bluuebunny/crossref_metadata_2025 huggingface dataset:
LMM-22: An Enhanced Linear Mixed Model (LMM) Approach for Genome-Wide Association Studies (GWAS) for the Prediction of Diseases and Traits among Humans from Genomics Data
Authors: Sharma Siddharth
Published: May 2020

Increasingly, genomics is being used for the prediction of specific traits and diseases (phenotypes) among humans. Wider availability of genomics data through multiple research projects (such as International HapMap Project1 and 1000 Genomes2) has been a catalyst in that direction. With the recent advances in machine learning and big data analysis, data computation resources and data models needed for genomics data analysis are readily available. However, the prediction of traits and diseases has its own challenges in terms of computational requirements and computational analysis, statistical analysis (example: confounding variables), and limited quality of data collection. Linear Mixed Models (LMM, a type of linear regression) is a common approach for Genome-wide Association Studies (GWAS) for the prediction of common traits among humans using genomics. This paper researches the existing LMM-based approaches for Genome-wide Association Studies (GWAS), describes the experiment performed on FaST-LMM approach from Microsoft Research, and then proposes an enhanced approach (called LMM-22) on how to address computational and statistical issues. LMM-22 focuses on the parallelization of LMM computations and execution of LMM-22 on General Purpose Graphics Processing Units (GPU) as against CPUs to accelerate the LMM approach for GWAS studies.
CORINE Land Cover Data and Actual Arrangement of Buildings in Research on Processes of Concentration and Dispersion of Settlement: Example of Poland
Authors: Śleszyński Przemysław , Gibas Piotr , Sudra Paweł
Published: May 2020

The article describes the results of comparison of occurence of buildings (and address points) in Poland with delimitations of land use belonging to particular classes in the CORINE Land Cover (CLC) 2018 dataset. Large discrepancies have been identified, which reach on average approx. 34% of addresses and 35% of buildings located outside class 1 (artificial surfaces), mainly on terrains of class 2 (agricultural areas). Among single-family buildings it was 37% and among new addresses (forecasted or ‘under construction’ buildings) – as much as 50%. This puts a question mark over the possibility of using CLC data with resolution of 25 ha for monitoring of spatial planning and development in Poland for purposes of the diagnosis and assessment of the scale of dispersion of built-up areas. It is worth carrying out similar analyses in other countries, known for the deconcentration processes and a relatively large share of dispersed settlement e.g. other CEE countries, Spain, Portugal, Italy.
Rural Smallholder Farmers' Awareness and Use of ICT-Based Market Information Sources in South Africa
Authors: Nwafor Christopher , van der Westhuizen Carlu , Ogundeji Abiodun
Published: May 2020

The utility of ICTs for providing market information to rural smallholder farmers is growing rapidly, and access to reliable information and sources is considered crucial for beneficial market interaction. This study explored critical factors contributing to usage of electronic sources for market information search among rural smallholder livestock farmers. Using data collected from 129 respondents through a non-random sampling technique; descriptive and regression analysis was applied to identify key factors responsible for their awareness and use of ICT-based market information sources. Level of education was found to be a driver of awareness of ICT-based sources, and use of these sources was influenced by farmer-specific characteristics such as household size, education, income, membership of cooperatives and herd-size. The key ICT tools used was radio and mobile phones, widely available in the study area. Identified constraints to use of these ICTs include cost and patchy network signals in some areas. Policy interventions to reduce cost of mobile phone services and expansion of base stations; including practical recommendations for improved programming in radio and television offerings, are considered indispensable for greater uptake of e-information sources among smallholder livestock farmers.
Grey Wolf Based Wang’s Demons for Retinal Image Registration
Authors: Chakraborty Sayan , Pradhan Ratika , Ashour Amira S. , Moraru Luminita , Dey Nilanjan
Published: May 2020

Image registration has an imperative role in medical imaging. In this work, a grey-wolf optimizer (GWO) based non-rigid demons registration is proposed to support the retinal image registration process. A comparative study of the proposed GWO-based demons registration framework with cuckoo search, firefly algorithm, and particle swarm optimization- based demons registration is conducted. In addition, a comparative analysis of different demons registration methods, such as Wang’s demons, Tang’s demons, and Thirion’s demons which are optimized using the proposed GWO is carried out. The results established the superiority of the GWO-based framework which achieved 0.9977 correlation, and fast processing compared to the use of the other optimization algorithms. Moreover, GWO-based Wang’s demons performed better accuracy compared to the Tang’s demons and Thirion’s demons framework. It also achieved the best less registration error of 8.36×10-5.
Epidemic Peak for COVID-19 in India, 2020
Authors: Wagh Chaitanya S. , Mahalle Parikshit N. , Wagh Sanjeev J.
Published: May 2020

In India the first case of coronavirus disease 2019 (COVID-19) reported on 30 January 2020, and thereafter cases were increasing daily after the last week of Feb. 2020. COVID-19 identified as family member of coronaviridae where previously Middle East Respiratory Syndrome MERS and Severe Acute Respiratory Syndrome SARS belongs to same family. The COVID-19 attacks on respiratory system signing fever, cough and breath shortness, in severe cases may cause pneumonia, SARS or some time death. The aim of this study work is to develop model which predicts the epidemic peak for COVID-19 in India by using the real-time data from 30 Jan to 10 May 2020. There are uncertainties while identifying the population information due to the incomplete and inaccurate data, we initiate the most popular model for epidemic prediction i.e Susceptible, Exposed, Infectious, & Recovered SEIR initially the compartmental model for the prediction. Based on the solution of the state estimation problem for polynomial system with Poisson noise, we estimate that the epidemic peak may reach the early-middle July 2020, initializing recovered R0 to 0 and Infected I0 to 1. The outcomes of the model will help epidemiologist to isolate the source of the disease geospatially and analyze the death. Also government authorities will be able to target their interventions for rapidly checking the spread of the epidemic.
Multiple Indirect ELISAs for Serological Detection of SARS-CoV-2 Antibodies
Authors: Algaissi Abdullah , Alfaleh Mohamed A. , Hala Sherif , Abujamel Turki S. , Alamari Sawsan	S. , Alluhaybi Khalid A. , Hobani Haya I. , Alsulaiman Reem M. , Alharbi Rahaf H. , El-Assouli Mohammad Z. , Abdulaal Wesam H. , AL-Somali Afrah A. , Alofi Fadwa S. , Khogeer Asim A. , Mahmoud Ahmad Bakur , Alkayyal Almohanad A , Almontashiri Naif A.M. , Pain Arnab , Hashem Anwar M.
Published: May 2020

As the coronavirus disease 2019 (COVID-19), which is caused by the novel coronavirus SARS-CoV-2, continues to spread rapidly around the world, there is an urgent need for validated serological assays to evaluate viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological tests to study the antibody response in COVID-19 patients. In order to validate the assays, we determined the cut-off values, sensitivity and specificity of the developed assays using sera collected from COVID-19 patients in Saudi Arabia at different time points after disease onset, as well as sera that are seropositive to other human CoVs; namely MERS-CoV, hCoV-OC43, hCoV-NL63, hCoV-229E, and hCoV-HKU1. The SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N) ELISAs that we developed here not only showed high specificity and sensitivity, but also did not show any cross-reactivity with other CoVs. We also showed that all RT-PCR confirmed COVID-19 patients included in our study developed both virus specific IgM and IgG as early as one week after the onset of disease. The availability of these validated assays will enable us to determine the nature and duration of the antibody response mounted in response to SARS-CoV-2 infection. It will also allow conducting large-scale epidemiological studies to determine evidence of previous exposure to the virus and assess the true extent of virus spread within communities.
Governança aplicada às tecnologias sociais para populações em situação de risco socioeconômico associada ao paradigma da sustentabilidade
Authors: Castilhos Alexandre , Silva Tania Nunes da
Published: May 2020

O objetivo deste artigo é apresentar os resultados de uma pesquisa, estruturada a partir de uma perspectiva qualitativa, a fim de identificar os parâmetros iniciais para o desenvolvimento de uma abordagem de governança das tecnologias sociais associada à sustentabilidade, considerando a perspectiva multinível. A revisão de literatura compreendeu os eixos temáticos relacionados à governança, tecnologias sociais e abordagem multinível. O modelo analítico buscou relacionar informações obtidas junto às Instituições de Tecnologias Sociais no Brasil e, em um segundo momento, com as verificadas junto a outros dois grupos: i) as Instituições Formuladoras de Políticas Públicas em Tecnologias Sociais no Brasil e ii) as Instituições que Adotam Governança em Tecnologias Sociais no Brasil. Os resultados apontam para uma abordagem que busca uma nova forma de olhar a dinâmica das tecnologias sociais, problemas, inovações, modelos, estágios, transições, desafios e mudanças, a fim de contribuir para novos modelos de desenvolvimento social sustentável no Brasil.
“E Agora, José?” Decisões Coletivas e Relações Familiares em Finanças Solidárias
Authors: Tavares do Nascimento Ives Romero , Scalfoni Rigo Ariádne
Published: May 2020

Este Caso de Ensino visa promover a reflexão sobre o outro agir econômico e modelos de gestão alternativos baseados nas relações de proximidade e confiança presentes nas finanças solidárias através de uma experiência de um Comitê de Avaliação de Crédito (CAC) de um Banco Comunitário de Desenvolvimento (BCD) brasileiro, que precisou decidir pela concessão ou não de um microcrédito num contexto onde as relações familiares foram bastante consideradas no julgamento da solicitação. O que se espera é que o professor possa, através deste instrumento, proporcionar aos seus alunos a realidade que os bancos comunitários brasileiros possuem, oportunizando o debate sobre como a gestão social e a economia solidária, por exemplo, podem ser as respostas para essas situações. Ao final, as notas de ensino oferecem o aporte teórico-metodológico para o docente melhor utilizar o caso em sala de aula, apontando a decisão real tomada na experiência-base do texto e suas possíveis alternativas. Por fim, são indicadas referências que podem contribuir com a reflexão da situação aqui descrita e com a compreensão das temáticas abordadas.
Avaliação da Eficiência dos Gastos Públicos com Educação dos Municípios de Santa Catarina
Authors: Santos Rodolfo Rocha , De Freitas Marcelo Machado , Flach Leonardo
Published: May 2020

Esse artigo teve como objetivo verificar os fatores que afetam o nível de eficiência na aplicação dos recursos públicos em educação básica dos municípios de Santa Catarina. Para tanto, utilizou-se o método não paramétrico de análise envoltória de dados. Posteriormente, aplicou-se um modelo de regressão Tobit. Pode-se inferir, ao nível de significância de 10%, que a qualidade de vida de um município afeta positivamente a eficiência na aplicação dos recursos públicos com educação dos municípios catarinenses. O PIB apresentou uma relação negativa com a escala de eficiência, podendo-se afirmar que, ao nível de significância de 5%, municípios que apresentaram maior poder econômico foram menos eficientes. Por fim, a densidade demográfica apresentou uma relação positiva com a eficiência dos municípios catarinenses ao nível de significância de 10%, se entende que municípios mais densamente povoados podem apresentar uma maior demanda com educação sem a necessidade de uma maior aplicação de recursos.
De la teoría del lugar a la teoría del paisaje: no-lugar, distalidad y carácter
Authors: Riesco Chueca Pascual
Published: May 2020

Se intenta situar conceptualmente el lugar y su contrafigura, el no-lugar, en el marco de la teoría del paisaje. Para ello se comparan los atributos que han venido aplicándose a la noción de lugar con las dos dimensiones, apego e interacción, que sustentan nuestra matriz clasificatoria del paisaje. Dicha matriz, libremente inspirada en la teoría cultural “grid-group”, distingue cuatro tipos de paisaje. Un objeto del presente artículo es aclarar la posible ubicación de lugar y no-lugar dentro de la citada matriz. La discusión consiguiente muestra que tanto la clasificación como el propio concepto de paisaje encuentran en las dinámicas de lo contemporáneo un potente vector desestabilizador, que derrite los límites entre tipos, crea disrupción entre los atributos del paisaje y problematiza el concepto de carácter paisajístico.
Three monthly doses of 60 mg/kg praziquantel for Schistosoma haematobium infection is a safe and effective treatment regimen.
Authors: Darko Samuel Nkansah , Hanson Henry , Ankrah Sampson Twumasi , Baffour Sandra , Adjei-Kusi Priscilla , Yar Denis , Owusu-Dabo Ellis
Published: May 2020

Background: Praziquantel (PZQ) is the standard treatment for Schistosomiasis in sub-Saharan Africa. However, there is evidence suggesting praziquantel treatment failure in Schistosome infections with associated potential renal impairment. The objective of this study was to determine the effect of three monthly doses of 60 mg/kg/day PZQ on schistosome egg count, liver and renal function during the treatment of urinary schistosomiasis in Ghana.Methods: A nested case-control study was designed from a cohort screened for schistosomiasis; 28 schistosomiasis positive cases by microscopy matched with 53 healthy controls by age and gender. The study population was urban dwellers from the Asokwa sub-metropolitan area, Kumasi in Ghana. Participants were within the age range of 6 to 30 years. We assessed Schistosoma haematobium egg counts in urine and its associated impact on liver and renal function at baseline, treatment and post-treatment phases using serum. Results: Of the 28 cases and 53 controls, 78.6% and (81.1% were males respectively. Globulin levels before treatment was higher in cases [36.7 (32.8, 40.1) vrs 30.5 (22.4, 33.8), p=0.005] at pre-treatment but not at post-treatment [35.8 (31.2, 39.1) vrs 37.4 (29.7, 43.0), p= 0.767]. Estimated cure rate was 42.9%, 46.4% and 96.4% after first, second and third dose respectively. Schistosome egg counts dropped significantly (p= 0.001) from before second dose to post-treatment. Similarly, levels of alanine aminotransferase (p=0.001), aspartate aminotransferase (p=0.028) and gamma glutamyl transferase (p=0.001) significantly declined towards post-treatment. Estimated glomerular filtration rate significantly improved from before second dose to post-treatment using both the Chronic Kidney Disease Epidemiology Program (p=0.001) and 4-variable Modification of Diet in Renal Disease (p=0.002) equations. Conclusion: Treatment of urinary Schistosoma hematobium infections with a repeated high monthly dose of 60 mg/kg of praziquantel for 3 months is safe and effective.
Using Pulse Oximetry Waveforms to Detect Coarctation of the Aorta
Authors: Sorensen Matthew , Sadiq Ismail , Clifford Gari D. , Maher Kevin O. , Oster Matthew E.
Published: May 2020

Background Coarctation of the aorta is a common form of critical congenital heart disease that remains challenging to diagnose prior to clinical deterioration. Despite current screening methods infants with coarctation may present with life threatening cardiogenic shock requiring urgent hospitalization and intervention. We sought to improve critical congenital heart disease screening by using a novel pulse oximetry waveform analysis, specifically focused on detection of coarctation of the aorta. Methods and Results Over a 2-year period, we obtained pulse oximetry waveform data on 18 neonates with coarctation of the aorta and 18 age-matched controls hospitalized in the cardiac intensive care unit at Children’s Healthcare of Atlanta. Patients with coarctation were receiving Prostaglandin E1 and had a patent ductus arteriosus. By analyzing discrete features in the waveforms, we identified statistically significant differences in the maximum rate of fall between patients with and without coarctation. This was accentuated when comparing the difference between the upper and lower extremities, with the lower extremities having a shallow slope angle when a coarctation was present (p-value 0.001). Postoperatively, there were still differences in the maximum rate of fall between the repaired coarctation patients and controls; however, these differences normalized when compared with the same individual’s upper vs. lower extremities. Coarctation patients compared to themselves (preoperatively and postoperatively), demonstrated waveform differences between upper and lower extremities that were significantly reduced after successful surgery (p-value 0.028). This screening algorithm had an accuracy of detection of 72% with 0.61 sensitivity and 0.94 specificity. Conclusions We were able to identify specific features in pulse oximetry waveforms that were unique to patients with coarctation and further demonstrated that these changes normalized after surgical repair. Pulse oximetry screening for congenital heart disease in neonates may thus be improved by including waveform analysis, aiming to identify coarctation of the aorta prior to critical illness. Further large-scale testing is required to validate this screening model among patients in a newborn nursery setting who are low risk for having coarctation.
The Effect of Transtheoretical Model-lead Intervention for Knee Osteoarthritis in Older Adults: A Cluster Randomized Trial
Authors: Wang Limin , Chen Hongbo , Lu Han , Wang Yunlin , Liu Congying , Dong Xu , Chen Jieru , Liu Nan , Yu Fang , Wan Qiaoqin , Shang Shaomei
Published: May 2020

Background: Knee osteoarthritis (KOA) is a common joint disease in people over 60 years old. Exercise therapy is one of the most effective non-pharmacological treatments for KOA, but low exercise adherence needs to be improved. The present study aimed to evaluate the effect of the Transtheoretical Model-lead home exercise intervention (TTM-HEI) program on exercise adherence, KOA symptoms, and knee function in older adults with KOA. Methods: A two-arm, superiority, assessor-blinded, cluster randomized trial was conducted. Community-dwelling older adults with KOA were recruited from 14 community centers in Beijing, China, via print and social media advertisements from April to October 2018. The present study lasted 48 weeks, with an intervention duration of 0–24 weeks and follow-up time of 24–48 weeks. The intervention was a two-stage and 24-week TTM-based exercise program, and the control group underwent a same-length exercise program guidance without any exercise-adherence interventions. The primary outcome was exercise adherence to the prescribed home exercise program and was measured using an 11-point numerical (0=not at all through and 10=completely as instructed) self-rating scale at week 4, 12, 24, 36, and 48 after the program started. KOA symptoms (pain intensity and joint stiffness) were measured using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and knee function (lower limb muscle strength and balance) was measured using the Five-Times-Sit-to-Stand Test (FTSST) and the Timed Up and Go Test (TUG) at baseline, week 24 and week 48. Latent growth model (GLM), repeated measures ANOVA, and independent t-test were the main statistical tests used.Results: A total of 189 older adults (intervention group: n = 103, control group: n = 86) were enrolled. Differences of any outcome measures at baseline were not significant between groups. The growth rate of exercise adherence in the intervention group increased 2.175 units compared with the control group (unstandardized coefficient of slope on group B2 = 2.175, p < 0.001), and the intervention program maintained participants’ exercise adherence with 5.56 (SD = 1.00) compared with 3.16 (SD = 1.31) in the control group at week 48. In addition, TTM-HEI program showed significant effects on relieving KOA symptoms and improving knee function.Conclusion: Over time, TTM-HEI could improve participants’ exercise adherence, KOA symptoms, and knee function.Trial registration: This study was approved by the ethics committee (IRB00001052-17066) in July 2017 and was registered at Chinese Clinical Trails Registry (website: www.chictr.org.cn, registry number: ChiCTR1800015458).
Prion peptide-mediated calcium level alteration governs neuronal cell damage through AMPK-autophagy flux
Authors: Moon Ji-Hong , Park Sang-Youel
Published: May 2020

Background The distinctive molecular structure of the prion protein, PrPsc, is established only in mammals with infectious prion diseases. Prion protein characterizes either the transmissible pathogen itself or a primary constituent of the disease. Our report suggested that prion-mediated neuronal cell death is triggered by the autophagy flux. However, the alteration of intracellular calcium levels, AMPK activity in prion models has not been described. This study is focused on the effect of the changes in intracellular calcium levels on AMPK/autophagy flux pathway and PrP (106–126)-induced neurotoxicity. Methods Western blot and Immunocytochemistry was used to detect AMPK and autophagy-related protein expression. Flow cytometry and a TdT-mediated biotin-16-dUTP nick-end labeling (TUNEL) assay were used to detect the percentage of apoptotic cells. Calcium measurement was employed using fluo-4 by confocal microscope. Results We examined the effect of calcium homeostasis alterations induced by human prion protein on the autophagy flux in neuronal cells. Treatment with human prion protein increased the intracellular calcium concentration and induced cell death in primary neurons as well as in a neuronal cell line. Using pharmacological inhibitors, we showed that the L-type calcium channel is involved in the cellular entry of calcium ions. Inhibition of calcium uptake prevented autophagic cell death and reduction in AMP-activated protein kinase (AMPK) activity induced by human prion protein. Conclusion Our data demonstrated that prion protein-mediated calcium inflow plays a pivotal role in prion protein-induced autophagic cell death, and reduction in AMPK activity in neurons. Altogether, our results suggest that calcium influx might play a critical role in neurodegenerative diseases, including prion diseases.
A daf-7-related TGF-β ligand (Hc-tgh-2) shows important regulations on the development of Haemonchus contortus
Authors: He Li , Liu Hui , Zhang Biying , Li Fangfang , Di Wenda , Wang Chunqun , Zhou Caixian , Liu Lu , Li Tingting , Zhang Ting , Fang Rui , Hu Min
Published: May 2020

Background In most multicellular organisms, transforming growth factor-β (TGF-β) signalling pathway is involved in regulating the growth and stem cell differentiation. Previous studies have demonstrated the importance of three key molecules in this pathway in the parasitic nematode Haemonchus contortus , including one TGF-β type I receptor ( Hc-tgfbr1 ), one TGF-β type II receptor ( Hc-tgfbr2 ), and one co-Smad ( Hc-daf-3 ), which regulated the developmental transition from the free-living to the parasitic stages of this parasite. However, almost nothing is known about the function of the TGF-β ligand ( Hc-tgh-2 ) of H. contortus . Methods Here, the temporal transcription profiles of Hc-tgh-2 at eight different developmental stages and spacial expression patterns of Hc- TGH-2 in adult female and male worms of H. contortus have been examined by real-time PCR and immunohistochemistry, respectively. In addition, RNA interference (RNAi) by soaking was employed to assess the importance of Hc-tgh-2 in the development from exsheathed third-stage larvae (xL3s) to fourth-stage larvae (L4s) in H. contortus . Results Hc-tgh-2 was continuously transcribed in all eight developmental stages of H. contortus studied with the highest level in the infective third-stage larvae (iL3) and Hc -TGH-2 was located in the muscle of the body wall, intestine, ovary of adult females and testes of adult males. Silencing Hc-tgh-2 by the specific double-stranded RNA (dsRNA), decreased the transcript level of Hc-tgh-2 and resulted in fewer xL3s developing to L4s in vitro. Conclusions These results suggested that the TGF-β ligand, Hc -TGH-2, could play important roles in the developmental transition from the free-living (L3s) to the parasitic stage (L4s). Furthermore, it may also take part in the processes such as digestion, absorption, host immune response and reproductive development in H. contortus adults.
Nontuberculous Mycobacterial Endophthalmitis: Case Series and Review Literature
Authors: Pinitpuwadol Warinyupa , Tesavibul Nattaporn , Boonsophon Sutasinee , Sakiyalak Darin , Sarunket Sucheera , Choopong Pitipol
Published: May 2020

Background: To report three cases of nontuberculous mycobacterial (NTM) endophthalmitis following multiple ocular surgeries and to review previous literature in order to study the clinical profile, treatment modalities, and visual outcomes among patients with NTM endophthalmitis.Methods: Clinical manifestation and management of patients with NTM endophthalmitis in the Department of Ophthalmology, Faculty of Medicine, Siriraj hospital, Mahidol University, Bangkok, Thailand were described. In addition, a review of previously reported cases and case series from MEDLINE was performed. The clinical information and type of NTM from the previous studies and our cases were summarized.Results: We reported three cases of NTM endophthalmitis caused by M. haemophilum, M. fortuitum and M. abscessus and a summarized review of 95 additional cases previously published. Of 98 patients, there were 85 exogenous endophthalmitis (86.7%) and 13 endogenous endophthalmitis (13.3%). The patients’ age ranged from 13 to 89 years with mean of 61.1±18.7 years with no gender predominance. Exogenous endophthalmitis occurred in both healthy and immunocompromised hosts, mainly caused by cataract surgery (62.4%). In contrast, almost all endogenous endophthalmitis patients were either primary or secondary immunocompromised. Among all patients, previous history of tuberculosis infection was identified in 4 cases (4.1%). Rapid growing NTMs were responsible for exogenous endophthalmitis, while endogenous endophthalmitis were commonly caused by slow growers. Treatment regimens consisted of macrolides, fluoroquinolones or aminoglycosides, which were continued for up to 12 months. Initial and final vision were generally worse than 6/60. There were no significant differences of initial and final vision between exogenous and endogenous causes (p=1.000, 0.446, respectively).Conclusions: NTM endophthalmitis is a serious intraocular infection that leads to irreversible loss of vision. The presentation can mimic a chronic recurrent or persistent intraocular inflammation. History of multiple intraocular surgeries or immune-deficiency in patient with chronic panuveitis should raise the practioner’s suspicion of NTM endophthalmitis. Appropriate diagnosis and treatment are important to optimize visual outcome.
Live Poultry Market Closure and Avian Influenza A (H7N9) infection in cities of China, 2013-2017: An ecological study
Authors: Chen Ying , Cheng Jian , Xu Zhiwei , Hu Wenbiao , Lu Jiahai
Published: May 2020

Background Previous studies have proven that the closure of live poultry markets (LPMs) was an effective intervention to reduce human risk of avian influenza A (H7N9) infection, but evidence is limited on the impact of scale and duration of LPMs closure on the transmission of H7N9. Method Five cities (i.e., Shanghai, Suzhou, Shenzhen, Guangzhou and Hangzhou) with the largest number of H7N9 cases in mainland China from 2013-2017 were selected in this study. Data on laboratory-confirmed H7N9 human cases in those five cities were obtained from the Chinese National Influenza Centre. The detailed information of LPMs closure (i.e., area and duration) was obtained from the Ministry of Agriculture. We used a generalized linear model with a Poisson link to estimate the effect of LPMs closure, reported as relative risk reduction (RRR). We used classification and regression trees (CARTs) to select and quantify the dominant factor of H7N9 infection. Results All five cities implemented the LPMs closure, and the risk of H7N9 infection decreased significantly after LPMs closure with RRR ranging from 0.80-0.93. Respectively, a long-term LPMs closure for 10-13 weeks elicited a sustained and highly significant risk reduction of H7N9 infection (RRR = 0.98). Short-time LPMs closure with 2 weeks in every epidemic did not reduce the risk of H7N9 infection (p>0.05). Partially closed LPMs in some suburbs contributed only 35% for reduction rate (RRR=0.35). Shenzhen implemented partial closure for first 3 epidemics (p>0.05) and all closure in the latest 2 epidemic waves (RRR=0.64). Conclusion Our findings suggest that LPMs all closure in whole city can be a highly effective measure comparing with partial closure (i.e. only urban closure, suburb and country remain open). Extend the duration of closure and consider permanently closing the LPMs will help improve the control effect. The effect of LPMs closure is greater than that of meteorology on H7N9 transmission.
Efficacy of Chloroquine versus Lopinavir/Ritonavir in mild/general COVID-19: a prospective, open-label, multicenter randomized controlled clinical study
Authors: Liu Xi , Chen Huili , Shang Yuqi , Zhu Hongqiong , Chen Gongqi , Chen Yuanli , Liu Shaoxuan , Zhou Yaoyong , Huang Mingxing , Hong Zhongsi , Xia Jinyu
Published: May 2020

Background The outbreak of novel coronavirus pneumonia is very serious, and no effective antiviral treatment has been confirmed. The fresh drug research and development cycle is too long to meet clinical emergency needs, and "old drugs and brand new applications" have a huge therapeutic potential. During our previous treatment, we found that the lopinavir/ritonavir treatment recommended in the Fifth edition of the treatment plan had little effect. Earlier studies have shown that chloroquine can inhibit coronavirus replication through multiple mechanisms. Our previous use of chloroquine to treat patients with SARS-CoV-2(novel coronavirus)-infected pneumonia has a higher negative rate of nucleic acid in throat swabs within 5 days after administration than that using lopinavir/ritonavir. However, the half-life and side effects of chloroquine vary greatly among individuals. Methods/design We plan to conduct a prospective, open-label, multicenter randomized controlled, comprehensive treatment clinical study. The study consisted of three phases: a screening period of 1-110 days, a treatment period of no more than 28 days, and a follow-up period of 1 month. Participants will be assessed at baseline and on days 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 21, and 28 after the intervention begins. In this study, chloroquine and lopinavir/ritonavir tablets were used to treat patients with eligible novel coronavirus pneumonia diagnosed at various centers between February 12, 2020 and May 31, 2020. The efficacy and safety of chloroquine and lopinavir/ritonavir are to be evaluated. At the same time, explore the correlation between patient genetic polymorphisms and chloroquine steady-state concentration, therapeutic effects and adverse reactions in the body. It is an anti-virus for pneumonitis caused by novel coronavirus. The optimization and update of the antiviral treatment plan provides evidence-based evidence. Disscussion Our study is a prospective, open-label, multicenter randomized controlled, comprehensive treatment clinical study to evaluate the efficacy and safety of chloroquine phosphate and lopinavir/ritonavir in patients with mild/general COVID-2019. The results of this study will provide valuable clinical evidence for the treatment of novel coronavirus pneumonia.
Revealing the full-length transcriptome of caucasian clover rhizome development
Authors: Yin Xiujie , Yi Kun , Zhao Yihang , Hu Yao , Li Xu , He Taotao , Liu Jiaxue , Cui Guowen
Published: May 2020

Background: Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant up-regulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.
Adherence to Highly Active Antiretroviral Therapy and Its Association with HIV Disclosure status among People Living with HIV/AIDS in Ethiopia: A systematic review and Meta-Analysis.
Authors: Azagew Abere Woretaw , Mekonnen Chilot Kassa , Ferede Abebaw Jember , Yazew Kassahun Gebeyehu , Tezera Zewdu Baye
Published: May 2020

Background:Adherence to Highly Active Antiretroviral Therapy (HAART) medication is the pressing public health problem worldwide. Non-adherence to HAART leads to treatment failure, immunologic failure, and virological failure. Despite different interventions made; still, HAART medication adherence among adult people living with HIV/AIDS (PLWHA) is inconsistent across studies and the effect of HIV disclosure status was not well studied. Therefore this study determines the pooled prevalence of HAART adherence and its relationship with HIV disclosure status among Adult PLWHA.MethodsWe searched 3247 both published and unpublished original articles from January 2016 to November 2019 in Ethiopia using different search engines. Data were extracted using Microsoft excel. New Castle Ottawa Scale quality assessment tool was used. STATA software version 11 was used for analysis. A random-effects meta-analysis was performed. Cochran Q statistics and I2 were used to estimate heterogeneity. Eggers and Begg’s test was used to assess the publication bias.ResultsA total of 15 studies for systematic review and four studies for Meta-analysis were used. The pooled prevalence of HAART medication adherence is found to be 81.19% (80.132, 82.248). In the subgroup analysis, the pooled prevalence of HAART adherence was 79.82% (73.19, 86.45) in the Oromia region, 82.51% ( 73.14, 91.87) in the Amhara region, and 72.7% (63.78, 81.61) in the SNNPR. HIV disclosure improves HAART adherence by nearly three times compared to non-HIV disclosed HAART users (AOR=2.99, 95%CI: 1.88, 4.77).Conclusions﻿The pooled prevalence of HAART adherence among adult PLWHA was found to be low. Having HIV disclosure improved HAART medication adherence.
Clinical parameters predictive for sphincter-preserving surgery and prognostic outcome in patients with locally advanced low rectal cancer
Authors: Partl Richard , Magyar Marton , Hassler Eva , Langsenlehner Tanja , Kapp Karin Sigrid
Published: May 2020

Background Although controversial, there are data suggesting that clinical parameters can predict the probability of sphincter preserving procedures in rectal cancer. The purpose of this study was to investigate the association between clinical parameters and the sphincter-preserving surgery rate in patients who had undergone neoadjuvant combination therapy for advanced low rectal cancer. Methods In this single center study, the charts of 540 patients with locally advanced rectal cancer who had been treated with induction chemotherapy-and/or neoadjuvant concomitant radiochemotherapy (nRCT) over an 11-year period were reviewed in order to identify patients with rectal cancer ≤6 cm from the anal verge, who had received the prescribed nRCT only. Univariate and multivariate analyses were used to identify pretreatment patient- and tumor associated parameters correlating with sphincter preservation. Survival rates were calculated using Kaplan-Meier analyses.Results 280 of the 540 patients met the selection criteria. Of the 280 patients included in the study, 158 (56.4%) underwent sphincter-preserving surgery. 164 of 280 patients (58.6%) had a downsizing of the primary tumor (ypT < cT) and 39 (23.8%) of these showed a complete histopathological response (ypT0 ypN0). In univariate analysis, age prior to treatment, Karnofsky performance status, clinical T-size, relative lymphocyte value, CRP value, and interval between nRCT and surgery, were significantly associated with sphincter-preserving surgery. In multivariate analysis, age (hazard ratio (HR)=1.05, CI95%: 1.02-1.09, p=0.003), relative lymphocyte value (HR=0.94, CI95%: 0.89-0.99, p=0.029), and interval between nRCT and surgery (HR=2.39, CI95%: 1.17-4.88, p=0.016) remained as independent predictive parameters. A significant longer disease-free (p =0.009) and overall survival (p =0.004) were observed in the sphincter-preserving surgery group. Conclusions These clinical parameters can be considered in the prognostication of sphincter-preserving surgery in case of low rectal adenocarcinoma. More future research is required in this area.
Current status of periodontitis and its association with tobacco use among adult population of Sunsari district, Nepal
Authors: Goel Khushboo , Sharma Shivalal , Baral Dharnidhar , Agrawal Santosh
Published: May 2020

Background: Tobacco products are considered significant but preventable factors related to initiation and progression of periodontal diseases. We assessed the prevalence of periodontitis and evaluated its association with tobacco use and other factors among the adult population of eastern Nepal.Methods: A community-based cross-sectional study was conducted in the rural municipalities in the province one of eastern Nepal. A total of 440 individuals were interviewed with a set of a standardized pre-tested semi-structured questionnaire. Data on social demographics, adverse oral habits followed by periodontal clinical examination were recorded. Prevalence of periodontitis was assessed by a case definition given by CDC-AAP. Univariate and multivariate logistic regression analysis was used to measure the association between tobacco use and other factors with periodontitis.Results: The overall prevalence of periodontitis was found to be 71.6%. Majority (85.4%) of tobacco users had periodontitis and they were significantly associated with the disease and its severity. The study identified age groups, 45-65 years (AOR=7.585, 95% CI, 3.938-14.610), plaque index (AOR=1.017, 95% CI, 1.005- 1.029), smoking (AOR=3.149, 95% CI, 1.364- 7.270), khaini users (smokeless tobacco, AOR=2.275, 95% CI, 1.122-4.613) and teeth loss (AOR=2.025, 95% CI, 1.211-3.387) as the significant factors associated with periodontitis. Conclusion: Almost three-quarters of the adult population had some form of periodontitis. Oral hygiene awareness programs, educational efforts and tobacco cessation policies targeted to limit the modifiable factors should be considered immediately at the community level.
Importance of GWAS risk loci and clinical data in predicting asthma using machine-learning approaches
Authors: Liang Si-Qiao , Long Jian-Xiong , Deng Jingmin , Wei Xuan , Yang Mei-Ling , Tang Shao-Jie , Qin Hua-jiao , Zhou Jian-Peng , Li Hai-Li
Published: May 2020

Asthma is a serious immune-mediated respiratory airway disease. Its pathological processes involve genetics and the environment, but it remains unclear. To understand the risk factors of asthma, we combined genome-wide association study (GWAS) risk loci and clinical data in predicting asthma using machine-learning approaches. A case–control study with 123 asthma patients and 100 healthy controls was conducted in Zhuang population in Guangxi. GWAS risk loci were detected using polymerase chain reaction, and clinical data were collected. Machine-learning approaches (e.g., extreme gradient boosting [XGBoost], decision tree, support vector machine, and random forest algorithms) were used to identify the major factors that contributed to asthma. A total of 14 GWAS risk loci with clinical data were analyzed on the basis of 10 times of 10-fold cross-validation for all machine-learning models. Using GWAS risk loci or clinical data, the best performances were area under the curve (AUC) values of 64.3% and 71.4%, respectively. Combining GWAS risk loci and clinical data, the XGBoost established the best model with an AUC of 79.7%, indicating that the combination of genetics and clinical data can enable improved performance. We then sorted the importance of features and found that the top six risk factors for predicting asthma were rs3117098, rs7775228, family history, rs2305480, rs4833095, and body mass index. Asthma-prediction models based on GWAS risk loci and clinical data can accurately predict asthma and thus provide insights into the disease pathogenesis of asthma. Further research is required to evaluate more genetic markers and clinical data and predict asthma risk.
Outcomes of and factors associated with partner notification and HIV testing in Northeastern Tanzania.
Authors: Lyamuya Furaha Seraphin , Muro Eva Prosper , Manongi Rachel , Mushi Declare , Kiwelu Irene , Katzenstein Terese , Theilgaard Zahra
Published: May 2020

Background: There is growing evidence of high effectiveness of partner notification (PN) in reaching previously undiagnosed sexual partners. As a result, there is increasing implementation of PN in sub-Saharan Africa. Tanzania, like other countries in the region, has recently expanded PN in HIV testing services. However, this approach is unlikely to yield the expected results if not well implemented. This study aimed to identify gaps and provide recommendations to improve routine implementation of PN in Tanzania.Methods: A cross-sectional study was conducted across seven care and treatment centers (CTCs) in the Kilimanjaro region from November 2018 to April 2019. A total of 297 newly diagnosed HIV infected clients with sexual partner(s) in the past 24 months were recruited at 2 months of their CTC enrollment. Interviews using structured questionnaires were conducted. Descriptive statistics, bivariate and multivariate regression analyses were done.Results: Two-thirds (195) were females. The majority 165 (85%) of those counseled and had partner(s) not previously tested for HIV consented to PN. They all chose passive PN with 102 (62%) reporting successful HIV status disclosure to their partner(s). Reporting disclosure was associated with; being married adjusted odds ratio (aOR 5.1, 95%CI: 2.4–10.9, p < 0.001), in a relationship for > 10 years (aOR 4.9, 95%CI: 1.3–17.6, p = 0.02) and living with the partner(s) (aOR 3.4, 95%CI: 1.3–9.1, p = 0.02). Fifty-three clients (27%) of those with partners not previously tested for HIV reported partner HIV testing following PN, associated with being married (aOR 3.4, 95%CI: 1.3-9, p < 0.02) and living with the partner (aOR 4.5, 95%CI: 1.3–15, p < 0.02). Male partner(s) had lower odds of successful HIV testing (aOR 0.4, 95%CI: 0.2–0.9, p = 0.02). Thirty-seven (67%) of those tested were HIV infected.Conclusions: Detection rate of previously undiagnosed HIV infection among clients referred for HIV-testing through PN was high. However, a significant number of partners did not report for HIV testing after 2 months of index clients CTC enrollment. Initiatives to improve PN are needed with special attention towards those who are single, not living with their partners, in a relationship for < 10 years as well as male sexual partners.
A Mokken Scale Analysis of the Kessler-6 Screening Measure among Chinese Elderly Population: Findings from a national survey
Authors: Zhang Lisong , Li Zhongquan
Published: May 2020

Background
The ageing population increases rapidly across the world. Timely and effective screening of their mental health problems is important to individuals, families and the whole society. The Kessler-6 screening measure (K6) is a very popular instrument for non-specific psychological distress. However, few studies have focused on the psychometric properties of this instrument in the elderly population.
Methods
The present study employed Mokken scale analysis to evaluate its dimensionality and structure, and employed differential item functioning (DIF) to examine whether the same structure existed across sex in a national representative sample of old Chinese people. Data were drawn from a public data set, the 2010 China Family Panel Studies (CFPS2010), and responses from a total of 6450 participants aged 60 years old and above (3136 males and 3314 females) were included in the final analysis.
Results
Mokken scale analysis supported the unidimensional structure of the K6. Differential item functioning (DIF) analysis revealed that two of the six items ("Hopeless" and "Everything was an effort") were marked for DIF based on the Chi-square. However, their impacts were negligible in term of McFadden's pseudo R2.
Conclusions
The K6 demonstrates adequate psychometric properties in the old Chinese population. The sum of all six items can be used as an indicator of non-specific psychological distress. Differences in the indicator across gender should be considered as a real difference in psychological distress between the female and the male.