bluuebunny/crossref_metadata_2025 huggingface dataset:
Upregulation of LncRNA SNHG15 indicates an unfavourable prognosis and clinical features of patients in multiple malignancies: a meta-analysis and bioinformatics
Authors: Chen Caizhi , Feng Yeqian , Wang Jingjing , Liang Ye , Zou Wen
Published: May 2020

Background: A snoRNA host gene named SNHG15 which produces a short half-lived lncRNA has been reported to be dysregulated in multiple cancers and correlated with tumor progression in published researches recently. So this meta-analysis was performed to evaluate the generalized prognostic effect of SNHG15 on malignancies because of the discrepant data amongst different studies.Methods: Four public databases were utilized for identifying eligible studies. The association between prognostic indicators and clinical features were extracted and pooled for estimation of the hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs). Publication bias and the stability of pooled results were measured by Begg’s test, Egger’s test and sensitivity analysis respectively. Additionally, Online database based on The Cancer Genome Atlas (TCGA) was screened and further validate our results.Results: Totally eleven studies including 1087 patients were ultimately enrolled in our paper. Promoted SNHG15 expression was associted with worse OS and DFS.Moreover, increased SNHG15 expression suggested advanced TNM stage and LNM but not correlated with age, gender and tumor size. No publication bias and instability of result were observed. SNHG15 was significantly upregulated in seven cancers and elevated expression of SNHG15 indicated shorter OS and DFS in five malignancies according to the validation using GEPIA (Gene Expression Profiling Interactive Analysis).Conclusions: Promoted expression of lncRNA SNHG15 was markedly related to worse prognosis and clinical features, suggesting that SNHG15 might serve as a novel factor in various cancers.
Initial Real-life Experience From a Designated COVID-19 Centre in Athens, Greece. A Proposed Therapeutic Algorithm
Authors: Baraboutis Ioannis , Gargalianos Panagiotis , Aggelonidou Eleni , Adraktas Andreas
Published: May 2020

We report our initial experience with the management of a mixed group of patients with COVID-19 infection, admitted and treated in a designated COVID-19 centre in the Athens Metropolitan area over a 4-week period. The SARS-CoV-2 pandemic presented a huge challenge to the Greek National Healthcare System and healthcare workers. Their response so far has been miraculously effective. Since there are essentially no therapeutic guidelines yet for this disease, we relied mainly on our medical intuition, our empathy for our patients and team work to do the best possible for 49 people with this infection. We present the therapeutic algorithm we gradually developed (on the job) and applied in our patients, based on continuous creative brainstorming and monitoring of the literature.
Association Between Meat Intake and Semen Parameters Among Iranian Infertile Men: A Cross-sectional Study
Authors: Ghiasvand Reza , haeri farahnaz , ShariatPanahi SeyyedPayam , Marvast Laleh Dehghan
Published: May 2020

Objective: Previous studies have proven the effect of dietary patterns on semen quality indicators, but research on the relationship between meat intake and semen quality is limited. Therefore, this study was conducted to investigate the relationship between Meat intake with semen quality.Methods: In this cross sectional study, 400 infertile men were recruited into study during their fertility investigation in Yazd Reproductive Sciences Institute Diagnosed by an andrologist according to the inclusion criteria. Multivariate logistic regression was used to determine the relationship between meat intake and semen parameters. All data were analyzed using SPSS V. 22 software.Results: We found that intake of canned tuna can have two different effects on sperm motility in infertile male. Intake of canned tuna according to the serving size stated in quartile 2, leads to a decrease in the percentage of immotile sperm from 52.93 (CI95%, 51.15-54.71) to 46.55 (CI95%, 44.56-48.54)(Ptrend=0.036). On the other hand, there is an increase in the percentage of immotile sperm from 46.55 (CI95%, 44.56-48.54) to 52.88 (CI95%, 50.94-54.82) in the highest quartile of canned tuna intake.Also, no significant relationship was observed between intake other types of meats and sperm quality indices.Conclusions: We found that intake of canned tuna,base on serving size of quartile 2, is associated with lower percentage of immotile sperm, on the other hand high intake of canned tuna increase percentage of immotile sperm in Iranian infertile men. More extensive studies are recommended in this regard.
Weighting National Survey Data: why, how and which weight?
Authors: Hakim Ferdous , Bhuiyan Rijwan , Akter Mst. Khaleda , Kamal Md. Mohit , Alam Md. Faruq , Karim Md. Rizwanul , Zaman Mohammad Mostafa
Published: May 2020

Background Weighting of national data is a procedure that enables the sample to be more representative of the target population. Weighting procedure is a thorough exercise and yields several types of weights. However, considerable variation exists among authors on which weight to use leaving the researchers baffled. In this article we share our experience on weighting for a few recent national surveys in Bangladesh. Methods We generated four weights: the base weight calculated from probabilities of selection, and non-response adjustments, population calibration, and trimmed weights. Finally we checked weighted means, medians, ranges, standard errors, confidence intervals, variances, multiplicative effects, design effects and prevalence of a key variable of the survey to decide on which weight to use. Results Compared to unweighted distribution, weighting makes the sample distribution to conform to the population. Among the four calculated weights, the trimmed weight had narrow standard error and variance, and smallest design and multiplicative effects. It yielded an acceptable prevalence and distribution of a core variable. Conclusion Though weighting is a time intensive exercise, it had a favorable effect on the sample distribution to comply with the Bangladeshi population. Among the four weights, we show that the trimmed weight met all parameters of good quality and precision. Therefore, we recommend to use this weight for national level surveys in Bangladesh.
Comparing two methods for deriving dietary patterns associated with risk of metabolic syndrome among middle-aged and elderly Taiwanese adults with impaired kidney function
Authors: Kurniawan Adi Lukas , Hsu Chien-Yeh , Lee Hsiu-An , Rau Hsiao-Hsien , Paramastri Rathi , Syauqy Ahmad , Chao Jane C-J
Published: May 2020

Background: Dietary patterns were associated with the risk of chronic disease development and outcome-related diseases. In this study, we aimed to compare the correlation between dietary patterns and metabolic syndrome (MetS) using two methods for identifying dietary patterns.Methods: The participants (n = 25,569) aged ≥ 40 years with impaired kidney function were retrieved from Mei Jau (MJ) Health Screening database from 2008 to 2010. Dietary patterns were identified by principal component analysis (PCA) and reduced rank regression (RRR) from twenty-two food groups using PROC FACTOR and PROC PLS functions.Results: We identified two similar dietary pattern characteristics (high intakes of deep fried foods, preserved or processed foods, dipping sauce, meat, sugary drinks, organ meats, jam/honey, fried rice/flour products, instant noodles and eggs) derived by PCA and RRR. Logistic regression analysis revealed that RRR-derived dietary pattern scores were positively associated with an odds ratio (OR = 1.70, 95% CI: 1.56, 1.86) of having MetS than PCA-derived dietary pattern scores (OR = 1.38, 95% CI: 1.27, 1.51). The correlations between RRR-derived dietary pattern scores and elevated systolic and diastolic blood pressure (OR = 1.30 for both) or low high density lipoprotein cholesterol in women (OR = 1.32) were statistically significant but not significant in PCA-derived dietary pattern scores.Conclusions: Our findings suggest that RRR gives better results when studying behavior related dietary patterns in association with MetS. RRR may be more preferable to provide dietary information for developing dietary guidelines among people with MetS. Further studies with prospective measurements are needed to verify whether RRR is a useful analytic tool for the association between dietary patterns and other chronic diseases.
IUD Contraceptive Use Among Women of Reproductive Age: Experiences, Motivators and barriers in a General Hospital, Uganda
Authors: Teddy Nambalirwa , Olwit Connie , Osingada Charles , Kiguli Juliet , Nyashanu Mathew , Mbalinda Scovia Nalugo
Published: May 2020

BackgroundDespite availing contraceptives, IUD uptake remains low in family planning service provision. Yet there is evidence that access to family planning reduces Maternal mortality especially in developing countries like Uganda. The study explored the reasons for low uptake of IUD among women of reproductive age.MethodologyFocus-groups and in-depth interviews with women in reproductive was employed to explore experiences, barriers and for low use of IUD. A thematic analysis was used to analyse the data.ResultsThis study explored women’s experiences, their motivations and barriers to IUD use. The positive experiences reported included; IUD is a long-term method of family planning; un affected libido, body image, reassurance from the health providers. The negative experiences included; pain on insertion; discomfort and bleeding and fear of strings. The motivators were; availability of IUD services at the facility, unaffected body image, information from the health workers and the barriers included; mistrust of health providers, financial constraints, myth and misconceptions and lack of social support.ConclusionThe experiences were both positive and negative, the motivators were their drivers to use the method and barriers were reported to influence the IUD use. There is need for mothers who have used IUD and are satisfied with the method to talk to other mothers so that we can increase IUD use as a method of family planning and health care providers have role to play to demystify the myth and misconceptions the mother have.
Fecal Microbiota Transplantation for Grade IV Steroid Refractory GI-GvHD: Interim Results a Non-randomized, Open-label, Phase 1 Clinical Study
Authors: Zhao Ye , Li Xue-wei , Zhou Yu-jing , Ma Xiao , Chen Feng , Hu Xiao-hui , Jin Song , He Xue-feng , Gao Jin , Zhu Bao-li , Wu De-pei , qi xiaofei
Published: May 2020

BackgroundGastrointestinal (GI) tract graft-vs-host disease (GvHD) is a major cause of post-allo-HCT morbidity and mortality. Patients with steroid-refractory GI-GvHD face a poor prognosis and limited therapeutic options. Here, we report an interim analysis on the safety and efficacy of fecal microbiota transplantation (FMT) in treating steroid-refractory GI-GvHD.MethodsWe did a non-randomized, open-label, phase 1 clinical study on patients with grade IV steroid-refractory GI-GVHD. FMT efficacy was evaluated using indexes of abdominal pain, diarrhea and bloody purulent stool at 14 and 21 days after the diagnosis of steroid-refractory GI-GvHD. The primary outcomes referred to clinical complete remission or partial remission. Secondary outcomes referred to PFS and OS at Day 90 and the end of the research. Safety was evaluated according to adverse events during FMT and the whole follow-up period. The study was registered with ClinicalTrials.gov as #NCT03148743.ResultsA total of 56 patients with steroid-refractory GI-GvHD were enrolled. Of them, 24 patients with grade IV steroid-refractory GI-GvHD were assigned to FMT and 18 to the control group. The characteristics of the two group patients at baseline were similar. At Day 14 after FMT, 13 (54.2%) patients in FMT group and none (0%) of 18 control group achieved clinical remission (p<0.05), while 20(83%) patients in FMT group and 7(39%) in control group showed effective response (clinical remission+partial remission) (RR 7.86, 95% CI 1.88–32.9; p=0.005). At Day 21, the clinical remission was significantly greater in FMT group than in control group (14 (58.3%) of 24 vs 3(16%) of 18; RR 6.0, 95% CI 1.22–29.45; p=0.027). Within a follow up of 90 days, the FMT group showed better OS (HR, 7.0; 95% CI, 1.53-32.08; p=0.012). At the end of the research, the median survival time was >600 days in FMT group and 107 days in control group (HR, 4.73; 95% CI, 1.58-14.14; p=0.005). Both the PFS (HR, 0.24; 95% CI, 0.06-0.95; p=0.055) and OS (HR, 5.97; 95% CI, 1.52-23.43; p=0.01) kept increasing during the follow-up in FMT group. Overall, the mortality rate was lower in FMT group (HR, 5.97; 95% CI, 1.52-23.43; p=0.01). No difference was observed in the occurrence of other side effects, such as hemorrhagic cystitis, infection of bacteria & fungi, CMV&EBV, septicemia, TMA, cardiac events, thrombocytopenia and epilepsy.ConclusionsThe diversity of intestinal microbiota can be affected by allo-HSCT. FMT is effective and safe in treating grade IV steroid refractory GI–GvHD.
Animalcules: Interactive Microbiome Analytics and Visualization in R
Authors: Zhao Yue , Federico Anthony , Faits Tyler , Manimaran Solaiappan , Monti Stefano , Johnson W. Evan
Published: May 2020

Background: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data.Results: To address some of these challenges, we have developed Animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis are enhanced in the toolkit, while new methods such as biomarker identification are introduced. Powerful interactive and dynamic figures generated by Animalcules enable users to understand their data and discover new insights. Animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface.Conclusions: We present Animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. Animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/animalcules.html).
Plasmodium infection prevents recurrence and metastasis of hepatocellular carcinoma potentially via inhibiting EMT
Authors: Liang Yun , Chen Xiao , Tao Zhu , Ma Meng , Adah Dickson , Li Xiaofen , Dai Lingling , Ding Wenting , Fanuel Songwe , Zhao Siting , Qin Li , Chen Xiaoping , Zhang Xiaowen
Published: May 2020

Background: Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer mortality worldwide and is characterized by a high rate of recurrence. We have previously reported Plasmodium infection inhibits tumor development and metastasis in a murine Lewis lung cancer model. In the current study, we aimed to examine the effects of Plasmodium infection on HCC metastasis and recurrence.Methods: Antitumor effects of Plasmodium infection were determined using two murine orthotopic HCC models, the non-resection model for investigating the effect of Plasmodium infection on liver tumor progression and metastasis, the resection model for investigating the effect of Plasmodium infection on the tumor recurrence after tumor was removed. Tumor tissues derived from tumor-bearing mice treated with or without Plasmodium infection were harvested after 15 days of tumor inoculation. The biomarkers related to epithelial-mesenchymal transition (EMT) and molecules associated with CCR10-mediated PI3K/Akt/GSK-3β/Snail pathway signaling were identified by qRT-PCR and western blot. Results: We found that Plasmodium infection significantly suppressed progression, recurrence and metastasis of HCC and prolonged the survival of tumor-bearing mice in both models. The expression levels of E-cadherin were significantly higher in Plasmodium treated group compared with those in control group, whereas the expression levels of Snail were significantly lower in the treated group than those in control group. Furthermore, Plasmodium infection inhibited the activation of Akt and GSK-3β in the tumor tissues by downregulating the expression of CCR10, thereby suppressing the accumulation of Snail and potentially contributed to the suppression of EMT and the prevention of tumor recurrence and metastasis.Conclusion: This study suggested that Plasmodium infection inhibited recurrence and metastasis, improved the prognosis of HCC potentially via suppression of CCR10‑mediated PI3K/Akt/GSK‑3β/Snail signaling, and prevention of EMT. These findings may be important in the development of novel therapy for HCC recurrence and metastasis especially for patients during the perioperative period.
Total Cholesterol Concentration Predicts the Effect of Plasmapheresis on Hypertriglyceridemic Acute Pancreatitis
Authors: chen zhu , Huang xiaolong , Han na , Guo Yanxia , Chen Jing , Ning yaogui , zhang minwei
Published: May 2020

Background The clinical efficacy of plasmapheresis (PP) in patients with hypertriglyceridemic acute pancreatitis (HLAP) might affected by total cholesterol (TC). The objective of this study is to determine the relationship of TC and the Triglyceride (TG)-lowing effect in patients on either non-PP or PP therapy.MethodsPatients were categorized into high total cholesterol (HTC) /low total cholesterol (LTC) groups based on TC level of 12.4 mmol/l. The primary outcome was TG reduction to below 500mg/dl within 48 hours. Linear mixed-effect model and logistic regression analyses were used to assess the association of TC and different therapy groups on TG-lowing efficacy.ResultsCompared with LTC group, patients with HTC showed more severe imaging manifestations(p<0.001) and higher APACH Ⅱ scores (p=0.036). Deaths occurred only in HTC groups. Significant interaction of time sequence with the 2 TGs-lowing therapy groups on TG level was only found in HTC group (p < 0.001). In patients with elevated TC level, primary outcome occurred in 66.67% of patients in the PP group, and 27.91% in the non-PP group. After adjustment for age, gender, CT grade and APACH II score, the odd ratio remain significant (OR 5.47, 95% confidence interval [CI] 1.84-16.25, p = 0.002). Furthermore, in patients with lower TC level, primary outcome occurred in 81.25% of patients in the PP group, and 62.30% in the non-PP group (adjusted OR 2.05; 95% CI 0.45–9.40; p = 0.353).Conclusions: TC could be a potential biomarker to predict the effects of TG-lowing therapy in patients with HLAP.
Prevalence and Correlates of Transactional Sex Among Women of Low Socioeconomic Status in Portland, Oregon
Authors: Menza Timothy W , Lipira Lauren , Bhattarai Amisha , Cali-DeLeon Victoria , Orellana Roberto
Published: May 2020

Background: Women who report transactional sex are at increased risk for HIV and other sexually transmitted infections (STIs). However,in the United States, social, behavioral, and trauma-related vulnerabilities associated with transactional sex are understudied and data on access to biomedical HIV prevention among women who report transactional sex is limited. Methods: In 2016, we conducted a population-based, cross-sectional survey of women of low socioeconomic status recruited via respondent-driven sampling in Portland, Oregon. We calculated the prevalence and,assessed the correlates of, transactional sex using generalized linear models accounting for sampling design. We also compared health outcomes,HIV screening, and knowledge and uptake of HIV pre-exposure prophylaxis (PrEP) between women who did and did not report transactional sex.Results: Of 334 women, 13.6% reported transactional sex (95% confidence interval [CI]: 6.8%, 20.5%). Women who reported transactional sex were older, more likely to identify as black, to identify as lesbian or bisexual, to experience childhood trauma and recent sexual violence, and to have been homeless. Six percent(95%CI: 1.8%, 10.5%) of women with no adverse childhood experiences (ACEs) reported transactional sex compared to 23.8%(95%CI: 13.0%, 34.6%)of women who reported eleven ACEs (P<0.001). Transactional sex was strongly associated withcombination methamphetamine and opiate use as well ascondomless sex. Women who reported transactional sex were more likely to report being diagnosed with a bacterial STI and hepatitis C; however, HIV screening and pre-exposure prophylaxis knowledge and use were low. Conclusions:In a sample ofwomen of low socioeconomic status in Portland, Oregon, transactional sex was characterized by marginalized identities, homelessness, childhood trauma, sexual violence, substance use, and sexual vulnerability to HIV/STI. Multi-level interventions that address these social, behavioral, and trauma-related factors and increase access to biomedical HIV prevention are critical to the sexual health of women who engage in transactional sex.
Influence of workload, mental health and professional quality of life on healthcare workers’ hand hygiene behavior in medical aid during COVID-19 pandemic
Authors: Zhou Qian , Zhang Xinping
Published: May 2020

BackgroundAppropriate hand hygiene behavior is much crucial during COVID-19 pandemic, which is influenced by workload, mental health and professional quality of life. The increasing workload, worse mental health and negative professional quality of life are severe challenges for healthcare workers, whereas the evidence of mechanism between them and hand hygiene behavior are limited. This study aimed to understand and model how HCWs’ hand hygiene behaviors were influenced by workload, mental health and professional quality of life.MethodsA total of 1,734 healthcare workers were investigated, covering self-reported hand hygiene behavior, mental health, workload, professional quality of life and socio-demographic characteristics. Structural equation modelling was conducted to confirm interrelationships and parameters among the variables.Findings The final model had a good fit (CFI=0.980; TLI=0.941; RMSEA=0.055). Higher workload was linked to worse mental health (β = 0.165, p < 0.001) and higher burnout (β = 0.183, p < 0.001). Worse mental health was linked to higher burnout (β = 0.339, p < 0.001). The higher burnout was associated with worse self-reported hand hygiene behavior (β = -0.302, p < 0.001).ConclusionWorkload is positively associated with mental health and burnout; mental health is positively related to burnout; burnout is negatively associated with hand hygiene behavior. Thus, hand hygiene behavior can be promoted by the strategy to decrease the workload, burnout and enhance mental health.
COVID-19 In Shang Hai: It is Worth Learning from the Successful Experience in Preventing and Controlling the Overseas Epidemic Situation
Authors: Dang Qi , Miao Rui , Yong Liang
Published: May 2020

BackgroundCOVID-19 first appeared in Wuhan, Hubei Province, China in late December 2019 and spread rapidly in China. Currently, the spread of local epidemics has been basically blocked. The import of overseas epidemics has become the main form of growth in China ’s new epidemic. As an important international transportation hub in China, Shanghai is one of the regions with the highest risk of imported cases abroad. Due to imported of overseas cases are affected by the international epidemic trend. The traditional infectious disease model is difficult to accurately predict the cumulative trend of cumulative cases in the Shanghai areas. It is also difficult to accurately evaluate the effectiveness of the international traffic blockade.MethodsIn this situation, this study takes Shanghai as an example to propose a new type of infectious disease prediction model. The model first uses the sparse graph model to analyze the international epidemic spread network to find countries and regions related to Shanghai. Next, multiple regression models were used to fit the existing COVID-19 growth data in Shanghai. Finally, the model predicts the growth curve of the COVID-19 epidemic in Shanghai without an international traffic blockade.ResultsIn this study, by constructing a sparse graph network model, 30 countries and regions related to Shanghai's overseas epidemic input were obtained, such as the United States. Moreover, the three regression models in this paper have obtained a good fitting effect. Finally, using data from 30 countries and regions related to Shanghai from April 4 to April 19 for a 15-day short-term forecast and comparing with real data, the results show that Shanghai’s international traffic blockade is effective and necessary.ConclusionThis research show that the control measures taken by Shanghai are very effective. At present, more and more countries and regions will face the current situation in Shanghai. We recommend that other countries and regions learn from Shanghai ’s successful experience in preventing overseas imports in order to fully prepare for epidemic prevention and control.
The influence of meteorology and air quality on parkrun athletic performance
Authors: Hodgson James Robert , Elliott Stephanie , Chapman Lee , Hudson Chris , Pope Francis D
Published: May 2020

Background

Despite increased awareness of climate change and urban air pollution, little research has been performed to examine the influence of meteorology and air quality on athletic performance of the general public and recreational exercisers. Anecdotal evidence of increased temperatures and wind speeds as well as higher relative humidity conditions resulting in reduced athletic performance has been presented in the past, whilst urban air pollution can have negative short- and long-term impacts on health. Furthermore, pollutants such as Ozone, Nitrogen Dioxide and Particulate Matter can cause respiratory and cardiovascular distress, which can be heightened during physical activity. Previous research has examined these impacts on marathon runners, or have been performed in laboratory settings. Instead, this paper focuses on the potential impacts on the general public. With the rise of parkrun events (timed 5 km runs) across the UK and worldwide concerns regarding public health in relation to both air quality and activity levels, the potential influence of air quality and meteorology on what is viewed as a ‘healthy’ activity has been investigated. A weekly dataset of parkrun participants at fifteen events, located in London UK, from 2011–2016 alongside local meteorological and air quality data has been analysed.
Results

The biggest influencer on athletic performance is meteorology, particularly temperature and wind speed. Regression results between parkrun finishing times and temperature predominantly show positive relationships, supporting previous laboratory tests. Increased relative humidity also causes slower finishing times but in several cases is not statistically significant. Higher wind speeds also result in slower times and in contrast to temperature and relative humidity, male participants are more influenced than female by this variable. Although air quality does influence athletic performance to an extent, the heterogeneity of pollutants within London and between parkrun events and monitoring sites makes this difficult to prove decisively.
Conclusions

It has been determined that temperature and relative humidity can have the largest detrimental impact on parkrun performance, with Ozone also having an impact. The influence of other variables cannot be discounted however and it is recommended that modelling is performed to further determine the extent to which ‘at event’ meteorology and air quality has on performance. In the future, there results can be used to determine safe operating and exercise conditions for parkrun and other public athletics events.
The HIV Epidemic In Colombia: Spatial And Temporal Trends Analysis﻿
Authors: Montana Jhon Freddy , Ferreira Glenda Roberta Oliveira Naiff , Cunha Carlos Leonardo Figueiredo , de Queiroz Ana Angelica Rego , Fernandes Wellington Augusto Andrade , Polaro Sandra Helena Isse , Gonçalves Lucia Hisako Takase , Couto Danielle Costa Carrara , Gir Elucir , Reis Renata Karina , Sorensen Wiliam , Botelho Elia Pinheiro
Published: May 2020

BACKGROUND – Colombia occupies 4th place among all Latin American countries in HIV/AIDS incidence rates, which have been increasing since the 1980s. There is a paucity of studies which address this trend. In this study we employed spatial and temporal trend analyses to study how the epidemic behaves in Colombian territory. METHODS - Our sample was composed of 72,994 HIV/AIDS cases and 21,898 AIDS-related deaths reported to the National Ministry of Health between 2008 and 2016. We employed the joinpoint regression model to analyze the annual HIV/AIDS incidence and AIDS mortality rates. In the spatial analysis we used univariate autocorrelation techniques and the Kernel density estimator. RESULTS – While the HIV/AIDS incidence had an increasing trend in Colombia, the AIDS mortality was stabilized. There was a downward trend in HIV/AIDS incidence and AIDS mortality among people between 0 to 14 years of age. An upward trend was observed for HIV/AIDS incidence in people older than 15 years of age and with the highest trend in 65 years and over group. AIDS mortality showed an increased trend in those 65 years old or over. The high-high clusters of HIV/AIDS incidence and AIDS mortality were located in the Andean and Caribbean regions. The HIV epidemic expanded from the North Caribbean region to Midwest Colombia.CONCLUSION – Sexual tourism and internal or external immigration might be responsible for the highest HIV/AIDS incidence and AIDS mortality rates observed in the Caribbean and Andean regions. Our results showed that Colombia needs to invest in specific and comprehensive public health policies to end HIV by 2030.
Development and validation of a nomogram to predict perioperative blood transfusion for gastric cancer surgery
Authors: Huang Haoquan , Han Zhixiao , Liang Xia , Liu Zhongqi , Cheng Shi , Cao Minghui
Published: May 2020

Background

This study aimed to construct and validate a nomogram composed of preoperative variables to predict perioperative blood transfusion for gastric cancer surgery.
Methods

600 gastric cancer patients undergoing gastrectomy between January 2010 and December 2015 were selected as primary cohort. 399 patients from January 2016 to June 2019 were collected as validation cohort. In the primary cohort, univariate and multivariate analyses were performed to identify independent risk factors for blood transfusion. Using Akaike information criterion, selected variables were incorporated to construct a nomogram. Validations of the nomogram were performed in the primary and validation cohort. Discrimination of the nomogram was assessed by the concordance index (C-index) and calibration of the nomogram was assessed by calibration curve and Hosmer–Lemeshow goodness-of-fit test.
Results

The following independent risk factors for transfusion were identified: Charlson comorbidity index score over 3 (odds ratio (OR) 2.15), tumor location (diffuse vs upper: OR 1.50), pTNM stage (III vs I: OR 3.17), type of gastrectomy (subtotal vs total gastrectomy: OR 0.58), extragastric organ resection (OR 2.03) and preoperative hemoglobin less than 80 g/l (vs over 120 g/l: OR 66.03). C-index was 0.863 and 0.901 in the primary and validation cohort, respectively, indicating good discrimination of the nomogram. Both calibration curves and Hosmer–Lemeshow goodness-of-fit tests (P-value 0.716 and 0.935) demonstrated high agreement between prediction and actual outcome.
Conclusion

A nomogram composed of preoperative variables to predict blood transfusion for gastric cancer surgery was developed and validated. This nomogram could be used to improve utilization of packed red blood cells.
Predictors of Failure on Second-line Antiretroviral Therapy with Protease Inhibitor Mutations in Uganda
Authors: Musana Hellen , Thaddeus Ssensamba Jude , Nakafeero Mary , Mugerwa Henry , Kiweewa Flavia Matovu , Serwadda David , Ssali Francis
Published: May 2020

Introduction Failure on second-line antiretroviral therapy (ART) with protease inhibitor (PI) mutations is on the rise. However, there is a paucity of information on the factors associated with this observation in the context of low-income countries. Knowledge of underlying factors is key if we are to minimize the number of PLHIV switched to costly third-line ART. Our study investigated the factors associated with failure on second-line ART with PI mutations. Methods We conducted a matched case-control analysis of patients' records kept at the Joint Clinical Research Center, starting from January 2008 to May 2018. We matched records of patients who failed the second-line ART with major PI mutations (cases) with records of patients who were virologically suppressed (controls) by a ratio of 1:3. Data analysis was conducted using STATA Version 14, and descriptive statistics comparing cases and controls were generated. Categorical variables were compared with the outcome, failure on second line ART with PI mutations using the Chi-square and Fisher's exact tests where appropriate. Conditional logistic regression for paired data was used to assess the association between the outcome and exposure variables, employing the backward model building procedure was done. Results Of the 340 reviewed patients' records, 53% were women, and 6.2% had previous Tuberculosis treatment. Males (aOR 2.64 CI: 1.0-4.64), type of second-line ART (aOR 3.92 CI: 1.15-13.38), and Tuberculosis treatment while on second-line ART (aOR7.08 CI: 2.35-21.29) highly predicted failure on second-line ART with PI mutations. Conclusion Males and patients concomitantly on Tuberculosis treatment while on second-line ART are at a higher risk of failing on second-line ART with PI mutations. HIV/AIDS response programs should give special attention to this group of people if we are to minimize the need for expensive third-line ART. More extensive explorative studies to ascertain underlying factors are recommended.
Distinct gut microbial communities and metabolic functions are associated with cachexia in lung cancer patients
Authors: Ni Yueqiong , Lohinai Zoltan , Heshiki Yoshitaro , Dome Balazs , Moldvay Judit , Dulka Edit , Gallfy Gabriella , Berta Judit , Weiss Glen , Sommer Morten , Panagiotou Gianni
Published: May 2020

Background

Cachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in the clinical setting by integrating shotgun metagenomics and plasma metabolomics of 38 lung cancer patients, with known cachexia status.
Results

The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, as well as vitamins, were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of plasma BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with the gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in the cancer cachectic patients. The involvement of gut microbiome in cachexia was further observed in a high-performance machine learning model that uses solely gut microbial taxonomic and pathway features to differentiate cachectic from non-cachectic cancer patients.
Conclusions

Our study demonstrates the links between host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible future therapeutic applications.
Fermented Astragalus in diet improved laying performance, egg quality, antioxidant and immunological status and intestinal microbiota in laying hens
Authors: Shi Hongtao , Wang Baiyu , Bian Chuanzhou , Han Yingqian , Qiao Hongxing
Published: May 2020

In the era of increased antibiotic resistance and ever stricter control on antibiotic use, it is urgent to develop green, safe and non-residue alternatives to antibiotics applied to the poultry industry. To this end, we supplied the potential Lactobacillus Plantarum (L. Plantarum) fermented Astragalus in the diet of laying hens, with a final addition of 3‰. Its effects have been assessed on laying performance, egg quality, antioxidant and immunological status and intestinal microbiota, and are compared to the control group, to the Astragalus group containing 3‰ unfermented Astragalus, and to the L. Plantarum group containing 2% L. Plantarum (1 × 108 CFU/mL). During the second half of the experimental period (15 to 28 days), the egg production rate was significantly higher in the fermented Astragalus group than that in the other groups, with the fermented Astragalus group having the lowest feed conversion ratio. No significant difference (P > 0.05) was observed among treatments on egg quality. Fermented Astragalus-treated hens exhibited significantly increased catalase (CAT), glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) in serum, and reduced malondialdehyde (MDA) in serum. Furthermore, fermented Astragalus supplementation resulted in a significant increase in ileal microbiota abundance relative to control. In conclusion, feeding laying hens with L. Plantarum fermented Astragalus has beneficial effects on production, antioxidant potential, immunity and ileal microbiota. L. Plantarum fermented Astragalus is expected to be a novel feed additive used in poultry production.
Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome
Authors: KIRUNGU Joy Nyangasi , MAGWANGA Richard Odongo , SHIRAKU Margaret Linyerera , Pu LU , MEHARI Teame Gereziher , Yuanchao XU , Yuqing HOU , AGONG Stephen Gaya , Yun ZHOU , Xiaoyan CAI , Zhou Zhongli , Kunbo WANG , Fang LIU
Published: May 2020

Background
Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genome, map A derived from an F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map 188 individual plants were used.
Results
The consensus linkage map had 1,492 markers across the 13 linkage groups; with a map size of 1,467.445 cM and average marker distance of 1.0370 cM. Chromosome D502 had the highest percentage of SD with 58.621% followed by Chromosome D507 with 47.887%. Six thousand and thirty eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2,308 and 3,730 genes were mined, respectively and were found to belong to 1,117 domains out of which 622 domains were common across the two chromosomes. Moreover, the first 9 domains were members of the plant resistance genes (R genes), while Pkinase; Protein kinase domain (PF00069) was the dominant group with 188 genes. Further analysis on the dominant domains revealed that 287 miRNAs were found to target various genes, such as the gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions in addition their higher expression at different stages fiber development.
Conclusion
The result obtained provided an indication of the important role of the SDRs in the evolution of significant genes in plants.
Brain tissue transcriptomic analysis of SIV-infected macaques identifies Poly (ADP-ribose) polymerases (PARPs) as potential biomarkers for neuropathogenesis.
Authors: Mavian Carla , Ramirez-Mata Andrea S , Dollar James Jarad , Nolan David J , Rich Shannan N , White Kevin , Magalis Brittany Rife , Cash Melanie N , Marini Simone , Prosperi Mattia , Amador David Moraga , Riva Alberto , Williams Kenneth C , Salemi Marco
Published: May 2020

Background. Despite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals’ quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified.Results. We investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n=11), with or without CD8+ lymphocyte depletion, based on detectable (n=6) or non-detectable (n=5) presence of the virus in frontal cortex tissues. S ignificant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion . In addition, transcripts of four poly (ADP-ribose) polymerases ( PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction.Conclusions. Our results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology .
A Composite Index Predicts Disease Progression in Early Stages of COVID-19: a Propensity Score-matched Cohort Study
Authors: Xu Jianjun , Hu Shaobo , Li Suzhen , Wang Weimin , Wu Yuzhe , Su Zhe , Zhou Xing , Cheng Xiang , Gao Yang , Zheng Qichang
Published: May 2020

Background: Thus far, studies on COVID-19 have focused on the epidemiology of the disease and clinical characteristics of patients (14-19), as well as on the risk factors associated with mortality during hospitalization in critical COVID-19 cases. However, no research has been performed on the prediction of progression in patients in the early stages of the disease. The aim of this work was to identify the early predictors of COVID-19 progression.Methods: The study included 338 patients with COVID-19 treated at two hospitals in Wuhan, Chian, from December, 2019 to March, 2020. Predictors of the progression of COVID-19 from mild to severe stages were selected by the logistic regression analysis. The predictive accuracy was evaluated further in the propensity score-matched cohort.Results: COVID-19 progression to severe and critical stages was confirmed in 78(23.1%) patients. The average value of the neutrophil-to-lymphocyte ratio (NLR) was higher in patients in the disease progression group than in the improvement group. Multivariable logistic regression analysis revealed that elevated NLR, LDH, and IL-10, were independent predictors of disease progression. The optimal cut-off value of NLR for predicting the progression of COVID-19 was 3.75. In the propensity score-matched cohort, NLR ≥ 3.75 was still an independent predictor of COVID-19 progression after multivariate analysis.Conclusions: The performed analysis demonstrates that NLR qualiﬁes as an independent predictor of disease progression in COVID-19 patients at the early stage of the disease. The combined evaluation of NLR and LDH improved the accuracy of the prediction of COVID-19 progression. Assessment of predictors might facilitate early identification of COVID-19 patients at high risk for disease progression and ensure timely administration of appropriate treatment to prevent mild cases from becoming severe.
Molecular Characterization of Plasmodium Falciparum DNA-3-Methyladenine Glycosylase
Authors: Pinthong Nattapon , Limudomporn Paviga , Vasuvat Jitlada , Adisakwattana Poom , Rattaprasert Pongruj , Chavalitshewinkoon-Petmitr Porntip
Published: May 2020

Background The emergence of artemisinin-resistant malaria parasite highlights the need for novel drugs and their targets. Alkylation in purine bases can hinder DNA replication if remained unsolved would eventually resulting in cell death. DNA-3-methyladenine glycosylase is an enzyme responsible for the repair of those alkylated lesions. Based on the AT-rich genome of Plasmodium falciparum and unexplored Plasmodium falciparum DNA-3-methyladenine glycosylase (PfMAG), therefore PfMAG should be characterized for its potential candidate for antimalarial drug development.Methods Bioinformatics analysis of PfMAG was performed. The native PfMAG from crude extract of chloroquine and pyrimethamine resistant Plasmodium falciparum strain K1 was partially purified using three columns. The existence of PfMAG activity leads to the cloning and expression of PfMAG for further characterization. The PfMAG was amplified, cloned to expression vector (pBAD202/D-TOPO), and expressed in Escherichia coli. The molecular weight of recombinant PfMAG was analyzed by SDS-PAGE and Western blot. Both functional and biochemical properties of the recombinant enzyme were characterized.Results PfMAG activity was most prominent in schizont. Native PfMAG was partially purified with a specific activity of 147.36 units/mg protein. The DNA sequence of amplified PfMAG showed an insertion of three nucleotides coding for asparagine compared to strain 3D7 and only 16% similarity compared to the human enzyme was observed. After cloning, the 74-kDa recombinant PfMAG was expressed and identified. PfMAG showed a larger size than its human counterpart twice. PfMAG preferred a double-stranded DNA substrate. Glycosylase activity was detected in a broad range of pH 5–8. The quite narrow optimal salt concentration was observed between 100–200 mM NaCl, whereas 250 mM NaCl reduces its activity. Divalent cations are not required for its glycosylase activity; on the contrary, they inhibited glycosylase activity in a concentration-dependent manner.Conclusion PfMAG activity increases according to parasite development. Native PfMAG was partially purified, the recombinant PfMAG was successfully expressed and characterized. An insertion of AAT coding for asparagine was found compared with that of strain 3D7. PfMAG differs from the human counterpart in a twice larger size and a wide range of optimal pH. Results obtained from this study will be a benefit for exploring and investigating of candidate targets toward antimalarial drug design in the future.