bluuebunny/crossref_metadata_2025_split huggingface dataset:
Researchers’ perceptions of malaria eradication: findings from a mixed-methods analysis of a large online survey
Authors: Brew Joe , Pradhan Menno , Broerse Jacqueline , Bassat Quique 
Published: October 2020

Abstract
Background
The value of malaria eradication, the permanent reduction to zero of the worldwide incidence of malaria infection caused by human malaria parasites, would be enormous. However, the expected value of an investment in an intended, but uncertain, outcome hinges on the probability of, and time until, its fulfilment. Though the long-term benefits of global malaria eradication promise to be large, the upfront costs and uncertainty regarding feasibility and timeframe make it difficult for policymakers and researchers to forecast the return on investment.

Methods
A large online survey of 844 peer-reviewed malaria researchers of different scientific backgrounds administered in order to estimate the probability and time frame of eradication. Adjustments were made for potential selection bias, and thematic analysis of free text comments was carried out.

Results
The average perceived likelihood of global eradication among malaria researchers approximates the number of years into the future: approximately 10% of researchers believe that eradication will occur in the next 10 years, 30% believe it will occur in the next 30 years, and half believe eradication will require 50 years or more. Researchers who gave free form comments highlighted systemic challenges and the need for innovation as chief among obstacles to achieving global malaria eradication.

Conclusions
The findings highlight the difficulty and complexity of malaria eradication, and can be used in prospective cost–benefit analyses to inform stakeholders regarding the likely return on eradication-specific investments.
Age-dependent carriage of alleles and haplotypes of Plasmodium falciparum sera5, eba-175, and csp in a region of intense malaria transmission in Uganda
Authors: Agwang Constance , Erume Joseph , Okech Brenda , Olobo Joseph , Egwang Thomas G. 
Published: October 2020

Abstract
Background
The development of malaria vaccines is constrained by genetic polymorphisms exhibited by Plasmodium falciparum antigens. The project the age-dependent distribution of alleles or haplotypes of three P. falciparum malaria vaccine candidates, Circumsporozoite Protein (csp), Erythrocyte Binding Antigen 175 (eba-175) and Serine Repeat Antigen 5 (sera5) in a region of intense malaria transmission in Uganda.

Methods
A cross-sectional study was carried out between August and November 2009 in which 250 study participants were selected from a population of 600. Finger prick blood samples were collected after informed consent from participants below 5 years, 5–10 years, and above 10 years of age. Blood was used for microscopy, RDT and dried blood spots. Plasmodium falciparum DNA was extracted by chelex method. Alleles of sera5 and eba-175 were determined by polymerase chain reaction (PCR) amplification followed by resolution of products by agarose gel electrophoresis. Allele calling was done using gel photographs from ethiduim bromide stained gels. Haplotypes of csp were identified by sequencing 63 PCR products using the P. falciparum 7G8 laboratory strain sequence as a reference. The data were analysed using SPSS 16, EQX for windows and Chi-square test was used to calculate associations (P-values), Excel was used to generate graphs. The BioEdit and NCBI blast software programs were used to analyse the sequences from which csp haplotypes map was constructed.

Results
Eba-175 FCR3 (48/178) and CAMP (16/178) alleles were observed, the FCR3 (24/67) allele being predominant among children aged below 5 years old while the CAMP (12/67) allele was predominant among older participants. Sera5 alleles ORI (6/204) and ORII (103/204) were observed in the population, ORII was more prevalent and was significantly associated with age (P values < 0.0001), parasite density (P-value < 0.0001) and clinical outcomes (P value = 0.018). There was marked csp diversity in the Th2/Th3 region. Out of 63 sequences, 16 conformed to the reference strain and one (1/16) was similar to a West African haplotype and the majority (14/16) of the haplotypes were unique to this study region. There was an age-dependent distribution of csp haplotypes with more haplotypes being harbored by children < 5-year of age, (10/16) compared to adults (2/16). Interestingly, the csp haplotype corresponding to 3D7 whose prototypical sequence is identical to the sequence of the leading malaria vaccine candidate RTS, S was not observed.

Conclusion
This data suggest that the eba-175 FCR3 allele, sera5 ORII allele, and csp haplotypes are targets of host immunity and under immune selection pressure in Apac District. These molecules could provide alternative malaria vaccine candidates as sub-unit vaccines.
Malaria serology data from the Guiana shield: first insight in IgG antibody responses to Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae antigens in Suriname
Authors: Labadie-Bracho Mergiory Y. , van Genderen Farah T. , Adhin Malti R. 
Published: October 2020

Abstract
Background
Suriname has accomplished a steep decline in malaria burden, even reaching elimination levels. Plasmodium serology data are not available for Suriname and even extremely scarce within the region, therefore malaria serology testing was introduced, country customized cut-off values were determined and a study was performed to explore the antibody status for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae.

Methods
A cross-sectional survey was conducted between July 2017 and March 2018 in two areas of the interior with different malaria settings: Stoelmanseiland, representing Maroon villages and Benzdorp, a gold mining area, with mostly Brazilian miners. Dried blood spots (DBS) were collected (n = 197) and antibody presence against seven Plasmodium antigens was detected using a multiplex bead-based, IgG antibody assay. Demographic information was gathered through a questionnaire. Country customized cut-off values were generated from a Surinamese malaria-naïve reference population (n = 50).

Results
Serological analysis for the reference population revealed cut-off values ranging from 14 MFI for LSA-1 to 177 MFI for PmMSP-119. Seroprevalence against any of the three MSP-119 antibodies was similar in both regions and surpassed 75%. Single seropositivity against PfMSP-119 antibodies was higher in Stoelmanseiland (27.0%) than Benzdorp (9.3%), in line with the historical malaria burden of Stoelmanseiland, while the reverse was observed for PvMSP-119 antibodies. Despite sporadic reports of P. malariae infections, PmMSP-119 antibody presence was 39.6%. A more detailed examination of P. falciparum serology data displayed a higher seroprevalence in villagers (90.7%) than in Brazilians (64.6%) and a highly diverse antigenic response with 22 distinct antibody combinations.

Conclusions
The results on the malaria antibody signature of Maroon villagers and Brazilian miners living in Suriname displayed a high Plasmodium seroprevalence, especially for P. falciparum in villagers, still reflecting the historical malaria burden. The seroprevalence data for both regions and the observed combinations of P. falciparum antibodies provided a valuable dataset from a historically important region to the international malaria serology knowledge. First insight in malaria serology data for Suriname indicated that the use of other target groups and assessment of age-dependent seroprevalence are required to successfully use malaria serology as tool in the national elimination strategy.
Spatial distribution of iron rich foods consumption and its associated factors among children aged 6–23 months in Ethiopia: spatial and multilevel analysis of 2016 Ethiopian demographic and health survey
Authors: Tiruneh Sofonyas Abebaw , Ayele Belete Achamyelew , Yitbarek Getachew Yideg , Asnakew Desalegn Tesfa , Engidaw Melaku Tadege , Gebremariam Alemayehu Digssie 
Published: October 2020

Abstract
Background
Micronutrient deficiencies are the most prevalent nutritional deficiencies that cause serious developmental problems in the globe. The aim of this study was to assess the spatial distribution of iron rich foods consumption and its associated factors among children aged 6–23 months in Ethiopia.

Methods
The data retrieved from the standard Ethiopian Demographic and Health Survey 2016 dataset with a total sample size of 3055 children aged 6–23 months. Spatial scan statistics done using Kuldorff’s SaTScan version 9.6 software. ArcGIS version 10.7 software used to visualize spatial distribution for poor consumption of iron rich foods. Multilevel mixed-effects logistic regression analysis employed to identify the associated factors for good consumption of iron-rich foods. Level of statistical significance was declared at a two-sided P-value < 0.05.

Results
Overall, 21.41% (95% CI: 19.9–22.9) of children aged 6–23 months had good consumption of iron rich foods in Ethiopia. Poor consumption of iron rich foods highly clustered at Southern Afar, Southeastern Amhara and Tigray, and the Northern part of Somali Regional States of Ethiopia. In spatial scan statistics, children aged 6–23 months living in the most likely cluster were 21% more likely vulnerable to poor consumption of iron rich foods than those living outside the window (RR = 1.21, P-value < 0.001). Child aged 12–17 months (AOR = 1.90, 95% CI: 1.45–2.49) and 18–23 months (AOR = 2.05, 95% CI: 1.55–2.73), primary (AOR = 1.42, 95% CI:1.06–1.87) and secondary and above (AOR = 2.26, 95% CI: 1.47–3.46) mother’s education level, rich (AOR = 1.49, 95% CI: 1.04–2.13) and middle (AOR = 1.83, 95% CI: 1.31–2.57) household wealth status, Amhara (AOR = 0.24, 95% CI: 0.09–0.60), Afar (AOR = 0.38, 95% CI: 0.17–0.84), and Harari (AOR = 2.11, 95% CI: 1.02–4.39) regional states of Ethiopia were statistically significant factors for good consumption of iron rich foods.

Conclusion
Overall, the consumption of iron rich foods was low and spatially non-random in Ethiopia. Federal Ministry of Health and other stakeholders should give prior attention to the identified hot spot areas to enhance the consumption of iron rich foods among children aged 6–23 months.
Features and associated factors of bacterial skin infections in hospitalized patients with pemphigus: a single-center retrospective study
Authors: Li Furong , Wu Yejun , Bian Wenjie , Huang Lei , Zhu Xuejun , Chen Xixue , Wang Mingyue 
Published: October 2020

Abstract
Background
Infections were the primary cause of death (34.3–55.5%) in patients with pemphigus. Skin was usually the origin of infections. The study aimed to explore features and associated factors of bacterial skin infections (BSIs) in inpatients with pemphigus.

Methods
One hundred and seventy-seven inpatients with pemphigus hospitalizing from November 2014 to April 2019 were continuously
recruited through Peking University First Hospital’s inpatient records inpatients with pemphigus hospitalizing from November 2014 to April 2019 were continuously recruited through Peking University First Hospital’s inpatient records. Then, we retrieved the clinical and laboratory data to explore the characteristics and associated factors of BSIs.

Results
Of patients enrolled, pemphigus vulgaris (PV, n = 142) and pemphigus foliaceus (PF, n = 9) were most common, followed by pemphigus erythematosus (PE, n = 25) and pemphigus vegetans (Pveg, n = 1). Eighty-seven of 177 (49.2%) inpatients developed BSIs, and they had a longer length of stay compared with inpatients without BSIs (median: 18.9 vs. 14.1 days, p = 0.008). Staphylococcus aureus was the most common bacteria (71.3%, 62/87) and highly resistant to penicillin (91.9%, 57/62). Higher levels of anti-Dsg1 autoantibodies (> 124.2 U/mL) (p < 0.001, odds ratio [OR] = 3.564, 95% confidence interval [CI]: 1.784–7.123) and anti-Dsg3 autoantibodies (> 169.5 U/mL) (p = 0.03, OR = 2.074, 95% CI: 1.084–3.969) were underlying risk factors of BSIs when analyzed by binary regression analysis. As for Gram’s stain of bacteria, females had a lower rate of Gram-positive infections (p = 0.03). Patients using oral antibiotics (p = 0.05) had a higher rate of Gram-negative infections. Inpatients who were hospitalized in other hospitals within 2 weeks before the current admission had a higher rate of Gram-negative and co-infections (p = 0.03).

Conclusions
Inpatients with pemphigus had a high incidence of BSIs. Some factors were associated with the susceptibility of BSIs and bacterial species.
Identification of a distinct luminal subgroup diagnosing and stratifying early stage prostate cancer by tissue-based single-cell RNA sequencing
Authors: Ma Xiaoshi , Guo Jinan , Liu Kaisheng , Chen Lipeng , Liu Dale , Dong Shaowei , Xia Jinquan , Long Qiaoyun , Yue Yongjian , Zhao Pan , Hu Fengyan , Xiao Zhangang , Pan Xinghua , Xiao Kefeng , Cheng Zhiqiang , Ke Zunfu , Chen Zhe-Sheng , Zou Chang 
Published: October 2020

Abstract
Background
The highly intra-tumoral heterogeneity and complex cell origination of prostate cancer greatly limits the utility of traditional bulk RNA sequencing in finding better biomarker for disease diagnosis and stratification. Tissue specimens based single-cell RNA sequencing holds great promise for identification of novel biomarkers. However, this technique has yet been used in the study of prostate cancer heterogeneity.

Methods
Cell types and the corresponding marker genes were identified by single-cell RNA sequencing. Malignant states of different clusters were evaluated by copy number variation analysis and differentially expressed genes of pseudo-bulks sequencing. Diagnosis and stratification of prostate cancer was estimated by receiver operating characteristic curves of marker genes. Expression characteristics of marker genes were verified by immunostaining.

Results
Fifteen cell groups including three luminal clusters with different expression profiles were identified in prostate cancer tissues. The luminal cluster with the highest copy number variation level and marker genes enriched in prostate cancer-related metabolic processes was considered the malignant cluster. This cluster contained a distinct subgroup with high expression level of prostate cancer biomarkers and a strong distinguishing ability of normal and cancerous prostates across different pathology grading. In addition, we identified another marker gene, Hepsin (HPN), with a 0.930 area under the curve score distinguishing normal tissue from prostate cancer lesion. This finding was further validated by immunostaining of HPN in prostate cancer tissue array.

Conclusion
Our findings provide a valuable resource for interpreting tumor heterogeneity in prostate cancer, and a novel candidate marker for prostate cancer management.
Measuring the prevalence of 60 health conditions in older Australians in residential aged care with electronic health records: a retrospective dynamic cohort study
Authors: Lind Kimberly E. , Raban Magdalena Z. , Brett Lindsey , Jorgensen Mikaela L. , Georgiou Andrew , Westbrook Johanna I. 
Published: October 2020

Abstract
Background
The number of older Australians using aged care services is increasing, yet there is an absence of reliable data on their health. Multimorbidity in this population has not been well described. A clear picture of the health status of people using aged care is essential for informing health practice and policy to support evidence-based, equitable, high-quality care. Our objective was to describe the health status of older Australians living in residential aged care facilities (RACFs) and develop a model for monitoring health conditions using data from electronic health record systems.

Methods
Using a dynamic retrospective cohort of 9436 RACF residents living in 68 RACFs in New South Wales and the Australian Capital Territory from 2014 to 2017, we developed an algorithm to identify residents’ conditions using aged care funding assessments, medications administered, and clinical notes from their facility electronic health record (EHR). We generated age- and sex-specific prevalence estimates for 60 health conditions. Agreement between conditions recorded in aged care funding assessments and those documented in residents’ EHRs was evaluated using Cohen’s kappa. Cluster analysis was used to describe combinations of health conditions (multimorbidity) occurring among residents.

Results
Using all data sources, 93% of residents had some form of circulatory disease, with hypertension the most common (62%). Most residents (93%) had a mental or behavioural disorder, including dementia (58%) or depression (54%). For most conditions, EHR data identified approximately twice the number of people with the condition compared to aged care funding assessments. Agreement between data sources was highest for multiple sclerosis, Huntington’s disease, and dementia. The cluster analysis identified seven groups with distinct combinations of health conditions and demographic characteristics and found that the most complex cluster represented a group of residents that had on average the longest lengths of stay in residential care.

Conclusions
The prevalence of many health conditions among RACF residents in Australia is underestimated in previous reports. Aged care EHR data have the potential to be used to better understand the complex health needs of this vulnerable population and can help fill the information gaps needed for population health surveillance and quality monitoring.
Gene correlation network analysis to identify regulatory factors in sepsis
Authors: Zhang Zhongheng , Chen Lin , Xu Ping , Xing Lifeng , Hong Yucai , Chen Pengpeng 
Published: October 2020

Abstract
Background and objectives
Sepsis is a leading cause of mortality and morbidity in the intensive care unit. Regulatory mechanisms underlying the disease progression and prognosis are largely unknown. The study aimed to identify master regulators of mortality-related modules, providing potential therapeutic target for further translational experiments.

Methods
The dataset GSE65682 from the Gene Expression Omnibus (GEO) database was utilized for bioinformatic analysis. Consensus weighted gene co-expression netwoek analysis (WGCNA) was performed to identify modules of sepsis. The module most significantly associated with mortality were further analyzed for the identification of master regulators of transcription factors and miRNA.

Results
A total number of 682 subjects with various causes of sepsis were included for consensus WGCNA analysis, which identified 27 modules. The network was well preserved among different causes of sepsis. Two modules designated as black and light yellow module were found to be associated with mortality outcome. Key regulators of the black and light yellow modules were the transcription factor CEBPB (normalized enrichment score = 5.53) and ETV6 (NES = 6), respectively. The top 5 miRNA regulated the most number of genes were hsa-miR-335-5p (n = 59), hsa-miR-26b-5p (n = 57), hsa-miR-16-5p (n = 44), hsa-miR-17-5p (n = 42), and hsa-miR-124-3p (n = 38). Clustering analysis in 2-dimension space derived from manifold learning identified two subclasses of sepsis, which showed significant association with survival in Cox proportional hazard model (p = 0.018).

Conclusions
The present study showed that the black and light-yellow modules were significantly associated with mortality outcome. Master regulators of the module included transcription factor CEBPB and ETV6. miRNA-target interactions identified significantly enriched miRNA.
Decreased expression of miR-29 family associated with autoimmune myasthenia gravis
Authors: Cron Mélanie A. , Payet Cloé A. , Fayet Odessa-Maud , Maillard Solène , Truffault Frédérique , Fadel Elie , Guihaire Julien , Berrih-Aknin Sonia , Liston Adrian , Le Panse Rozen 
Published: October 2020

Abstract
Background
Myasthenia gravis (MG) is a rare autoimmune disease mainly mediated by autoantibodies against the acetylcholine receptor (AChR) at the neuromuscular junction. The thymus is the effector organ, and its removal alleviates the symptoms of the disease. In the early-onset form of MG, the thymus displays functional and morphological abnormalities such as B cell infiltration leading to follicular hyperplasia, and the production of AChR antibodies. Type-I interferon (IFN-I), especially IFN-β, is the orchestrator of thymic changes observed in MG. As Dicer and miR-29 subtypes play a role in modulating the IFN-I signalization in mouse thymus, we investigated their expression in MG thymus.

Methods
The expression of DICER and miR-29 subtypes were thoroughly investigated by RT-PCR in human control and MG thymuses, and in thymic epithelial cells (TECs). Using miR-29a/b-1-deficient mice, with lower miR-29a/b-1 expression, we investigated their susceptibility to experimental autoimmune MG (EAMG) as compared to wild-type mice.

Results
DICER mRNA and all miR-29 subtypes were down-regulated in the thymus of MG patients and DICER expression was correlated with the lower expression of miR-29a-3p. A decreased expression of miR-29 subtypes was similarly observed in MG TECs; a decrease also induced in TECs upon IFN-β treatment. We demonstrated that miR-29a/b-1-deficient mice were more susceptible to EAMG without higher levels of anti-AChR IgG subtypes. In the thymus, if no B cell infiltration was observed, an increased expression of Ifn-β associated with Baff expression and the differentiation of Th17 cells associated with increased expression of Il-6, Il-17a and Il-21 and decreased Tgf-β1 mRNA were demonstrated in miR-29a/b-1-deficient EAMG mice.

Conclusions
It is not clear if the decreased expression of miR-29 subtypes in human MG is a consequence or a causative factor of thymic inflammation. However, our results from the EAMG mouse model indicated that a reduction in miR-29a/b1 may contribute to the pathophysiological process involved in MG by favoring the increased expression of IFN-β and the emergence of pro-inflammatory Th17 cells.
Prevalence and perceived importance of racial matching in the psychotherapeutic dyad: a national survey of addictions treatment clinical practices
Authors: Steinfeldt Jesse A. , Clay Shondra L. , Priester Paul E. 
Published: October 2020

Abstract
Background
Despite conflicting results in the literature concerning its efficacy in practice, racial matching has been identified as a component of culturally sensitive treatment.

Methods
This study examined the perceived importance and prevalence of racial matching by surveying a national sample of substance use disorder (SUD) centers from the Substance Abuse and Mental Health Services Administration (SAMHSA).

Results
Using univariate statistical analysis, results for the prevalence of racial matching revealed that in 58% of the clinics, there was the potential to match a counselor with a racially similar client, while in 39% of the clinics, there was no potential to provide such a match. Among the agencies that displayed a potential for racial matching, 26% of the respondents indicated that they never racially matched clients and therapists, 71% reported that they sometimes practice racial matching, 15% indicated that they usually racially match, and only 7% purported to always racially match clients and therapists. Results for the perceived importance of racial matching revealed that in both situations where treatment centers had the potential for racial matching and did not have the potential for racial matching, supervisors reported that it was relatively important to provide culturally sensitive treatment but that it was not as important to match clients in SUD centers with racially/ethnically similar counselors.

Conclusion
The topic of racial matching can be very complex and has shown variation amongst SUD centers; however, this study emphasizes the importance of providing culturally sensitive treatment and an appreciation of differences among members within each racial group.