bluuebunny/crossref_metadata_2025 huggingface dataset:
Intratumoural immune heterogeneity as a hallmark of tumour evolution and progression in hepatocellular carcinoma
Authors: Nguyen Phuong , Ma Siming , Phua Cheryl , KAYA Neslihan , Lai Hannah , Lim Chun Jye , Lim Jia Qi , Lai Liyun , Tam Wai Leong , Lim Kiat Hon , Wan Wei Keat , Loh Tracy , Leow Wei Qiang , Pang Yin Huei , Chan Chung Yip , Lee Ser Yee , Cheow Peng Chung , Toh Han Chong , Ginhoux Florent , Iyer Shridhar , Kow Alfred , Dan Yock Young , Chung Alexander , Goh Brian , Albani Salvatore , Chow Pierce Kah‐Hoe , Zhai Wei Wei , Chew Valerie
Published: July 2020

The clinical relevance of immune landscape intratumoural heterogeneity (immune-ITH) and its role in tumour evolution remain largely unexplored. Here, we uncovered significant spatial and phenotypic immune–ITH from multiple tumour sectors and deciphered its relationship with tumour evolution and disease progression in hepatocellular carcinomas (HCC). Immune–ITH was associated with RNA-ITH and distinct immune microenvironments. Tumours with low immune–ITH experienced higher immunoselective pressure and underwent escape mechanisms via loss of heterozygosity in human leukocyte antigens and immunoediting. Instead, the tumours with high immune-ITH were associated with a more immunosuppressive/exhausted microenvironment. This immune pressure gradient along with immune-ITH represents a hallmark of tumour evolution closely linked to the transcriptome-immune networks contributing to disease progression and immune inactivation. Remarkably, high immune-ITH and its transcriptomic signature were predictive for worse clinical outcome in HCC patients. This in-depth investigation of ITH provides novel evidence on tumour-immune co-evolution along HCC progression.
Molecular characteristics and pathogenicity of porcine epidemic diarrhea virus in some areas of China from 2015 to 2018
Authors: Yu Linyang , Dong Jianguo , Wang Shuangyun , Liu Yanling , Zhang Leyi , Liang Pengshuai , Wang Lei , Chen Bin , Huang Li , song Changxu
Published: July 2020

Background

Since 2010, porcine epidemic diarrhea virus (PEDV) has caused severe diarrhea disease in piglets, which has led to large economic losses in China. To understand the genetic characteristics of PEDV strains that have been circulating in some provinces of China from 2015 to 2018, 362 feces and small intestine samples in pigs were collected and tested.
Methods

The S gene of PEDV in collected samples were amplified by RT-PCR. A phylogenetic tree was constructed using MEGA6.0 software with the neighbor-joining method to analyze the evolutionary relationship. Nucleotide and deduced amino acid (AA) sequences of S were aligned using the MegAlign program of DNASTAR7.1 software to determine sequence homology. PEDV GDgh16 strain isolation, IFA identification and titer detection were performed in Vero cells. Six 4-day-old healthy colostrum deprived suckling piglets were used for challenging experiment of PEDV GDgh16 strain. Virus copies from the small intestine were detected by RT-qPCR. The other section was stained with the anti-N protein McAb at 1:1000 dilution for immunohistochemical (IHC) examinations.
Results

The results showed that 160 samples tested positive and the PEDV-positive prevalence was 44.20%. Phylogenetic tree analysis of entire S genes showed that these strains were clustered into four subgroups, G1-b, G1-c, G2-a and G2-b, and that the G2-b strains had become dominant in recent years. Compared with previous strains, these strains had multiple variations in the SP and S1-NTD domains and in the neutralizing epitope of the S protein. Furthermore, we successfully isolated and identified a new virulent G2-b strain, GDgh16, which was well adapted to Vero cells and had a high mortality rate in piglets through challenge experiments.
Conclusions

Our study provides full insights into the genetic characteristics of prevalent PEDV strains in parts of China, suggesting that the development of novel effective vaccines is necessary and urgent.
The prevalent RNA modification on SARS-CoV-2 RNAs may confound the SNP profile and evolutionary patterns revealed by previous studies
Authors: Wang Yan , Gai Yanhong , Li Yuefan , Li Chunxiao , Li Ziliang , Wang Xuekun
Published: July 2020

Background

The recent outbreak of SARS-CoV-2 has caused severe damage to the world. The concomitant papers on the evolutionary patterns of SARS-CoV-2 is continuously emerging. Studies has utilized the publically available RNA-seq data to find out the so-called SNPs in the virus genome and analyzed their selection patterns.
Methods

We downloaded a set of RNA-seq data and performed a well-established but modified variant calling pipeline to allow the identification of multiple clustered mutations.
Results

We found prevalent “putative” but reliably detected A-to-G RNA modifications in the RNA-seq data of SARS-CoV-2 with high signal to noise ratios, presumably caused by the host’s deamination enzymes. Importantly, since SARS-CoV-2 is an RNA virus, it is technically impossible to truly distinguish SNPs and RNA modifications from the RNA-seq data alone.
Conclusions

The technically indistinguishable RNA modifications and SNPs of SARS-CoV-2 have complicated the situation where many researchers intend to unveil the evolutionary patterns behind the mutation spectrum. This is not a problem for DNA organisms but should be seriously considered when we are investigating the RNA viruses.
The influence of South East Asia Forest Fires on ambient Particulate Matter concentrations in Singapore: An Ecological Study using Random Forest and Vector Autoregressive Models
Authors: Rajarethinam Jayanthi , Aik Joel , Tian Jing
Published: July 2020

Background In recent decades, haze, due to biomass burning, has become a recurring problem in Southeast Asia (SEA). Haze degrades air quality, thus, causing detrimental effects on human health. Exposure to atmospheric particulate matter (PM) remains an important public health concern.Methods In this paper, we examined the long-term seasonality of PM2.5 and PM10 in Singapore. To study the association between forest fires in SEA and air quality in Singapore, we built two machine learning models, including the random forest (RF) model and the vector autoregressive (VAR) model, using a benchmark air quality dataset containing daily PM2.5 and PM10 from 2009 to 2018. Furthermore, we incorporated weather parameters as independent variables, to understand their effects on air quality.Results We observed two annual peaks, one in the middle of the year and one at the end of the year for both PM2.5 and PM10. Singapore was more affected by fires from Kalimantan compared to fires from other SEA countries. In our experimental results, VAR models performed better than RF with Mean Absolute Percentage Error (MAPE) values being 0.8% and 6.1% lower for PM2.5 and PM10, respectively.Conclusions Our study findings suggest that air quality in Singapore can be reasonably anticipated with predictive models that incorporate information on forest fires and weather variations. The public communication of anticipated air quality at the national level benefit who are at higher risk of experiencing poorer health due to poorer air quality.
Clinical Variables Responsible for Early and Late Diagnosis of Foreign Body Aspiration in Pediatrics age Group
Authors: Goyal Samarth , Jain Shubhika , Rai Guruprasad , Vishnu Rajkamal , Kamath Ganesh Sevagur , Bishnoi Arvind Kumar , Gaude Yogesh , Kumara Vijaya , Joshi Harshil , Reddy Revanth
Published: July 2020

Background
Incidence of foreign body aspiration ( FBA ) has been noticed maximally in age group ranging from 12 months-3 years. Foreign body in the trachea is a medical emergency as presentation is of respiratory distress. Obstruction of only one main or distal bronchus, leads to severe cough, choking sensation and breathlessness. Without early intervention it can lead to collapse, consolidation and pneumonia of the affected lung.
Methods
We retrospectively analysed 37 pediatric case records who presented from January 2014-December 2018 with FBA. Our primary aim was to assess the parameters responsible for early and late diagnosis of FBA. We concluded with a diagnostic algorithm for management of FBA on the basis of this outcomes.
Results
Around 32.5% came with a history of aspiration, 43% were referred from primary centers with a suspicion for the same and the rest came our tertiary care hospital directly. Those who presented within a week came with complaints of wet cough, wheeze and tachypnea where as those who came in after a week had dry cough and fever as their main complaint. Majority of ingested foreign body was vegetative type (80%) as compared to the non -vegetative material (20%).
Conclusion
Unlike adults, FBA in children is most commonly diagnosed on history, suspicion and clinical findings. Chest x ray has been the primary investigation of choice but in majority of the cases it was normal with subtle changes. Early diagnosis is the key to avoid complication.
Analysis of Evidence-Rating Systems Used in Meta-Analyses of Pharmacotherapy
Authors: Pérez-Surio Alberto Frutos , Hernando José Manuel Vinuesa , Mendoza Mercedes Arene , Bandrés María Ángeles Allende , López María Aránzazu Alcácera , Gómez Tránsito Salvador
Published: July 2020

Background: Evidence-rating systems (ERSs) provide a framework for the systematic evaluation of the quality of individual interventional or observational studies and the overall body of evidence in meta-analyses. Authors and users of meta-analyses require a familiarity with ERSs to determine the level of confidence in the application of results. Many ERSs have been published, but no consensus exists regarding best practice for their use. Objective: The aim is to describe patterns of use of ERSs in meta-analyses of drug therapy published in contemporary high-impact medical journals.Methods: We design a review. Medline / PubMed was searched to identify meta-analyses evaluating drug therapy from the top 5 ranked general medical journals from 2012 to 2016. Methods of full-texts were reviewed to ensure the meta-analyses evaluated drug therapy and to identify the ERS used to rate individual studies and the overall body of evidence. Frequency of ERS use was analyzed using descriptive statistics.Results: The top-ranked journals were Ann Intern Med, BMJ, JAMA, Lancet and PLoS Medicine. Of the 309 results, manual review excluded 111 meta-analyses. In 198 evaluated meta-analyses, 86.4% (171) utilized an ERS; the most commonly used was the Cochrane Risk of Bias Tool in 80.7% (138) of all meta-analyses. An ERS was used to evaluate the body of literature in 19.1% (38) of meta-analyses; the most commonly used of three systems was the GRADE methodology. Overall, 14 unique ERSs, including author-defined systems, were usedConclusions: Most meta-analyses of drug effects in high-impact medical journals evaluated individual studies with an ERS, most commonly the Cochrane Risk of Bias Tool, while the use of ERSs to evaluate the body of literature was less frequent. The familiarity of authors and users of meta-analyses with commonly used ERSs may facilitate the evaluation and application of findings of meta-analyses.
MicroRNA-219c-5p Regulates Bladder Fibrosis by Targeting FN1
Authors: Liu Bowen , Ding Yafei , Li Peng , He Siyuan , Wang Tao , Jia Zhankui , Yang Jinjian
Published: July 2020

BackgroundWe found that the bladders of multiple sclerosis mice were significantly fibrotic. This study aimed to investigate the relationship between fibronectin 1 (FN1) and bladder fibrosis, as well as the microRNAs involved in FN1 regulation. Methods The degree of bladder smooth muscle fibrosis was observed by immunohistochemistry. In addition, we used quantitative real-time polymerase chain reaction (RT-qPCR) and Western blotting to determine FN1 expression in bladders with different grades of fibrosis. Bioinformatics analysis revealed that miR-199a-3p, miR-219c-5p and miR-3572-3p could inhibit FN1 synthesis. Therefore, miR-199a-3p, miR-219c-5p and miR-3572-3p were overexpressed or knocked down in bladder smooth muscle cells (BSMCs), and the respective transfection and FN1 knockdown efficiencies were detected by RT-qPCR. Only miR-219c-5p overexpression and knockdown produced the expected results. A dual luciferase reporter assay was used to determine the targeting relationship between miR-219c-5p and FN1. Flow cytometry and Cell Counting Kit 8 (CCK8) experiments confirmed that miR-219c-5p reduced FN1 expression and affected the biological activity of smooth muscle cells. Agomir and anagomir of miR-219c-5p were transfected in vivo to observe the change of bladder fibrosis in mice.ResultsWith increasing bladder fibrosis, FN1 expression increased, while miR-199a-3p, miR-219c-5p, and miR-3572-3p expression levels decreased. The RT-qPCR results after transfection showed that only miR-219c-5p could regulate FN1. Indeed, the dual luciferase reporter assay results indicated that miR-219c-5p targeted FN1 directly. CCK8 and cell cycle assays showed that miR-219c-5p overexpression inhibited BSMC proliferation, while miR-219c-5p knockdown promoted BSMC proliferation. An apoptosis assay showed that miR-219c-5p overexpression promoted apoptosis, while miR-219c-5p knockdown inhibited BSMC apoptosis. The agomir and anagomir transfected with miR-219c-5p in vivo found that the bladder fibrosis of the mice in the agomir group was reduced, and the anagomir group was worse.ConclusionsOur findings indicate that FN1 up-regulation and miR-219c-5p down-regulation play an important role in the development of bladder fibrosis, and miR-219c-5p participates in bladder fibrosis by regulating FN1 expression. Thus, a novel antifibrotic function of miR-219c-5p is proposed, which may represent a potential target for the diagnosis and treatment of bladder fibrosis.
Value of Biopsy in a Cohort of Children with High-Titer Celiac Serologies: Observation of Dynamic Policy Differences between Europe and North America
Authors: Badizadegan Kamran , Vanlandingham David M. , Hampton Wesley , Thompson Kimberly M.
Published: July 2020

Background: Healthcare systems implement change at different rates because of differences in incentives, organizational processes, key influencers, and management styles. A comparable set of forces may play out at the national and international levels as demonstrated in significant differences in the diagnostic management of pediatric Celiac Disease (CD) between European and North American practioners. Methods: We use retrospective clinical cohorts of 27,868 serum tissue transglutaminase (tTG) immunoglobulin A levels and 7,907 upper gastrointestinal endoscopy pathology reports to create a dataset of 793 pathology reports with matching tTG results between July 1 of 2014 and July 1 of 2018. We use this dataset to characterize histopathological findings in the duodenum, stomach and esophagus of patients as a function of serum tTG levels. In addition, we use the dataset to estimate the local and national cost of endoscopies performed in patients with serum tTG levels greater than 10 times the upper limit of normal. Results: Using evidence from a US tertiary care center, we show that in the cohort of pediatric patients with high pre-test probability of CD as determined by serum tTG levels, biopsy provides no additional diagnostic value for CD, and that it counter-intuitively introduces diagnostic uncertainty in a number of patients. We estimate that using the European diagnostic algorithms could avoid between 4,891 and 7,738 pediatric endoscopies per year in the US for evaluation of CD. Conclusions: This study considers the North American and European management guidelines for the diagnosis of pediatric CD and highlights the slow adoption in North America of evidence-based algorithms developed and applied in Europe for triage of endoscopy and biopsy. We suggest that the forces that maintain the status quo in North America go beyond medical evidence and include a variety of social and economic factors. This work contributes to the growing body of evidence that suggests that the dynamics that largely favor maintaining status quo management policies extend to clinical medicine and influence a variety of clinical decisions at the level of individual patients and the population.
First Report of New Delhi Metallo-β-Lactamase-1 (NDM-1) Among Escherichia Coli Strains Isolated from Leukemia Patients in Iran
Authors: Roshani Mahdane , Goodarzi Alireza , Dehbashi Sanaz , Afrasiabi Farhad , Goudarzi Hossein , Hashemi Ali , Arabestani Mohammad Reza
Published: July 2020

Background: Escherichia coli has appeared as an important opportunistic pathogen responsible for nosocomial infections in Patients with immunodeficiency particularly in leukemia patients. New Delhi metallo-β-lactamase (NDM-1) is an enzyme that class of beta-lactam antibiotics and is used in treatment of multi-drug resistant (MDR) infections. Case Presentation: In this study, 80 isolates of Escherichia coli and Klebsiella pneumoniae collected over the course of two years from two medical centers of Tehran, Iran. Production of carbapenemase was detected of the isolates using MHT. New Delhi metallo-beta-lactamase 1 (blaNDM-1) genes were detected by polymerase chain reaction (PCR) ampliﬁcation with speciﬁc primers 2 blaNDM-1 producing E.coli strains were isolated from 2 leukemia of patients, The isolates were resistant to carbapenems (imipenem, meropenem),two isolates were positive for carbapenemase production by Modified Hodge test.Conclusions: The emerging of NDM-1 producing E. coli is a threat for leukemia patients in Oncology and hematology departments. We concluded that the incidence of MDR pathogens increased amang patients with leukemia and is life threatening.
Radiofrequency ablation combined with conductive fluid-based dopants (saline normal and colloidal gold): Computer modeling and ex vivo experiments.
Authors: Castro-Lopez Dora Luz , Berjano Enrique , Romero-mendez Ricardo
Published: July 2020

Background: The coagulation zone volume created during radiofrequency ablation (RFA) is limited by the appearance of roll-off. Doping the tissue with conductive fluids, e.g. gold nanoparticles (AuNPs) could enlarge the coagulation zones by delaying the roll-off. Our goal was to characterize the electrical conductivity of a substrate doped with AuNPs and to study by computer modeling and ex vivo experiments the effect on coagulation zone volumes.Methods: The electrical conductivity of substrates doped with normal saline or AuNPs was assessed experimentally using agar phantoms. The computer models, built and solved on COMSOL Multiphysics, consisted of a cylindrical domain mimicking liver tissue and a spherical domain mimicking a doped zone with diameters of 2, 3 and 4 cm. Ex vivo experiments were conducted on bovine liver fragments and under three different doping conditions: 1) non-doped tissue (ND Group), 2 mL of 0.9% NaCl (NaCl Group), and 2 mL of AuNPs 0.1 wt% (AuNPs Group).Results: The theoretical analysis showed that adding normal saline or colloidal gold in concentrations lower than 10% only modify the electrical conductivity of the doped substrate with practically no change of the thermal characteristics. The computer results showed a relationship between doped zone size and electrode length regarding the created coagulation zone. We observed a good agreement between ex vivo and computational results in terms of transverse diameter of the coagulation zone.Conclusions: Both computer and ex vivo experiments showed that doping with AuNPs can enlarge the coagulation zone, specially the transverse diameter, hence achieving more spherical coagulation zones.
Voluntary Exercise in Mesothelioma: Effects on Tumour Growth and Treatment Response in a Murine Model
Authors: FISHER Scott A , Peddle-McIntyre Carolyn J , Burton Kimberley , Newton Robert U , Marcq Elly , Lake Richard A , Nowak Anna K
Published: July 2020

Objective
There is substantial evidence that exercise can safely reduce the risk of cancer and improve survival in different human cancer populations. Long latency periods associated with carcinogeninduced cancers like asbestos induced mesothelioma provide an opportunity to implement exercise as an intervention to delay or prevent disease development. However, there are limited studies investigating the ability of exercise to prevent or delay cancer, and exercise as a preventive strategy has never been assessed in models with a known carcinogen. We investigated the potential of voluntary exercise (VE) to delay development of asbestos related disease (ARD) in our well-characterised, asbestos induced MexTAg model of mesothelioma.
Results
Asbestos exposed MexTAg mice were given continuous or delayed access to VE and ARD assessed over time. We found that the addition of VE did not affect ARD development in asbestos exposed MexTAg mice. However, nonasbestos exposed, aged matched control mice participated in significantly more VE behaviours, suggesting subclinical development of ARD after asbestos exposure had a greater impact on VE participation than age alone. These data highlight the importance of model choice and the potential limitation that some preclinical studies may not accurately represent the clinical paradigm, particularly in the context of prevention studies.
Effects of hearing impairment and hearing aid use on the incidence of cognitive impairment among community-dwelling older adults: evidence from the Taiwan Longitudinal Study on Aging (TLSA)
Authors: Tai Chi-Jung , Tseng Tzyy-Guey , Hsiao Yu-Han , Kuo Tsu-Ann , Huang Ching-Ya , Yang Yi-Hsin , Lee Meng-Chih
Published: July 2020

Background: Previous studies have reported associations between hearing impairment (HI) and cognitive impairment, but the evidence is not conclusive while considering concurrent geriatric syndromes. Especially, evidence from previous studies rarely came from Asian studies. This study aimed to evaluate the independent effects of HI and hearing aid use on the incidence of cognitive impairment while considering most geriatric confounders.Methods: This population-based, propensity-score matched cohort study used cohort from Waves IV­–VII (1999–2011) survey of the Taiwan Longitudinal Study on Aging (TLSA). Cognitive impairment was identified based on Short Portable Mental Status Questionnaire (SPMSQ) scores. The hazard ratio (HR) was calculated using the Cox proportional hazard regression adjusting for age, sex, comorbidities, socioeconomic status, Center for Epidemiologic Studies Depression (CES-D) scores, the instrumental activities of daily living scale, mobility condition and quality of life. In addition, social support and participation were also considered as confounders in the analysis. To assess the robustness of our findings, we conducted a sensitivity analysis designed to access unmeasured confounding factors by calculating E-values.Results: After 1:1 propensity-score matching, we included 709 participants in both the HI and non-HI groups with a mean age of 73.4 years and 39.4% of participants were female. The mean follow-up was 8.9±3.9 years. The HI group had a higher incidence of cognitive impairment than the non-HI group (74.5% vs. 69.1%, respectively), with an adjusted HR of 1.16 (95% confidence interval [CI], 1.03–1.32) based on a 12-year follow up. The E-value was 1.45 for the estimate, which provided evidence for this study’s robustness. Although, a subgroup analysis showed that hearing aid use was associated with lower incidences of cognitive impairment (66.3% vs. 75.6%) when compared to non-users in the HI group, the adjusted HR of 0.82 (95% CI, 0.61–1.09) revealed no significant differences.Conclusions: HI was an independent risk factor of incident cognitive impairment on top of concurrent geriatric syndromes. Early HI detection may thus be effective for preventing cognitive decline. Further studies are needed to evaluate the effect of hearing aid use on the prevention of cognitive decline.
Towards Precision Health in Weight Reduction: Thematic Content Analysis of an Open-Ended Survey on Reasons Why Morbidly Obese Patients Want to Lose Weight.
Authors: Md-Ya Mazapuspavina , Ismail Ilham Ameera , Malek Khasnur Abd , Yusoff Khalid , Bulgiba Awang
Published: July 2020

Background: Addressing individuals’ motivation to lose weight among patients with morbid obesity is an essential entity in weight reduction. Failures to shift motivation into weight loss actions are common. These could be contributed by the inadequacy to identify and subsequently address the key reasons, that are of particular concern to the patient' individual needs. We aimed to understand the motivations better and identify the reasons why morbidly obese patients attending hospital-based weight management programmes (WMP) wanted to lose weight. Methods: The study used a qualitative approach to analyze part of a quantitative questionnaire of a more extensive study to understand factors influencing weight loss among morbidly obese patients. We used thematic content analysis to analyze responses from a self-administered open-ended question "What is the main factor why you want to lose your weight?”. A total of 225 new patients attending obesity clinics in two tertiary hospitals responded to the questionnaire. Results: Patients’ mean BMI was 45.6±8.05 kg/m2. Four themes emerged for the reasons why morbidly obese patients wanted to lose weight. Health was the most commonly inferred theme (84%). Patients were concerned about the impact obesity had on their health. Overcoming obesity was seen as a reward not just for physical health, but also for their psychological wellbeing. Patients regard being functional to care for themselves, their family members, as well as their religious and career needs as the next most crucial theme (25.8%). Patients raised the theme appearance (12.9%), especially with regards to wanting to look and feel beautiful. The last theme was perceived stigmatization for being morbidly obese as they were mocked and laughed at for their appearance (3.1%).Conclusion: Patients with morbid obesity in this study had expressed their main personal motivational reasons to lose weight. Concerns about the impact of morbid obesity on health, physical, social and obligatory function, appearance and perceived stigma warrant detailed exploration by the managing health professionals. Identifying and addressing these unique personal motivations in a focused approach is vital at the beginning and throughout a weight reduction program in this unique group.
Construction of Anti-codon Table of the Plant Kingdom and Evolution of tRNA Selenocysteine (tRNAsec)
Authors: Mohanta Tapan Kumar Kumar , Mishra Awdhesh Kumar , Hashem Abeer , Abd_Allah Elsayed Fathi , Al-Harrasi Ahmed
Published: July 2020

Background
The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not.
Results
Therefore, we analysed the tRNAnome of 128 species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNAMet has highest (5.039%) whereas CGC anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and it has undergone anti-codon switch during the course of evolution.
Conclusion
The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation.
A novel nanoemulsion based microalgal growth medium for enhanced biomass production
Authors: Nigam Harshita , Malik Anushree , Singh Vikram
Published: July 2020

Background: Microalgae are well-established feedstocks for applications ranging from biofuels to valuable pigments and therapeutic proteins. However, the low biomass productivity using commercially available growth mediums is a roadblock for its mass production. This work describes a strategy to boost the algal biomass productivity by using an effective CO 2 supplement.Results: In the present study, a novel nanoemulsion-based media has been tested for the growth of freshwater microalgae strain Chlorella pyrenoidosa. Two different nanoemulsion-based media were developed using 1% silicone oil nanoemulsion (1% SE) and 1% paraffin oil nanoemulsion (1% PE) supplemented in BG11 media During 12-day growth experiment, the 1% PE gave the highest biomass yield (3.2± 0.07gL -1 ), followed by 1%SE (2.75 ± 0.07 gL -1 ) and control (1.03±0.02 gL -1 ). The respective microalgal cell number measured using cell counter were (3.0 ± 0.21 x 10 6 cells ml -1 ), (2.4 ± 0.30 x 10 6 cells ml -1 ) and (1.34 ± 0.09 x 10 6 cells ml -1 ). Cell viability analysis using MTT assay showed that 1% PE also had higher viable cells (94%) compared to 1% SE (77%) and control (53%). The effective CO 2 absorption tendency of the emulsion was highlighted as the key mechanism for greater biomass production. On the biochemical characterization of the produced biomass, it was found that the nanoemulsion cultivated C. pyrenoidosa had increased lipid (1% PE=26.8%, 1% SE=23.6%) and carbohydrates (1% PE=17.2%, 1% SE=18.9%) content compared to the control (lipid=18.05%, carbohydrates=13.6%).Conclusions: This study provides a novel nanoemulsion which acts as an effective CO 2 supplement for microalgal growth media which increase the growth of microalgal cells. Importantly, nanoemulsions cultivated microalgal biomass possess increment in lipid and carbohydrate content. This approach also provides high microalgal biomass productivity without alteration of morphological characteristics like cell shape and cell size.
Impact of Shoulder Subluxation on Peripheral Nerve Conduction and Function of Hemiplegic Upper Extremity in Stroke Patients: A Retrospective, Matched-Pair Study
Authors: Li Xiangzhe , Yang Zhiwei , Wang Sheng , Xu Panpan , Wei Tianqi , Zhao Xiaomeng , Li Xifeng , Zhang Yanmei , Li Ying , Mei Na , Wu Qinfeng
Published: July 2020

Background: After stroke, the peripheral nerves of the hemiplegic upper extremity (HUE) could exist impairments which seriously delay the function recovery of the HUE. However, the impacts of shoulder subluxation (SS) on the HUE electromyography characteristics in post-stroke are rarely reported. Therefore, this study was to investigate the impact of SS on peripheral nerve conduction and function of the HUE in post-stroke patients.Methods: A retrospective, matched-pair study was conducted. 30 post-stroke in-patients (15 patients for each group) were selected and their peripheral nerves of bilateral upper limbs were used to be underdone by the electroneurographic examination. The characteristics of patients, such as age and type of stroke, were recorded and paired. The electroneurographic parameters of upper limb motor/sensory nerves contained: the compound muscle action potential (CMAP) amplitude and latency of suprascapular, axillary, musculocutaneous, radial, median and ulnar nerves; the motor conduction velocity/ the sensory nerve action potential (SNAP) amplitude and latency of median, ulnar and radial nerves. The Brunnstrom stage scale was used to evaluate the motor function of the HUE.Results: The CMAP amplitude of each nerve in the HUE of both groups was lower than that in the healthy side (P < 0.05). CMAP amplitude of peripheral nerves (except ulnar) in the HUE of SS group was decreased (P < 0.05). The CMAP latency of the suprascapular, axillary and musculocutaneous nerves was longer than that of the healthy side in the SS group (P < 0.05). The axillary nerve CMAP latency in the SS group was prolonged more (P < 0.05). The motor conduction velocity of the median nerve on the HUE in the SS group was lower than that of the HUE in the N-SS group (P < 0.05). The SNAP amplitudes of the nerves in the HUE in both groups were lower than those in the healthy side (P < 0.05). The Brunnstrom stage of HUE in the SS group was lower (P < 0.05).Conclusions: Stroke may lead to extensive damage of the HUE nerves, and SS may aggravate the damage of these nerves, delaying the recovery of upper limb function.
Magnitude and antimicrobial susceptibility patterns of extended-spectrum β-lactamase producing Enterobacteriaceae recovered from environmental samples at Tikur Anbessa Specialized Hospital, Ethiopia
Authors: Muktar Shemse Sebre , Erku Woldaregay , Mihret Wude , Seman Aminu , Awoke Tewachw , Desalegn Zelalem , Mihret Adane , Abebe Tamrat
Published: July 2020

Background

The hospital environment especially the intensive care units (ICUs) contributes to the spread of extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae, which are contributing to increasing morbidity and mortality rates. We aimed to assess the rate of environmental contamination of ESBL producing Enterobacteriaceae and their antimicrobial susceptibility patterns.
Methods

A Cross-sectional study was conducted at Tikur Anbessa Specialized Hospital (TASH) from June to July, 2018. A total of 65 environmental swab were taken from inanimate items. All isolates from the inanimate environment were cultured by using ESBL ChromoSelect Agar and identified using conventional bacteriological methods. All ESBL producing Enterobacteriaceae isolates were tested for their antimicrobial susceptibility using the disc diffusion method according to the methods and interpretive criteria of the Clinical and Laboratory Standards Institute (CLSI).
Results

From a total of 65 environmental swab samples, 16 (24.6%) were ESBL producing Enterobacteriaceae. The most predominant ESBL producing isolates were E. coli (8/16, 50%) and Klebsiella spp (6/16, 37.6%). The Pediatrics and Medical-Surgical ICU exhibited the highest ESBL producing Enterobacteriaceae, each with (37.5%, 6/16). Linens and ventilators were associated with high rates of ESBL isolates positivity each with equal 31.3% detection rate. ESBL producing Enterobacteriaceae isolates had significantly high resistance level to ampicillin (100%), ceftazidime (93.8%), cefepime (87.5%) and cefotaxime (86.7%). However, low resistance level was recorded against amikacin (18.8%).
Conclusion

The appearance of ESBL producing Enterobacteriaceae among ICUs hospital environment is posing a serious threat for the control of nosocomial infections. The high resistance found from this study shows the need for policies for devising infection control procedures and screening policies for ESBL on a routine basis.
Assessing the Effectiveness of Chagas Disease Education for Healthcare Providers in the United States
Authors: Granados Paula Stigler , Pacheco Gerardo J , Patlán Evangelina Núñez , Betancourt Jose , Fulton Lawrence
Published: July 2020

Background
Chagas disease is a zoonotic infection caused by the parasite Trypanasoma cruzi, which affects an estimated 8–11 million people globally. Chagas disease is almost always associated with poverty in rural areas and disproportionately impacts immigrants from Latin America living in the United States. Approximately 20–30% of people who are infected with Chagas disease will develop a chronic form of the infection that can be fatal if left untreated. Chagas disease is vastly underestimated in the United States, often goes undiagnosed and is not well understood by most U.S. healthcare providers. One of the most important ways at reducing barriers to improving diagnostics of Chagas disease in the U.S. is giving healthcare providers the most up-to-date information and access to leading experts.
Methods
An online webinar was conducted for healthcare providers, veterinarians and public health professionals using Chagas disease expert panelists. Pre and post tests were administered to participants (n = 57) to determine the efficacy in raising awareness and to determine key focus areas for improving knowledge. A Wilcoxon rank-sum was used for non-parametric variables equivalent and for questions that assessed knowledge the McNemar’s Chi-Square test was used.
Results
There were statistically significant learning increases in multiple categories including transmission (p = < .001), clinical presentation (p = 0.016), diagnostics (p = < .001), and treatment (p = < .001).
Conclusion
Providing easily accessible learning opportunities using validated testing and evaluations should be further developed for rural healthcare providers in the U.S. as well as healthcare providers serving under represented populations such as immigrants. There is a clear lack of knowledge and awareness surrounding Chagas disease in the United States and just by raising awareness and providing education on the topic, lives will be saved.
Reduced Metagenome Sequencing for strain-resolution taxonomic proles
Authors: Snipen Lars , Angell Inga-Leena , Rognes Torbjørn , Rudi Knut
Published: July 2020

Background: Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution, and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or do not explore the full potential of RMS data.Results: We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock-community data sets shows the potential to clearly separate between strains even when the 16S is 100% identical and genome-wide dierences is < 0:02, indicating RMS has a very high resolution. From a simulation study we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real data set of infants guts we show that RMS is capable of detecting a strain-diversity gradient for Escherichia coli across time.Conclusion: We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain-level. Like shotgun metagenomics, it requires a good database of reference genomes, and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.
Risk factors for postoperative delirium and subsyndromal delirium in older surgical patients in the general ward: a prospective observational study
Authors: Kanno Maya , Doi Mana , Kubota Kazumi , Kanoya Yuka
Published: July 2020

Background
Postoperative delirium (POD) among older patients is a common, serious disease and is associated with a high incidence of negative outcomes. For early detection of POD and subsyndromal delirium (SSD), this study was conducted to identify risk factors of POD and SSD in older patients in a general ward who were scheduled for surgery.
Methods
This was a prospective observational study. Study participants were older than 65 years, underwent urology surgery, and were hospitalized in the general ward between April and September 2019. Both POD and SSD were assessed by using the Confusion Assessment Method on the preoperative day, the day of surgery, and postoperative days 1–3. Personal characteristics, clinical data, cognitive function, physical functions, laboratory test results, medication use, type of surgery and anesthesia, and use of restraints were collected from medical records. Univariate and multivariate analyses were conducted to identify the risk factors for POD and SSD.
Results
A total of 101 participants (mean age 74.9 years) were enrolled; 19 (18.8%) developed POD and SSD. The use of bed sensors (odds ratio 10.2, p = .001) and preoperative level of C-reactive protein (CRP; odds ratio 1.5, p = .054) were identified as risk factors for POD and SSD.
Conclusions
POD and SSD among older patients in general wards were related to bed sensor use and the preoperative CRP level. Therefore, this study suggests that in order prevent POD and SSD for older patients in general wards, it is necessary to avoid bed sensor use as restraints and to assess the preoperative CRP level.
Giant mid-esophageal diverticulum treated with diverticular peroral endoscopic myotomy: a case report
Authors: Niu Qiong , Liu Fang , Cheng Xian-Yong , Shi Ning , Wang Kai , Li Yan-Min , Liu Cheng-Xia
Published: July 2020

Background

Esophageal diverticulum is rare and usually requires surgical treatment. Diverticular peroral endoscopic myotomy(D-POEM) is considered to be a novel technique that can be effectively used for septotomy in patients with esophageal diverticulum.
Case presentation:

A 73-year-old male patient was admitted to our hospital, complaining of recurrent dysphagia for more than 8 years and aggravated dysphagia for 2 months. Esophagogram revealed a sac in the anterior esophageal region and gastroscopy showed a giant diverticulum in the mid-esophagus. He was treated with D-POEM and had good clinical outcome. The patient was discharged 6 days after operation and has been doing well, and no recurrence was observed.
Conclusion

D-POEM is an effective and minimally invasive method for esophageal diverticulum, but long-term efficacy remains to be proved by more studies.
Machine Learning Based DWDM Design Using Regression Modelling
Authors: K Venkatesan , A Chandrasekar , P.G.V Ramesh
Published: July 2020

In this paper, we discuss the non-linearity problems such as Four Wave Mixing (FWM) and high signal distortion with low Output Signal to Noise Ratio (OSNR) in the design of a 64-channel DWDM system using Regression learning technique. The occurrence of FWM in a DWDM system with high number of channels reduces the performance of an optical fiber system in terms of bandwidth and increases computational complexity. High signal distortion with low OSNR reduces network throughput, energy efficiency and thus forces re-transmission. To overcome the above problems, DWDM system with higher number of channel necessitates an optimized design based on correlation factors of optical dependent and independent variable factors such as BER, Q-factor, signal power, noise power and OSNR. Proposed here is a regression optimized DWDM system design. Regression is used here for correlating and optimizing the optical parameters. In this paper, the problem of non-linearity is solved through optimized DWDM design based on correlated parameters in 16, 32 and 64- Channeled DWDM system. The regression based correlated DWDM design (R-DWDM) is improvised mechanism over the independent parameter based simulations and thus improves accuracy. The R-DWDM design system shows higher accuracy through the derived R-value for optical parameters such as input power, channel spacing, optical gain and data rate. The enhancement achieved through the regression based optimized DWDM design is evaluated in terms of optical measurements such as signal power, noise power, Q-factor and BER.
Interleukin-10 Expands Transit-Amplifying Cells While Depleting Lgr5+ Stem Cells via Inhibition of Wnt and Notch Signaling
Authors: Deng Fan , Hu Jingjuan , Yang Xiao , Wang Yifan , Liu Kexuan
Published: July 2020

Background & Aims: Epithelial regeneration is essential for homeostasis and mucosal barrier repair. In infectious and immune-mediated intestinal diseases, interleukin (IL)-10 is thought to enhance these processes. We aimed to define the mechanism by which IL-10 played in mucosal healing or injury.Methods: Intestinal stem cells (ISCs) cultures and mice were treated with recombinant mice IL-10 (rmIL-10). The level of cell proliferation, differentiation, death and related signaling pathways for self-renewal of ISCs were measured in vitro and in vivo.Results: It was uncovered that rmIL-10 increased the size and death, but reduced the total number of organoids. In addition, rmIL-10 depleted Lgr5+ ISCs and reduced epithelial proliferation, but enhanced the differentiation of epithelial cells and expanded numbers of transit-amplifying (TA) cells. These changes are related to the decrease of Wnt and Notch signals in vivo and in vitro. Meanwhile, increased expression of Paneth cells and decreased expression of enteroendocrine cells and goblet cells were induced by rmIL-10.Conclusions: IL-10 reduces the survival of Lgr5+ ISCs and proliferation of epithelial cells by inhibiting Notch and Wnt signaling, but promotes enhanced the differentiation of epithelial cells and expanded numbers of TA cells. Therefore, IL-10 acts as an anti-inflammatory factor, but may damage intestinal mucosa repair and maybe a potential target for the treatment of intestinal injury.
Prospective Study on a Fast-Track Training in Psychiatry for Medical Students: The Psychiatric Hat Game
Authors: Clément Anthony , Delage Raphaël , Chollier Marie , Josse Laure , Gaudry Stéphane , Zahar Jean-Ralph , Baubet Thierry , Degos Bertrand
Published: July 2020

Background: While medical students are losing interest in lectures in favor of other educational materials, many studies suggest the benefit of active learning, combined with gamified educational tools. The authors developed a psychiatric adaptation of the « Hat Game ». It was hypothesised that this game would increase both knowledge and motivation in medical students toward psychiatric semiology.Methods: This gamified fast-track training consisted of two teams and each team must guess as many psychiatric semiology terms as possible using different techniques (i.e. speech, mime). The study involved a pre- and post-evaluation of knowledge and a satisfaction survey.Results: Knowledge scores were significantly higher after the game than before. Improvement was maintained three months after the game. Satisfaction survey items highlighted that students enjoyed and would recommend this type of gamified training.Conclusions: The Psychiatric Hat Game improved knowledge of psychiatric semiology in medical students. Results suggest that it is a promising efficient tool to teach playfully medical semiology, with transferable features, utility and acceptability from one medical field to another. This study contributes to the growing body of knowledge advocating for serious games and gamified training in medical education.