bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative Analysis of Histopathological Images and Genomic Data in Colon Adenocarcinoma
Authors: Li Hui , Zeng Hao , Chen Linyan , Liao Qimeng , Ji Jianrui , Ma Xuelei 
Published: October 2020

Abstract
Background: Colon adenocarcinoma (COAD) is one of the highest morbidity cancers all over the world. Its 5-year survival is no more than 60% even in European countries with the highest survival rates. The histopathological information is crucial for the prognosis and therapy of COAD. Application of the digital whole slide imaging system enables us to read histopathological sections digitally. Apart from that, cancer genomics is also an important prognostic factor.Methods: To identify prognosis biomarkers of COAD, we downloaded whole-slide histopathological images from TCIA database. After processing these images, histopathological features were extracted by CellProfiler. Least Absolute Shrinkage and Selection Operator and Support Vector Machine Recursive Feature Elimination were followed applied, screening out 5 prognosis-related features. Weighted gene co-expression network analysis (WGCNA) was operated to find co-expression gene module correlated with prognosis-related features. The samples were divided into a training set and a testing set on a scale of 70% and 30%. Random forest was applied to construct histopathologic-genomic prognosis factor (HGPF) using prognosis-related features and genomic data. After that, we combined HGPF and clinical characteristics with nomogram and verify its predictive efficacy.Results: The time-dependent ROC was drawn to evaluate the efficacy of prognostic model. In the training set, 1-year, 3-year and 5-year AUCs are respectively 0.948, 0.916, 0.933. In the testing set, 1-year, 3-year and 5-year AUCs are respectively 0.913, 0.894, 0.924. In addition, patients were separated into high-risk survival group and low-risk survival group by HGPF. Survival analysis indicates that the low-risk patients’ survival was significantly better than high-risk patients’ in both training set and testing set. It is suggested that histopathological image features have certain ability to predict COAD survival, which can be further improved by means of multi-omics combination.Conclusions: In conclusion, this study constructs an integrative prognosis model based on histopathological and genomic features, which may have some guidance effect on prognosis and clinical decision of COAD patients. Furthermore, the underlying biological mechanisms of this multi-omics model require further study.
Red and Fallow Deer Determine the Density of Ixodes Ricinus Nymphs Containing Anaplasma Phagocytophilum
Authors: Takumi Katsuhisa , Hofmeester Tim , Sprong Hein 
Published: October 2020

Abstract
Background: The density of Ixodes ricinus nymphs infected with Anaplasma phagocytophilum is one of the parameters that determines the risk for humans and domesticated animals to contract anaplasmosis. For this, I. ricinus larvae need to take a blood meal from free-ranging ungulates, which are competent hosts for A. phagocytophilum.Methods: Here, we compared the contribution of four free-ranging ungulate species, red deer (Cervus elaphus), fallow deer (Dama dama), roe deer (Capreolus capreolus), and wild boar (Sus scrofa) to A. phagocytophilum infections in nymphs. We used a combination of camera and live trapping to quantify the relative availability of vertebrate hosts to questing ticks in nineteen Dutch forest sites. Additionally, we collected questing I. ricinus nymphs and tested these for the presence of A. phagocytophilum. Furthermore, we explored two potential mechanisms that could explain differences between species: 1) differences in larval burden, which we based on data from published studies, and 2) differences in associations with other, non-competent hosts.Results: Principal component analysis indicated that the density of A. phagocytophilum infected nymphs (DIN) was higher in forest sites with high availability of red and fallow deer, and to a lesser degree roe deer. Initial results suggest that these differences are not a result of differences in larval burden, but rather differences in associations with other species or other ecological factors.Conclusions: These results indicate that the risk for contracting anaplasmosis in the Netherlands is likely highest in the few areas where red and fallow deer are present. Future studies are needed to explore the mechanisms behind this association.
Improvement of Water Quality for Mass Anopheline Rearing: Evaluation of the Impact of Ammonia-capturing Zeolite on Larval Development and Adult Phenotypic Quality
Authors: AKPODIETE NWAMAKA OLUCHUKWU , Tripet Frederic 
Published: October 2020

Abstract
BackgroundVector control approaches that rely on mosquito releases such as the sterile insect technique (SIT) and suppression or replacement strategies relying on genetically modified mosquitoes (GMM) depend on effective mass production of Anopheles mosquitoes. For optimal development, Anophelines typically require relatively clean water which can be in short supply in some settings. Water replacement requires complex and onerous continuous-flow-systems and/or expensive water filtration systems like ultrafiltration and reverse osmosis. Thus, there is a need for simple cost-effective water management and treatment solutions. Zeolites are additives that have been extensively applied in fish and crustacean aquaculture to improve water quality because of their selective adsorption of ammonia and toxic heavy metals. The many advantages of zeolites include low cost, abundance in many parts of the world and their environmental friendliness, but so far they have not been exploited for mosquito rearing.MethodsThis study evaluated the independent effects of zeolite and daily water changes (to simulate a continuous flow system) on the rearing of An. coluzzii under two feed regimes (powder or solution feed) and larval densities (200 and 400 larvae per tray). The duration of larval development, adult emergence success and phenotypic quality (body size) were recorded to assess the impact of water treatments on mosquito numbers and phenotypic quality and to identify the optimal feeding regimes and density for zeolite use.ResultsOverall, mosquito emergence, duration of development and adult phenotypic quality was significantly better in treatments with daily water changes. In treatments without daily water changes, zeolite significantly improved water quality at the lower larval rearing density, resulting in higher mosquito emergence. Duration of development was significantly longer in zeolite treatments. At the lower larval rearing density, adult phenotypic quality did not significantly differ between zeolite treatment without water changes and those with daily changes. ConclusionsThese results suggest that treating rearing water with zeolite can improve mosquito production under some conditions, and thus offer a cheaper alternative to more expensive techniques such as ultrafiltration or reverse osmosis, which are often part of continuous water change systems. Further studies are needed to optimize its uses for rearing Anopheles gambiae s.l.
Factors Associated With Involuntary Psychiatric Hospitalization in Portugal
Authors: Silva Manuela , Antunes Ana , Azeredo-Lopes Sofia , Loureiro Adriana , Saraceno Benedetto , Caldas-de-Almeida José Miguel , Cardoso Graça 
Published: October 2020

Abstract
BackgroundIdentifying which factors contribute to involuntary psychiatric hospitalization may support initiatives to reduce its frequency. This study examines the sociodemographic, clinical, and contextual factors associated with involuntary hospitalization of patients from five Portuguese psychiatric departments in 2002, 2007 and 2012.MethodsData from all admissions were extracted from clinical files. A Poisson generalized linear model estimated the association between the number of involuntary hospitalizations per patient in one year and sociodemographic, clinical, and contextual factors.ResultsMale gender [exp(β̂) = 1.31; 95%CI:1.06-1.62, p<0.05], having secondary and higher education [exp(β̂) = 1.45; 95%CI:1.05-2.01, p<0.05, and exp(β̂) = 1.89; 95%CI:1.38-2.60, p<0.001, respectively], a psychiatric diagnosis of psychosis [exp(β̂) = 2.02; 95%CI:1.59-2.59, p<0.001], and being admitted in 2007 and in 2012 [exp(β̂) = 1.61; 95%CI:1.21-2.16, p<0.01, and exp(β̂) = 1.73; 95%CI:1.31-2.32, p<0.001, respectively] were associated with an increment of involuntary hospitalizations. Being married/cohabitating [exp(β̂) = 0.74; 95%CI:0.56-0.99, p<0.05], having experienced a suicide attempt [exp(β̂) = 0.26; 95%CI:0.15-0.42, p<0.001], and belonging to the catchment area of three of the psychiatric units evaluated [exp(n) =0.65; 95%CI:0.49-0.86, p<0.01, exp(β̂) = 0.67; 95%CI:0.49-0.90, p<0.01, and exp(β̂) = 0.67; 95%CI:0.46-0.96, p<0.05 for Hospital de Magalhães Lemos, Centro Hospitalar Psiquiátrico de Lisboa and Unidade Local de Saúde do Baixo Alentejo, respectively] were associated with a decrease in involuntary hospitalizations.ConclusionsThe findings suggest that involuntary psychiatric hospitalizations in Portugal are associated with sociodemographic, clinical, and contextual factors. This information may help to recognize high-risk patients, and to inform the development of better-targeted preventive interventions to reduce these hospitalizations.
Depression: Improving Health Processes and Outcomes Through Implementation Science Research in China
Authors: Premji Shahirose , Tao Fangbiao , Loli-Dano Laura , Ravindran Arun , Zhu Beibei , Wu Xiaoyan , Lu Mengjuan , Shao Shanshan , Dobson Keith , Yamamoto Shelby 
Published: October 2020

Abstract
Despite widespread recognition of the importance of mental health, services for assessment and treatment, in the People’s Republic of China, cannot currently meet the need. In this paper, we discuss the challenges associated with developing and validating evidence-based approaches to depression, including inertia and the need for culturally valued research. The potential role of implementation science is discussed in relation to the need for assessment and treatment of depression, and a recent initiative to fund and foster implementation research is detailed. The potential values of implementation research are highlighted, and several examples of projects are described to detail the scope of such work. We conclude with recommendations for further improvements of funding for mental health research in China. While we recognize several challenges to this initiative, we recommend further implementation science research to help meet the social need of mental health problems.
Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172
Authors: Tõlgo Monika , Hüttner Silvia , Thuy Nguyen Than , Than Vu Nguyen , Larsbrink Johan , Olsson Lisbeth 
Published: October 2020

Abstract
Background: Biomass-degrading enzymes with improved activity and stability can ameliorate substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate well low pH and high temperatures. Here, we aimed to illuminate the lignocellulose degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail.Results: We sequenced and analysed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. In total, 411 CAZy domains were found among 10,128 predicted genes. Compared to other fungi, auxiliary activity (AA) enzymes were particularly enriched. GC content was higher in coding sequences than in the overall genome. A high GC3 content was hypothesised to contribute to thermophilicity. T. terrestris employed mainly lytic polysaccharide monooxygenases (LPMOs) and glycoside hydrolase (GH) family 7 glucanases to attack cellulosic substrates, and conventional hemicellulases (GH10 and GH11) to degrade xylan. The observed co-expression and co-upregulation of AA9 LPMOs, other AA CAZymes, and (hemi)cellulases points to a complex and nuanced degradation strategy. Growth on more complex and heterogeneous substrates resulted in a more varied but generally lower gene expression. Conclusions: Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterisation of potential new enzymes for industrial biomass saccharification.
Cell membrane rupture: A novel test reveals significant variations among different brands of tissue culture flasks
Authors: Tchao Ruy 
Published: October 2020

Abstract
Objectives Loss of cytoplasmic molecules including protein controls, due to cell membrane rupture can cause errors and irreproducibility in research data. Previous results have shown that during the washing of a monolayer of cells with a balanced salt solution, the fluid force causes cell membrane rupture on some areas of the flasks/dishes. This fact shows the non-uniformity of the polystyrene surface in terms of cell culture. There is at present no simple test to monitor that surface. This paper presents a novel biologically based assay to determine the degree of heterogeneity of flasks supplied by various manufacturers. Results This paper shows that significant variation exists in polystyrene surface heterogeneity among several brands of tissue culture flasks, varying from 4% to 20% of the flask surface. There is also large variability within the production lot of a manufacturer. The assay method involves loading the cells with a cytoplasmic fluorescent marker that is released upon cell membrane rupture. Cell membrane rupture also causes the loss of marker proteins such as GAPDH used in Westernblots. This novel assay method can be used to monitor the batch consistency and the manufacturing process of flasks/dishes. It may also be used to test new biomaterials.
Development of the ‘REadiness SElf-Assessment (RESEA) Guide’ to assist low and middle-income countries with establishing safe and sustainable radiotherapy services: a pragmatic sequential mixed qualitative methods project
Authors: Donkor Andrew , Luckett Tim , Aranda Sanchia , Vanderpuye Verna , Phillips Jane L 
Published: October 2020

Abstract
Background: Improving access to radiotherapy services in low and middle-income countries (LMICs) is challenging. Many LMICs’ radiotherapy initiatives fail because of multi-faceted barriers leading to significant wastage of scarce resources. Supporting LMICs to self-assess their readiness for establishing radiotherapy services will help to improve cancer outcomes by ensuring safe, effective and sustainable evidenced-based cancer care. The aim of the study was to develop practical guidance for LMICs on self-assessing their readiness to establish safe and sustainable radiotherapy services.Methods: The Access to Radiotherapy for Cancer treatment (ARC) Project was a pragmatic sequential mixed qualitative methods design underpinned by the World Health Organisation’s ‘Innovative Care for Chronic Conditions Framework’ and ‘Health System Building Blocks Framework for Action’ conceptual frameworks. This paper reports on the process of overall data integration and meta-inference from previously published components comprising a systematic review and two-part qualitative study (semi-structured interviews and a participant validation process). The meta-inferences enabled a series of radiotherapy readiness self-assessment requirements to be generated, formalised as a REadiness SElf-Assessment (RESEA) Guide’ for use by LMICs.Findings: The meta-inferences identified a large number of factors that acted as facilitators and/or barriers, depending on the situation. ‘Commitment’, ‘cooperation’, ‘capacity’ and ‘catalyst’ were identified as the key domains enabling development of radiotherapy services. Across these four domains, the RESEA Guide included 37 requirements and 120 readiness questions that LMICs need to consider and answer as part of establishing a new radiotherapy service.Conclusions: The RESEA Guide provides a new resource for LMICs to self-assess their capacity to establish safe and sustainable radiotherapy services. Future evaluation of the acceptability and feasibility of the RESEA Guide is needed to inform further refinements.
Memory, Trauma, and the Maternal: Post-Apocalyptic View of the Chernobyl/Chornobyl/Charnobyl Nuclear Disaster
Authors: Chuchvaha Hanna 
Published: October 2020

Chornobyl/Chernobyl/Charnobyl has a symbolic meaning for several generations of east Europeans. It is a city that experienced a disastrous nuclear explosion in 1986 that bequeathed a post-apocalyptic landscape and an eloquent demonstration of the Anthropocene. The epistemological crisis for humanity provoked by the Chornobyl nuclear disaster led to the emergence of post-Chornobyl art, an art of acceptance and denial, an art of physical and emotional trauma, an art that symbolized humanity’s responsibility for the future.
This paper focuses on art works produced in the first two decades after the explosion at the Chornobyl nuclear plant. The range of art pieces examined in this paper is diverse, from representational art to conceptual installations. The article is an attempt to analyze the trend of post-Chornobyl art created by witnesses of the tragedy. They are Belarusian and Ukrainian artists for whom Chornobyl epitomizes the point of non-return, the overwhelming tragedy of their people, and the devastation of their land; and for whom Chornobyl is an inverted metaphor of the legitimacy of peaceful atom and the results of the Anthropocene. The paper employs Griselda Pollock’s theoretical approach to trauma and focuses on the art of the maternal created by artists of both genders
Risk factors for refusing to continue medical follow-up by tuberculosis patients detected in the penitentiary system of the Russian Federation
Authors: Lisovskiy S. N. , Turkina E. N. , Sterlikov S. A. , Mikhaylova Yu. V. 
Published: October 2020

One of the essential problem sisthelack of continuity of medical follow-up and treatment of tuberculosis patients released from the penitentiary units and transferred tocivilian medical services. Mostly it is due to the fact that patients released from prisons are reluctant to continue medical follow up needed for their disease of tuberculosis or risk of its reactivation.The objective of the study: to find out the predictors of avoidance behavior in tuberculosis patients released from the penitentiary system of Russia resulting in reluctance to continue medical follow-up.Subjects and methods. During the case-control study, the information about 75 patients was investigated; those patients were detected in the penitentiary system in the period with 2014 2018 and released by the moment when the study was conducted. Ofthem, 62 referred to TB dispensary to continue follow-up and 13 didn't. The following predictors of the failure to continue medical follow-up were found out: the lackofa regular place of residence or foreign citizen ship; tuberculosis with minimal lesions and the negative result of the sputum test; clinically cured tuberculosis at the moment of release (Group III of dispensary follow-up). The regular place of residence, certain concurrent somatic conditions, and virus hepatites contributed to the willingness of patients to continue follow-up in the civilian medical system including due to tuberculosis.
First report of Paratylenchus lepidus Raski, 1975 associated with green tea (Camellia sinensis (L.) Kuntze) in Vietnam
Authors: Le Thi Mai Linh , Nguyen Huu Tien , Nguyen Thi Duyen , Trinh Quang Phap 
Published: October 2020

Abstract
The pin nematodes, Paratylenchus spp., are relatively small nematodes that can feed on a wide range of host plants. The morphological identification of this nematode is greatly hampered by their small size and variable characters. This study provides the first report of Paratylenchus lepidus from Vietnam with a combination of morphological and molecular characterizations. The 28S rDNA phylogenetic tree of the genus and the first COI mtDNA barcode of this species are also provided.
CARACTERIZAÇÃO DA SÍFILIS DIAGNOSTICADA A PARTIR DA TECNOLOGIA TESTE RÁPIDO EM SERVIÇO DE REFERÊNCIA NA CAPITAL TERESINA
Authors: Alves Amorim de Sousa Karinna , Niege Meneses Damasceno Alana , Portela de Carvalho Rocha Cristiana , Sena Sousa Luciana , Romulo Leite Furtado Denis , De Sousa e Silva Meire Maria , Gomes Oliveira dos Reis Thais 
Published: October 2020

INTRODUÇÃO: A sífilis é uma Infecção Sexualmente Transmissível que atinge mais de 12 milhões de pessoas no mundo e sua eliminação continua a desafiar globalmente os sistemas de saúde. O Brasil, na última década, obteve aumento de notificações de sífilis adquirida. OBJETIVO: Estimar a prevalência da infecção e caracterizar a população diagnosticada com sífilis a partir de teste rápido realizado no Centro de Testagem e Aconselhamento em Teresina. MÉTODOS: Trata-se de um estudo descritivo, epidemiológico, de corte transversal realizado por meio dos dados disponíveis no SI-CTA (Sistema de informação do CTA), realizado a partir de levantamento dos registros da população atendida no serviço durante o ano de 2018. RESULTADOS: Foram atendidas 6.664 pessoas que realizaram teste rápido de sífilis, das quais 1.083 tiveram o diagnóstico confirmatório da doença, ocasionando uma prevalência de sífilis foi 16,25%. Sendo 77% no sexo masculino e 23% no feminino. Predominância entre pardos autorreferidos (51%), idade entre 18 a 28 anos (39%), solteiros (67%), com escolaridade entre 8 a 11 anos de estudo (56%). Em relação ao comportamento de risco, 62% realizava o teste pela primeira vez. Quanto à prática sexual, 59% afirmaram ter de um a cinco parceiros sexuais no último ano, apenas 6% relataram sempre usar preservativos, 27% afirmaram não usar camisinha por confiar no parceiro. O uso de álcool/drogas foi relatado por 57%. A maioria da população atendida foi de homossexuais (52%), exposição sexual de risco foi relatada por 44%. CONCLUSÃO: A prevalência encontrada justifica necessidade de ampliação do acesso ao diagnóstico e tratamento oportuno nas unidades básicas de saúde ou outros serviços com a implantação do teste rápido. O estudo possibilita deduzir a importância do CTA, pois agrega experiência com população mais vulnerável à sífilis, podendo ser referência para serviços na promoção de campanhas educativas e de detecção de casos.

Palavras-Chave: Sífilis. Sorodiagnóstico da sífilis. Epidemiologia.
LEVANTAMENTO EPIDEMIOLÓGICO DO HIV/AIDS NO MUNICÍPIO DE PARNAÍBA-PI, BRASIL, 1990-2018
Authors: Coelho de Resende Dias Francisco Irisvan , Lima Mascarenhas Diniz Cláudia , Sambuichi Rafael , Soares da Silva Lucélia , De Sousa Nogueira Francisco Jander , Ângelo Ventura Cláudio 
Published: October 2020

Objetivo: Descrever o perfil epidemiológico de HIV/AIDS no município de Parnaíba-PI, no período de 1980-2018. Métodos: Estudo descritivo, tipo seccional, realizado a partir de dados notificados no Sistema de Informação de Agravos de Notificação (SINAN), declarados no Sistema de Informações de Mortalidade (SIM). Resultados: Foram registrados 354 casos da Síndrome da Imunodeficiência Adquirida (AIDS) no município. Acerca da variável raça/cor, pode-se observar uma maior prevalência de registros na população parda 61,5% (N=134) seguida da raça branca 12,4% (N=27). Em relação à escolaridade evidenciou-se o nível fundamental incompleto 36,2% (N=79). Outro fator relevante diz respeito ao número de gestantes cerca de 12% (N=15) das mulheres da amostra. Acerca dos óbitos por AIDS, entre os anos de 1996 a 2018 foram registrados o número total de 28% (N=96) no período. Conclusão: O estudo permitiu discussões sobre o perfil epidemiológico de HIV/AIDS no município de Parnaíba-PI, concluiu-se a necessidade de avanços nas políticas públicas voltadas para esse público, como a melhoria da qualificação desses indicadores, investimento na qualificação dos profissionais, para que haja redução da morbimortalidade por esse agravo.