D1(negative) and Ki-67(2%+). The patient is alive without evidence of recurrence 3 months after surgery.Conclusions: Distant metastasis of low-grade endometrial stromal sarcoma is rare, especially involving large vessels or the heart. This case demonstrates that malignant tumor metastasis should be considered as a differential diagnosis of intracardiac and intravascular masses. The treatment rely on multidisciplinary cooperation.
Local Community Knowledge and Perceptions towards Amphibians in Urban and Rural Settings: Tools for Biological Conservation
Authors: Vergara-Ríos Danny , Montes-Correa Andrés Camilo , Urbina-Cardona J. Nicolás , De Luque-Villa Miguel Antonio , Cattan Pedro E. , Granda Hernan Dario 
Published: September 2020

Abstract
Background Human perceptions determine the degree to which people can coexist with biodiversity. It is, therefore, important to identify the sociodemographic factors that determine these local perceptions to adjust amphibian conservation strategies. In this research, the effect of the urban or rural location where people live, as well as their gender, age and educational level, concerning the knowledge and perceptions about amphibians was determined.Methods The data were collected through individual semi-structured surveys, which sought to evaluate changes in the perceptions, of 401 participants, about amphibians. We measured seven response variables through the Likert scale, which ranges from 1 (totally disagree) to 5 (totally agree): composition of taxonomic groups, number of known taxonomic groups, species composition of anurans, number of species of anurans, level of importance of amphibians in nature, positive perceptions about amphibians and negative beliefs about amphibians. For each response variable, a Bray-Curtis matrix was generated and multivariate analysis of variance (PERMANOVA).Results Ninety-two percent of people correctly recognized frogs and toads as amphibians, but there was confusion in classifying caecilians and salamanders within this group, or including reptiles (lizards, turtles and snakes) within the group of amphibians. This confusion was more evident for women from urban locality. No one recognized the five native species shown in the study, although the inhabitants of the rural locality recognized more species than those of the urban locality. Positive perceptions of amphibians varied between urban and rural locality for young adults, people with a high school education level, and people without formal education. Negative beliefs varied between urban and rural locations for women, adolescents, young adults, and professionals with undergraduate studies. Half of the people accepted information on the conservation of amphibians.Conclusion Positive perceptions of people about amphibians should be used as a flag to strengthen environmental educational strategies that seek to change negative attitudes about this group. Field activities are crucial to consolidating the positive perceptions of people about amphibians, mainly in urban locations. The results suggest that amphibian conservation plans that aim to inform and educate the public should be focused differently for age groups, genders, and educational level for people in urban and rural locations.
Efficient Isolation of Protoplasts from Rice Calli With Pause Points and its Application in Transient Gene Expression and Genome Editing Assays
Authors: Poddar Snigdha , Tanaka Jaclyn , Cate Jamie H. D. , Staskawicz Brian , Cho Myeong-Je 
Published: September 2020

Abstract
Background: An efficient in vivo transient transfection system using protoplasts is an important tool to study gene expression, metabolic pathways, and multiple mutagenesis parameters in plants. Although rice protoplasts can be isolated from germinated seedlings or cell suspension culture, preparation of those donor tissues can be inefficient, time consuming, and laborious. Additionally, the lengthy process of protoplast isolation and transfection needs to be completed in a single day. Results: Here we report a protocol for isolation of protoplasts directly from rice calli, without using seedlings or suspension culture. The method is developed to employ discretionary pause points during protoplast isolation and prior to transfection. Protoplasts maintained within a sucrose cushion partway through isolation, for completion on a subsequent day, per the first pause point, are referred to as S protoplasts. Fully isolated protoplasts maintained in MMG solution for transfection on a subsequent day, per the second pause point, are referred to as M protoplasts. Both S and M protoplasts, 1 day after initiation of protoplast isolation, had minimal loss of viability and transfection efficiency compared to protoplasts 0 days after isolation. S protoplast viability decreases at a lower rate over time than that of M protoplasts and can be used with added flexibility for transient transfection assays and time-course experiments. The protoplasts produced by this method are competent for transfection of both plasmids and ribonucleoproteins (RNPs). Cas9 RNPs were used to demonstrate the utility of these protoplasts to assay genome editing in vivo. Conclusion: The current study describes a highly effective and accessible method to isolate protoplasts from callus tissue induced from rice seeds. This method utilizes donor materials that are resource-efficient and easy to propagate, permits convenience via pause points, and allows for flexible transfection days after protoplast isolation. It provides an advantageous and useful platform for a variety of in vivo transient transfection studies in rice.
Senescent Accelerated Prone 8 (SAMP8) Mice as A Model of Age Dependent Neuroinflammation
Authors: Fernández Andrés , Quintana Elena , Velasco Patricia , de Andrés Belén , Gaspar Maria Luisa , Liste Isabel , Vilar Marcal , Mira Helena , Cano Eva 
Published: September 2020

Abstract
Background: Aging and age related diseases are strong risk factors for the development of neurodegenerative diseases. Neuroinflammation (NIF), as the brain's immune response, plays an important role in aged associated degeneration of central nervous system (CNS). The need of animal models that will allow us to understand and modulate this process is required for the scientific community. Methods: We have analyzed aging-phenotypical and inflammatory changes of brain myeloid cells (bMyC) in a senescent accelerated prone aged (SAMP8) mouse model, and compared with their resistant to senescence control (SAMR1). We have performed morphometric methods to evaluate the architecture of cellular prolongations and analyzed Iba1+ clustered cells with aging. To analyse specific constant brain areas we have performed stereology measurements of Iba1+ cells in the hippocampal formation. We have isolated bMyC from brain parenchyma (BP) and choroid plexus and meningeal membranes (m/Ch), and analyzed their response to systemic LPS- driven inflammation.Results: Aged 10 month old SAMP8 mice presents many of the hallmarks of aging-dependent neuroinflammation when compared with their senescence resistant control (SAMR1); ie, increase of protein aggregates, presence of Iba1+ clusters, but not increase in the number of Iba1+ cells. We have further observed and increased of main inflammatory mediator IL-1β, and augment of border MHCII+Iba1+ cells. Isolated CD45+ bMyC from brain parenchyma (BP) and choroid plexus and meningeal membranes (m/Ch) have been analyzed showing that there is not significant increase of CD45+ from the periphery. Our data support that aged-driven pro-inflammatory cytokine interleukin 1 beta (IL1β) transcription is mainly enhanced in CD45+BP cells. Furthermore, we are showing that LPS-driven systemic inflammation produces inflammatory cytokines mainly in the border bMyC, sensed to a lesser extent by the BP bMyC, and is enhanced in aged SAMP8 compared to control SAMR1.Conclusion: Our data validate the SAMP8 model to study age-associated neuroinflammatory events, but careful controls for age and strain are required. These animals show morphological changes in their bMyC cell repertoires associated to age, corresponding to an increase in the production of main pro inflammatory cytokines such as IL-1β, which predispose the brain to an enhanced inflammatory response after LPS-systemic challenge.
A Cost Analysis to Address Issues of Budget Constraints on the Implementation of the Indoor Residual Spray Program in Two Districts of Maputo Province, Mozambique
Authors: Canana Neide 
Published: September 2020

Abstract
Background : Over the past few years, the capacity of the government of Mozambique to sustain the operational cost of Indoor Residual Spraying (IRS) is facing numerous challenges due to restrictions of the Official Development Assistance (ODA), an external aid scheme of financing from the Mozambican government budget. Objectives: The objective of the study was to estimate the cost of IRS operationalization in two districts of Maputo Province (Matutuíne and Namaacha) in Mozambique, in 2014. Methods: The cost analysis followed an “ingredients based” approach from the provider perspective. The cost information was collected retrospectively, and both economic and financial costs were calculated. Results were tested using a “one-way” deterministic sensitivity analysis. Results : From the economic analysis, Matutuíne and Namaacha on average totaled an annual economic cost of US$117,351.34, with an average economic cost per household sprayed of US$16.35, and an average economic cost per person protected of US$4.09. In the financial analysis, both districts faced an average total annual financial cost of US$69,174.83, an average financial cost per household sprayed and per person protected of US$9.84 and US$2.46, respectively. Our findings indicate that vehicles, personnel salaries, and IRS consumables were components with a substantial cost for IRS operationalization. Conclusions : For our results, with resource constraints, it is important to focus on operationalizing IRS within the available budget by respecting the right timing for scheduled IRS spraying rounds and by paying attention to cost drivers in order to reduce the costs.
Systematic Comparison of High-Throughput Single-Cell RNAseq Methods for Immune Cell Profiling
Authors: Li Chi-Ming Kevin , Yamawaki Tracy M , Lu Daniel R , Ellwanger Daniel C , Bhatt Dev , Manzanillo Paolo , Zhou Hong , Yoon Oh-Kyu , Homann Oliver , Wang Songli 
Published: September 2020

Abstract
Background: Elucidation of immune populations with single-cell RNA-seq has greatly benefited the fieldof immunology by deepening the characterization of immune heterogeneity and leading to thediscovery of new subtypes. However, single-cell methods inherently suffer from limitations in therecovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropoutevents. This issue is often compounded by limited sample availability and limited prior knowledge ofheterogeneity, which can confound data interpretation.Results: Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. Weprepared 21 libraries under identical conditions of a defined mixture of two human and two murinelymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluatemethods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expressionsignatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5’v1 and 3’ v3 methods. We demonstrate that these methods have fewer drop-out events whichfacilitates the identification of differentially-expressed genes and improves the concordance of singlecellprofiles to immune bulk RNA-seq signatures.Conclusion: Overall, our characterization of immune cell mixtures provides useful metrics, which canguide selection of a high-throughput single-cell RNA-seq method for profiling more complex immunecellheterogeneity usually found in vivo.
Significance between Air pollutants, Meteorological Factors and COVID-19 Infections: Probable Evidences in India
Authors: Sahoo Mrunmayee M 
Published: September 2020

Abstract
SARS-CoV-2 (Coronavirus) disease represents the causative agent with a potentially fatal risk which is having great global human health concern. Earlier studies suggested that air pollutants and meteorological factors were considered as the risk factors for acute respiratory infection, which carries harmful pathogens and affects the immunity. The study intended to explore the correlation between air pollutants, meteorological factors and the daily reported infection cases caused by novel coronavirus in India. The daily positive infected cases, air pollution and meteorological factors in 288 districts were collected from January 30, 2020 to April 23, 2020 in India. Speraman’s correlation and generalised additive model were applied to investigate the correlations of four air pollutants (PM2.5, PM10, NO2 and SO2) and eight meteorological factors (Temp, DTR, RH, AH, AP, RF, WS and WD) with COVID-19 infected cases. The study indicated that a 10 µg/m3 increase during (Lag0-14) in PM2.5, PM10 and NO2 was resulted in 2.21% (95%CI: 1.13 to 3.29), 2.67% (95% CI: 0.33 to 5.01) and 4.56 (95% CI: 2.22 to 6.90) increase in daily counts of COVID 19 infected cases respectively. However, only 1 unit increase in meteorological factor levels in case of daily mean temperature and DTR during (Lag0-14) associated with 3.78% (95%CI: 1.81 to 5.75) and 1.82% (95% CI: -1.74 to 5.38) rise of COVID-19 infected cases respectively. In addition, SO2 and relative humidity were negatively associated with COVID-19 infected cases at Lag0-14 with decrease of 7.23% (95% CI: -10.99 to -3.47) and 1.11% (95% CI: -3.45 to 1.23) for SO2 and for relative humidity respectively. The study recommended that there is significant relationship between air pollutants and meteorological factors with COVID-19 infected cases, which substantially explain the effect of national lockdown and suggested positive implications for control and prevention of the spread of SARS-CoV-2 disease.