bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of amphibian SLC26A5 using RNA-Seq
Authors: Wang Zhongying , Wang Qixuan , Wu Hao , Huang Zhiwu 
Published: December 2020

Abstract
Background
Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Due to lacking of the 3D structure, most of the mechanism of prestin is from experiments using site-directed mutagenesis or domain-swapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs. Frog prestin is the only representative in amphibian lineage. The knowledge of frog SLC26A5 is quite limited with only one species has been identified.
Results
Here we report a new coding sequence of SLC26A5 for a frog species, the American bullfrog (Rana catesbeiana). In our study, the SLC26A5 gene of bullfrog has been mapped, sequenced and cloned successively using RNA-SEq. The comparative study revealed an alignment with nearly 40% identity among bullfrogs and mammalian species. The predicted 3D protein structure showed that the frog prestin possessed a transmembrane domain (TM) and a STAS domain similar to the mammalian prestin. The function of prestin crucially relies on its integration into the cell membrane. Such localization was observed when a prestin-EGFP fusion protein was expressed in HEK293T cells. We measured the nonlinear capacitance (NLC) of prestin both in the hair cells of frog’s inner ear and HEK293T cells transfected with this new coding gene. We observed that HEK293T cells expressing frog prestin showed electrophysiological features similar to that of hair cells from the amphibian’s inner ear.
Conclusions
We mapped and sequenced the SLC26A5 of the American bullfrog from its inner ear cDNA using RNA-SEq. The frog SLC26A5 cDNA was 2,292 bp long, encoding a polypeptide of 763 amino acid residues, with 40% identity to mammals. After isolating the prestin gene of the frog, we generated a stable cell line transfected with this new coding gene and found it possessing similar electrophysiological features as the hair cells from the frog’s auditory organ. Our experiment demonstrated that the new coding gene could encode a functionally active protein conferring NLC to both frog HCs and the mammalian cell line.
Predictors for oral and general health outcomes and quality of life among older people attending general practice (GP) clinics in South Australia
Authors: Balasubramanian Madhan , Keuskamp Dominic , Amarasena Najith , Brennan David 
Published: December 2020

Abstract
Background: As the proportion and number of older people in Australia continue to grow, innovative means to tackle primary care and prevention are necessary to combat the individual, social and economic challenges of non-communicable diseases.Objective: To assess risk factors (or predictors) for oral and general health outcomes and quality of life of older people (75+ yrs.) attending general practice (GP) clinics in South Australia.Methods: Data were collected from older people attending 48 GP clinics in metropolitan South Australia. Age, sex, education, living arrangement, material standards, chronic conditions and nutrition were assessed as risk factors. Global self-rated oral and general health and quality of life (OHIP Severity and EQ-5D Utility) were included as outcome measures.Results: A total of 459 participants completed the study; response rate was 78%. In the adjusted models, high satisfaction with material standards and good nutritional health were positively associated with all four oral and general health measures. Sex (β=-0.07), age (β=-0.09) and number of chronic conditions (β=-0.13) were negatively associated with EQ-5D, while living arrangement (β=0.06) was positively associated. Further, education level (PR:0.78), living arrangement (PR:0.75) and chronic conditions (PR:1.54) were significantly associated with self-rated general health.Conclusion: Satisfaction with material standards and nutritional risk were consistent predictors for oral and general health outcomes and quality of life of older people visiting GP clinics. Primary care teams involving general practitioners, nurses and allied health practitioners are well poised to assess risk factors for older people, and work alongside the dental team.
In Vitro: Natural Compounds (Thymol, Carvacrol, Hesperidine, And Thymoquinone) Against Sars-Cov2 Strain Isolated From Egyptian Patients
Authors: Seadawy Mohamed G , Gad Ahmed F. , Shamel Mohamed , Elharty Bassem , Mohamed Mostfa F. , Elfiky Abdo A. , Ahmed Aya , Zekri Abdel Rahman N. 
Published: December 2020

Abstract
Background: The current pandemic of the coronavirus disease-2019 (COVID-19) has badly affected our life during the year 2020. SARS-CoV-2 is the primary causative agent of the newly emerged pandemic. Natural flavonoids, Terpenoid and Thymoquinone are tested against different viral and host-cell protein targets. These natural compounds have a good history in treating Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV). Methods: Molecular docking combined with cytotoxicity and plaque reduction assay is used to test the natural compounds against different viral (Spike, RdRp, and Mpro) and host-cell (TMPRSS II, keap 1, and ACE2) targets. Results: The results demonstrate the binding possibility of the natural compounds (Thymol, Carvacrol, Hesperidine, and Thymoquinone) to the viral main protease (Mpro). Some of these natural compounds were approved to start clinical trail from Egypt Center for Research and Regenerative Medicine ECRRM IRB (Certificate No.IRB00012517)Conclusion: Development of an effective anti-viral for SARS-CoV-2 could help to limit the viral load. Benchmarking testing of those natural compounds against other potential antivirals for SARS-CoV-2 with alternative mechanisms of action would thus be important as soon as practicable.
Association between social trust and the risk of cardiovascular disease in older adults in Korea: a nationwide retrospective cohort study
Authors: Hwang Seo Eun , Choi Seulggie , Kim Kyuwoong , Lee Jong-Koo , Oh Juhwan , Park Sang Min 
Published: December 2020

Abstract
Background: Although social capital has been shown to be one of the important social determinants of health, the association between social trust and the risk of cardiovascular disease (CVD) is not clear yet. We aimed to investigate the association of social trust with CVD risk using a large Korean population based data.Methods: The data of this study was derived from the Korean National Health Insurance Service database. Community-level social trust was determined from the Korean Community Health Survey. The study population consisted of 2,156,829 participants. According to social trust index measured in the area of residence during 2011, participants were followed-up from 1 January 2012 to 31 December 2016. Multivariate Cox proportional hazards regression was used to determine the adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for CVD risk according to quintiles of social trust.Results: Compared to participants with the lowest quintile of social trust, those within the highest quintile had lower risk for CVD (aHR 0.91, 95% CI=0.89 to 0.93), CHD (aHR 0.92, 95% CI=0.89 to 0.95), and stroke (aHR 0.90, 95% CI=0.87 to 0.93). The risk-reducing association of high social trust on CVD risk was preserved after additional adjustments for lifestyle behaviors including smoking, alcohol consumption, and physical activity.Conclusion: Higher social trust was associated with reduced risk of CVD even after considering lifestyle behaviors. Social trust in a community level is an important determinant of CVD and enhancing social trust may lead to reduced risk of CVD.
Induction of autophagy mitigates TDP-43 pathology and translational repression of neurofilament mRNAs in mouse models of ALS/FTD&nbsp;
Authors: Kumar Sunny , Phaneuf Daniel , Cordeau Pierre , Boutej Hejer , Kriz Jasna , Julien Jean-Pierre 
Published: December 2020

Abstract
Background:TDP-43 proteinopathy is a pathological hallmark of many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). So far, there is no therapy available for these neurodegenerative diseases. In addition, the impact of TDP-43 proteinopathy on neuronal translational profile also remains unknown. Methods:Biochemical, immunohistology and assay-based studies were done with cell cultures and transgenic mice models. We also used Ribotag with microarray and proteomic analysis to determine the neuronal translational profile in the mice model of ALS/FTD.Results:Here, we report that oral administration of a novel analog (IMS-088) of withaferin-A, an antagonist of nuclear factor kappa-B (NF-ĸB) essential modulator (NEMO), induced autophagy and reduced TDP-43 proteinopathy in the brain and spinal cord of transgenic mice expressing human TDP-43 mutants, models of ALS/FTD. Treatment with IMS-088 ameliorated cognitive impairment, reduced gliosis in the brain of ALS/FTD mouse models. With the Ribotrap method, we investigated the impact of TDP-43 proteinopathy and IMS-088 treatment on the translation profile of neurons of one-year old hTDP-43A315T mice. TDP-43 proteinopathy caused translational dysregulation of specific mRNAs including translational suppression of neurofilament mRNAs resulting in 3 to 4-fold decrease in levels type IV neurofilament proteins. Oral administration of IMS-088 rescued the translational defects associated with TDP-43 proteinopathy and restored the synthesis of neurofilament proteins, which are essential for axon integrity and synaptic function. Conclusions:Our study revealed that induction of autophagy reduces TDP-43 pathology and ameliorates the translational defect seen in mice models of ALS/FTD. Based on these results, we suggest IMS-088 and perhaps other inducers of autophagy should be considered as potential therapeutics for neurodegenerative disorders with TDP-43 proteinopathies.
A tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda (Ailurus fulgens) and the Giant Panda (Ailuropoda melanoleuca)&nbsp;
Authors: Cserhati Matyas 
Published: December 2020

Abstract
Background: The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results: A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids as well as A. fulgens were also aligned to draw further phylogenetic inferences. The results from the whole genome study show that A. fulgens is a member of the mustelid clade (p = 9·10-97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10-62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study based on the sequence identity matrix seem to place A. fulgens into its own group.Conclusions: The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. The mitochondrial results could be due to differing mutational pressures compared to the nucleus. It cannot be said for sure, but it is likely that A. fulgens belongs to the mustelid clade.
The Herbst appliance and its modifications - prevalence and individuality
Authors: Karbach Mareike , Zöller Claudia , Zöller Georg , Wehrbein Heinrich , Erbe Christina 
Published: December 2020

Abstract
Objective: The aim of this study was to analyze the use of modified, cast splint Herbst appliances for the treatment of skeletal class II and as an alternative to surgical bite correction over a period of five years. Materials and methods: The patient cases all originate from the patients of the Department of Orthodontics at the University Medical Center of the Johannes Gutenberg University Mainz, Germany and the orthodontic practice Dres. Zöller, Kaiserslautern, Germany. Inclusion criteria were orthodontic treatment with the Herbst appliance and its modifications. The type of modification, number and frequency of the different modifications were determined on the basis of patient files, X-ray documents, photos and models. Results: Of a total of 2881 new admissions over a period of five years, 1751 patients came from the Department of Orthodontics at the University Medical Center of the Johannes Gutenberg University Mainz and 1130 from the orthodontic practice in Kaiserslautern. A total of 336 patients were treated with a Herbst appliance during the period mentioned. 14 (13 %) of the cases from the Herbst patient collective of the University Medical Center and 45 (19 %) of the cases from the orthodontic practice were classified as modifications. The following modifications could be determined in descending order: University Medical Center Mainz: Herbst for anchorage during space closure (65 %) > distalization (14 %) ≥ bar construction as a space maintainer (14 %) > Herbst applicance for anchoring for the adjustment of impacted teeth (7 %); orthodontic practice Kaiserslautern: Herbst appliance with quadhelix in the maxilla (42 %) > distalization (27 %) > space closure (15 %) > bar construction as a space maintainer (9 %) > adjustment of impacted teeth (7 %), multiple modifications occurred at 11 %. The combination of quadhelix and Herbst appliance as well as multiple modifications have not yet been used in the University Medical Center Mainz. As an alternative to dysgnathia surgery, 23 adult patients (> 18 years) from the University Medical Center and 22 from the orthodontic practice were treated with a Herbst appliance. Conclusion: Nearly 12 % of Herbst appliances are used in everyday orthodontic practice and almost 18 % of these are used with modification(s). The high anchoring quality and force-effect geometry of the Herbst appliance is suitable for combining and treating various other treatment tasks in addition to the classical treatment task of class II therapy.
Fast deep learning computer-aided diagnosis of COVID-19 based on digital chest x-ray images
Authors: Al-antari Mugahed A. , Hua Cam-Hao , Lee Sungyoung , Bang Jaehun 
Published: December 2020

Abstract
Coronavirus disease 2019 (COVID-19) is a novel harmful respiratory disease that has rapidly spread worldwide. At the end of 2019, COVID-19 emerged as a previously unknown respiratory disease in Wuhan, Hubei Province, China. The world health organization (WHO) declared the coronavirus outbreak a pandemic in the second week of March 2020. Simultaneous deep learning detection and classification of COVID-19 based on the full resolution of digital X-ray images is the key to efficiently assisting patients by enabling physicians to reach a fast and accurate diagnosis decision. In this paper, a simultaneous deep learning computer-aided diagnosis (CAD) system based on the YOLO predictor is proposed that can detect and diagnose COVID-19, differentiating it from eight other respiratory diseases: atelectasis, infiltration, pneumothorax, masses, effusion, pneumonia, cardiomegaly, and nodules. The proposed CAD system was assessed via five-fold tests for the multi-class prediction problem using two different databases of chest X-ray images: COVID-19 and ChestX-ray8. The proposed CAD system was trained with an annotated training set of 50,490 chest X-ray images. The regions on the entire X-ray images with lesions suspected of being due to COVID-19 were simultaneously detected and classified end-to-end via the proposed CAD predictor, achieving overall detection and classification accuracies of 96.31% and 97.40%, respectively. Most test images from patients with confirmed COVID-19 and other respiratory diseases were correctly predicted, achieving average intersection over union (IoU) greater than 90%. Applying deep learning regularizers of data balancing and augmentation improved the COVID-19 diagnostic performance by 6.64% and 12.17% in terms of the overall accuracy and the F1-score, respectively. It is feasible to achieve a diagnosis based on individual chest X-ray images with the proposed CAD system within 0.0093 s. Thus, the CAD system presented in this paper can make a prediction at the rate of 108 frames/s (FPS), which is close to real-time. The proposed deep learning CAD system can reliably differentiate COVID-19 from other respiratory diseases. The proposed deep learning model seems to be a reliable tool that can be used to practically assist health care systems, patients, and physicians.
gCAnno: a graph-based single cell type annotation method
Authors: Yang Xiaofei , Gao Shenghan , Wang Tingjie , Yang Boyu , Dang Ningxin , Ye Kai 
Published: December 2020

Abstract
BackgroundCurrent single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering outcome, often leading to incorrect cluster-level annotation or multiple runs of subsequent clustering steps. To address these limitations, methods based on well-annotated reference atlas has been proposed. However, these methods are currently not robust enough to handle datasets with different noise levels or from different platforms. ResultsHere, we present gCAnno, a graph-based Cell type Annotation method. First, gCAnno constructs cell type-gene bipartite graph and adopts graph embedding to obtain cell type specific genes. Then, naïve Bayes (gCAnno-Bayes) and SVM (gCAnno-SVM) classifiers are built for annotation. We compared the performance of gCAnno to other state-of-art methods on multiple single cell datasets, either with various noise levels or from different platforms. The results showed that gCAnno outperforms other state-of-art methods with higher accuracy and robustness. ConclusionsgCAnno is a robust and accurate cell type annotation tool for single cell RNA analysis. The source code of gCAnno is publicly available at https://github.com/xjtu-omics/gCAnno.
The Prevalence Rate of Sexual Violence Worldwide: A Trend Analysis
Authors: Borumandnia Nasrin , Khadembashi Naghmeh , Tabatabaei Mohammad , Majd Hamid Alavi 
Published: December 2020

Abstract
Background: The purpose of the present study is to showcase the image of Sexual Violence (SV) temporal trends through exploring differences in its prevalence rates during 1990-2017 across 195 countries and territories.Methods: The SV prevalence rates were derived from the Global Burden of Disease (GBD) database during 1990-2017, worldwide. First, the Latent Growth Model (LGM) was employed for assessing the change in SV prevalence rate over time in Asia, Africa, Europe, North America, South America, Australia & Oceania, for men and women separately. Then, the change in SV prevalence rate over time was determined within countries with high and low Human Development Index (HDI). Finally, the Latent Growth Mixture Models (LGMM) were applied for identifying classes where countries within each class have similar trend of SV prevalence rate over time.Results: The SV prevalence was higher among women than men and decreased in both genders over time across the world. The declining trend in SV prevalence against men is visible in both countries with high and low HDI, but SV prevalence against women in countries with low HDI shows an increase. The findings of LGMM identified six classes of SV prevalence trajectories. LGMM allocated Bermuda into the class with the highest decrease in SV prevalence against men, and Equatorial Guinea and Luxembourg into the class with the highest increase. Other countries had very slow declining trends. In terms of SV prevalence against women, LGMM allocated China, North Korea, and Taiwan into the class with the most increase among the countries in the world. Bermuda, Guyana, Mexico, Nigeria, and Saint Lucia were placed into the class which witnessed the largest decline and Angola, Congo, and Equatorial Guinea were ranked next. The trend in other countries was mostly decreasing.Conclusion: Given the high economic and social burden that SV has on victims and societies, the rate of SV in most countries does not seem to have dropped remarkably and requires special attention by relevant policymakers. The SV prevalence rate is highly heterogeneous among world countries which may be due to the definitions and tools used, and more importantly, the culture norms.
A Comprehensive Performance Analysis of Apache Hadoop and Apache Spark for Large Scale Data Sets Using HiBench
Authors: Ahmed Nasim , Barczak Andre L. C. , Susnjak Teo , Rashid Mohammad 
Published: December 2020

Abstract
Big Data analytics for storing, processing, and analyzing large-scale datasets has become an essential tool for the industry. The advent of distributed computing frameworks such as Hadoop and Spark oﬀers eﬃcient solutions to analyze vast amounts of data. Due to the application programming interface (API) availability and its performance, Spark becomes very popular, even more popular than the MapReduce framework. Both these frameworks have more than 150 parameters, and the combination of these parameters has a massive impact on cluster performance. The default system parameters help the system administrator deploy their system applications without much eﬀort, and they can measure their speciﬁc cluster performance with factory-set parameters. However, an open question remains: can new parameter selection improve cluster performance for large datasets? In this regard, this study investigates the most impacting parameters, under resource utilization, input splits, and shuﬄe, to compare the performance between Hadoop and Spark, using an implemented cluster in our laboratory. We used a trial-and-error approach for tuning these parameters based on a large number of experiments. In order to evaluate the frameworks of comparative analysis, we select two workloads: WordCount and TeraSort. The performance metrics are carried out based on three criteria: execution time, throughput, and speedup. Our experimental results revealed that both system performances heavily depends on input data size and correct parameter selection. The analysis of the results shows that Spark has better performance as compared to Hadoop when data sets are small, achieving up to 2 times speedup in WordCount workloads and up to 14 times in TeraSort workloads when default parameter values are reconfigured.