bluuebunny/crossref_metadata_2025_split huggingface dataset:
The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection
Authors: Onywera Harris , Williamson Anna-Lise , Cozzuto Luca , Bonnin Sarah , Mbulawa Zizipho Z. A. , Coetzee David , Ponomarenko Julia , Meiring Tracy L. 
Published: April 2020

AbstractBackgroundTo date, the microbiota of the human penis has been studied mostly in connection with circumcision, HIV risk and female partner bacterial vaginosis (BV). These studies have shown that male circumcision reduces penile anaerobic bacteria, that greater abundance of penile anaerobic bacteria is correlated with increased cytokine levels and greater risk of HIV infection, and that the penile microbiota is an important harbour for BV-associated bacteria. While circumcision has been shown to significantly reduce the risk of acquiring human papillomavirus (HPV) infection, the relationship of the penile microbiota with HPV is still unknown. In this study, we examined the penile microbiota of HPV-infected men as well as the impact of HIV status.ResultsThe penile skin microbiota of 238 men from Cape Town (South Africa) were profiled using Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene.CorynebacteriumandPrevotellawere found to be the most abundant genera. Six distinct community state types (CSTs) were identified. CST-1, dominated byCorynebacterium, corresponded to less infections with high-risk HPV (HR-HPV) relative to CSTs 2–6. Men in CST-5 had greater relative abundances ofPrevotella,Clostridiales, andPorphyromonasand a lower relative abundance ofCorynebacterium. Moreover, they were significantly more likely to have HPV or HR-HPV infections than men in CST-1. Using a machine learning approach, we identified greater relative abundances of the anaerobic BV-associated bacteria (Prevotella,Peptinophilus, andDialister) and lower relative abundance ofCorynebacteriumin HR-HPV-infected men compared to HR-HPV-uninfected men. No association was observed between HIV and CST, although the penile microbiota of HIV-infected men had greater relative abundances ofStaphylococcuscompared to HIV-uninfected men.ConclusionsWe found significant differences in the penile microbiota composition of men with and without HPV and HIV infections. HIV and HR-HPV infections were strongly associated with greater relative abundances ofStaphylococcusand BV-associated bacterial taxa (notablyPrevotella,PeptinophilusandDialister), respectively.It is possible that these taxa could increase susceptibility to HIV and HR-HPV acquisition, in addition to creating conditions in which infections persist. Further longitudinal studies are required to establish causal relationships and to determine the extent of the effect.
New mutation of the ceruloplasmin gene in the case of a neurologically asymptomatic patient with microcytic anaemia, obesity and supposed Wilson’s disease
Authors: Ondrejkovičová Mária , Dražilová Sylvia , Drakulová Monika , Siles Juan López , Zemjarová Mezenská Renáta , Jungová Petra , Fabián Martin , Rychlý Boris , Žigrai Miroslav 
Published: April 2020

Abstract
Background
Aceruloplasminaemia is a very rare autosomal recessive disorder caused by a mutation in the ceruloplasmin gene, which is clinically manifested by damage to the nervous system and retinal degeneration. This classical clinical picture can be preceded by diabetes mellitus and microcytic anaemia, which are considered to be early manifestations of aceruloplasminaemia.

Case presentation
In our report, we describe the case of a patient with aceruloplasminaemia detected in an early stage (without clinical symptoms of damage to the nervous system) during the search for the cause of hepatopathy with very low values of serum ceruloplasmin.
Molecular genetic examination of the CP gene for ceruloplasmin identified a new variant c.1664G > A (p.Gly555Glu) in the homozygous state, which has not been published in the literature or population frequency databases to date. Throughout the 21-month duration of chelatase treatment, the patient, who is 43 years old, continues to be without neurological and psychiatric symptomatology. We observed a decrease in the serum concentration of ferritin without a reduction in iron deposits in the brain on magnetic resonance imaging.

Conclusion
Currently, there is no unequivocal recommendation of an effective treatment for aceruloplasminaemia. Early diagnosis is important in the neurologically asymptomatic stage.
The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers
Authors: Orjuela Stephany , Menigatti Mirco , Schraml Peter , Kambakamba Patryk , Robinson Mark D. , Marra Giancarlo 
Published: April 2020

Abstract
Background
Identifying molecular differences between primary and metastatic colorectal cancers—now possible with the aid of omics technologies—can improve our understanding of the biological mechanisms of cancer progression and facilitate the discovery of novel treatments for late-stage cancer. We compared the DNA methylomes of primary colorectal cancers (CRCs) and CRC metastases to the liver. Laser microdissection was used to obtain epithelial tissue (10 to 25 × 106 μm2) from sections of fresh-frozen samples of primary CRCs (n = 6), CRC liver metastases (n = 12), and normal colon mucosa (n = 3). DNA extracted from tissues was enriched for methylated sequences with a methylCpG binding domain (MBD) polypeptide-based protocol and subjected to deep sequencing. The performance of this protocol was compared with that of targeted enrichment for bisulfite sequencing used in a previous study of ours.

Results
MBD enrichment captured a total of 322,551 genomic regions (249.5 Mb or ~ 7.8% of the human genome), which included over seven million CpG sites. A few of these regions were differentially methylated at an expected false discovery rate (FDR) of 5% in neoplastic tissues (primaries: 0.67%, i.e., 2155 regions containing 279,441 CpG sites; liver metastases: 1%, i.e., 3223 regions containing 312,723 CpG sites) as compared with normal mucosa samples. Most of the differentially methylated regions (DMRs; 94% in primaries; 70% in metastases) were hypermethylated, and almost 80% of these (1882 of 2396) were present in both lesion types. At 5% FDR, no DMRs were detected in liver metastases vs. primary CRC. However, short regions of low-magnitude hypomethylation were frequent in metastases but rare in primaries. Hypermethylated DMRs were far more abundant in sequences classified as intragenic, gene-regulatory, or CpG shelves-shores-island segments, whereas hypomethylated DMRs were equally represented in extragenic (mainly, open-sea) and intragenic (mainly, gene bodies) sequences of the genome. Compared with targeted enrichment, MBD capture provided a better picture of the extension of CRC-associated DNA hypermethylation but was less powerful for identifying hypomethylation.

Conclusions
Our findings demonstrate that the hypermethylation phenotype in CRC liver metastases remains similar to that of the primary tumor, whereas CRC-associated DNA hypomethylation probably undergoes further progression after the cancer cells have migrated to the liver.
An exploratory study of the acceptability of indoor residual spraying for malaria control in upper western Ghana
Authors: Suuron Vitalis Mwinyuri , Mwanri Lillian , Tsourtos George , Owusu-Addo Ebenezer 
Published: April 2020

Abstract
Background
Despite the implementation of the World Health Organisation’s recommended indoor residual spraying (IRS) intervention in the upper west region of Ghana to reduce malaria morbidity and mortality, the uptake of this intervention remains low. This study explores the facilitators and barriers to the acceptability and community uptake of indoor residual spraying in a highly endemic region of Ghana.

Methods
The health belief model (HBM) and realist evaluation framework were used to inform the study. A qualitative enquiry was conducted between April to October 2016. Data were collected through focus group discussions and semi-structured interviews with program stakeholders including community members, AngloGold Ashanti malaria control (AGA Mal) spray operators, and AGA Mal officials.

Results
A total of 101 people participated in the study. Considerable barriers to community acceptance of indoor residual spraying (IRS) were found, including, dislike of spray insecticides, inadequate information, religious and cultural beliefs, perceived low efficacy of IRS, difficulties with packing, unprofessional conduct of IRS spray operators, and other operational barriers to spraying. Facilitators of IRS uptake included a perceived effectiveness of IRS in preventing malaria and reducing mosquito bites, incidental benefits, respect for authority, training and capacity building, and sensitization activities.

Conclusion
The numerous barriers to indoor residual spraying acceptance and implications show that acceptance levels could be improved. However, measures are required to address householders’ concerns and streamline operational barriers to increase community uptake of indoor residual spraying.
Relationship between body composition indicators and risk of type 2 diabetes mellitus in Chinese adults
Authors: Chen Yongchun , He Dongliang , Yang Tingting , Zhou Hao , Xiang Siyun , Shen Lijun , Wen Jing , Chen Shengcai , Peng Songxu , Gan Yong 
Published: April 2020

Abstract
Background
Body composition is a crucial factor associated with the incidence of type 2 diabetes mellitus. However, no study on this relationship has been performed in the Chinese population. This study aimed to investigate the relationship between body composition indicators and risk of type 2 diabetes mellitus among Chinese adults undergoing medical examination.

Methods
Between January 2018 and July 2018, a retrospective cross-sectional study was performed on 3367 (2307 male and 1060 female) participants aged ≥18 years undergoing medical examination in Zhengzhou. Logistic regression analysis was performed to explore the relationship between body composition indicators and risk of type 2 diabetes mellitus. A receiver operating characteristic curve was used to calculate cutoff points and the predictive power of each indicator.

Results
Among the 3367 participants, 12.53% were diagnosed with type 2 diabetes mellitus. Multivariate logistic analysis indicated that male participants (odds ratio [OR] = 1.68, 95% confidence interval [CI]: 1.29–2.19), older participants (OR = 1.05, 95% CI: 1.04–1.06), participants with a waist-to-hip ratio above the reference value (OR = 1.56, 95% CI: 1.18–2.07), participants with body fat percentage above the reference value (OR = 1.62, 95% CI: 1.01–2.68), and participant with a large visceral fat area (OR = 1.01, 95% CI: 1.01–1.02) had a high risk of type 2 diabetes mellitus. Waist-to-hip ratio, body fat percentage, and visceral fat area were the best indicators of type 2 diabetes mellitus (P < 0.001) with cutoff values of 0.90, 25.02%, and 92.00 cm2, respectively.

Conclusion
This study suggests a predictive relationship between type 2 diabetes mellitus and body composition indicators of waist-to-hip ratio, body fat percentage, and visceral fat area, which are valuable for screening diabetes and providing effective health education and behavioral intervention for high-risk populations.
Cancer symptom and risk factor awareness in Malaysia: findings from a nationwide cross-sectional study
Authors: Schliemann Désirée , Ismail Roshidi , Donnelly Michael , Cardwell Christopher R. , Su Tin Tin 
Published: April 2020

Abstract
Background
Cancer incidence in Malaysia is expected to double by 2040. Understanding cancer awareness is important in order to tailor preventative efforts and reduce the cancer burden. The objective of this research was to assess nationwide awareness about the signs and symptoms as well as risk factors for various cancers in Malaysia and identify socio-demographic factors associated with awareness.

Methods
This cross-sectional study was conducted from March–November 2014 in the form of a telephone survey. Participants aged 40 years and above were randomly selected across Malaysia and interviewed using the validated Awareness Beliefs about Cancer (ABC) measurement tool. Linear regression was conducted to test the association between symptom and risk factor recognition and socio-demographic variables.

Results
A sample of 1895 participants completed the survey. On average, participants recognised 5.8 (SD 3.2) out of 11 symptoms and 7.5 (SD 2.7) out of 12 risk factors. The most commonly recognised symptom was ‘lump or swelling’ (74.5%) and the most commonly recognised risk factor was ‘smoking’ (88.7%). Factors associated with prompted awareness were age, ethnicity, education and smoking status.

Conclusion
Recognition of symptom and risk factors for most cancers was relatively low across Malaysia compared to previous studies in high-income countries and to studies conducted in Malaysia. There is a need to conduct regular public health campaigns and interventions designed to improve cancer awareness and knowledge as a first step towards increasing the early detection of cancer.
Autoimmune pulmonary alveolar proteinosis developed during immunosuppressive treatment in polymyositis with interstitial lung disease: a case report
Authors: Sato S. , Akasaka K. , Ohta H. , Tsukahara Y. , Kida G. , Tsumiyama E. , Kusano K. , Oba T. , Nishizawa T. , Kawabe R. , Yamakawa H. , Amano M. , Matsushima H. , Takada T. 
Published: April 2020

Abstract
Background
Pulmonary alveolar proteinosis (PAP) is characterized by the accumulation of surfactant proteins within the alveolar spaces. Autoimmune PAP (APAP) caused by elevated levels of GM-CSF autoantibodies (GM-Ab) is very rarely associated with systemic autoimmune disease. Here we report a case of APAP manifested during immunosuppressive treatment for polymyositis with interstitial lung disease.

Case presentation
A 52-year-old woman treated at our hospital because of polymyositis with interstitial pneumonia had maintained remission by immunosuppressive treatment for 15 years. She had progressive dyspnea subsequently over several months with her chest CT showing ground-glass opacities (GGO) in bilateral geographic distribution. Her bronchoalveolar lavage fluid with cloudy appearance revealed medium-sized foamy macrophages and PAS-positive amorphous eosinophilic materials by cytological examination. We diagnosed her as APAP due to an increased serum GM-CSF autoantibody level. Attenuating immunosuppression failed to lead GGO improvement, but whole lung lavage (WLL) was effective in her condition.

Conclusions
PAP should be considered as one of the differential diseases when the newly interstitial shadow was observed during immunosuppressive treatment. WLL should be regarded as the treatment option for APAP concurred in connective tissue disease (CTD).
The use of complementary and alternative medicine (CAM) in Europe
Authors: Fjær Erlend L. , Landet Erling R. , McNamara Courtney L. , Eikemo Terje A. 
Published: April 2020

Abstract
Background
While the use of complementary and alternative medicine (CAM) has become increasingly popular in western societies, we do not understand why CAM use is more frequent in some countries than in others. The aim of this article is to examine the determinants of CAM use at the individual and country-level.

Methods
Logistic multilevel regressions were applied analyzing data from 33,371 respondents in 21 European countries (including Israel) from the seventh round of the European Social Survey. We examined CAM in terms of overall use and also dichotomized treatments into physical and consumable subgroups.

Results
At the individual level, we found CAM use to be associated with a range of socioeconomic, demographic and health indicators. At the country level, we found that countries’ health expenditures were positively related to the prevalence of overall and physical CAM treatments.

Conclusions
A common predictor for CAM use, both at the individual (in terms of education and financial strain) and country-level (in terms of health expenditures per capita), is greater resources.
Constructing fine-grained entity recognition corpora based on clinical records of traditional Chinese medicine
Authors: Zhang Tingting , Wang Yaqiang , Wang Xiaofeng , Yang Yafei , Ye Ying 
Published: April 2020

Abstract
Background
In this study, we focus on building a fine-grained entity annotation corpus with the corresponding annotation guideline of traditional Chinese medicine (TCM) clinical records. Our aim is to provide a basis for the fine-grained corpus construction of TCM clinical records in future.

Methods
We developed a four-step approach that is suitable for the construction of TCM medical records in our corpus. First, we determined the entity types included in this study through sample annotation. Then, we drafted a fine-grained annotation guideline by summarizing the characteristics of the dataset and referring to some existing guidelines. We iteratively updated the guidelines until the inter-annotator agreement (IAA) exceeded a Cohen’s kappa value of 0.9. Comprehensive annotations were performed while keeping the IAA value above 0.9.

Results
We annotated the 10,197 clinical records in five rounds. Four entity categories involving 13 entity types were employed. The final fine-grained annotated entity corpus consists of 1104 entities and 67,799 tokens. The final IAAs are 0.936 on average (for three annotators), indicating that the fine-grained entity recognition corpus is of high quality.

Conclusions
These results will provide a foundation for future research on corpus construction and named entity recognition tasks in the TCM clinical domain.
Identifying no-harm incidents in home healthcare: a cohort study using trigger tool methodology
Authors: Lindblad Marléne , Unbeck Maria , Nilsson Lena , Schildmeijer Kristina , Ekstedt Mirjam 
Published: April 2020

Abstract
Background
Patient safety in home healthcare is largely unexplored. No-harm incidents may give valuable information about risk areas and system failures as a source for proactive patient safety work. We hypothesized that it would be feasible to retrospectively identify no-harm incidents and thus aimed to explore the cumulative incidence, preventability, types, and potential contributing causes of no-harm incidents that affected adult patients admitted to home healthcare.

Methods
A structured retrospective record review using a trigger tool designed for home healthcare. A random sample of 600 home healthcare records from ten different organizations across Sweden was reviewed.

Results
In the study, 40,735 days were reviewed. In all, 313 no-harm incidents affected 177 (29.5%) patients; of these, 198 (63.2%) no-harm incidents, in 127 (21.2%) patients, were considered preventable. The most common no-harm incident types were “fall without harm,” “deficiencies in medication management,” and “moderate pain.” The type “deficiencies in medication management” was deemed to have a preventability rate twice as high as those of “fall without harm” and “moderate pain.” The most common potential contributing cause was “deficiencies in nursing care and treatment, i.e., delayed, erroneous, omitted or incomplete treatment or care.”

Conclusion
This study suggests that it is feasible to identify no-harm incidents and potential contributing causes such as omission of care using record review with a trigger tool adapted to the context. No-harm incidents and potential contributing causes are valuable sources of knowledge for improving patient safety, as they highlight system failures and indicate risks before an adverse event reach the patient.
Factors contributing to post-stroke health care utilization and costs, secondary results from the life after stroke (LAST) study
Authors: Døhl Øystein , Halsteinli Vidar , Askim Torunn , Gunnes Mari , Ihle-Hansen Hege , Indredavik Bent , Langhammer Birgitta , Phan Ailan , Magnussen Jon 
Published: April 2020

Abstract
Background
The result from the Life After Stroke (LAST) study showed that an 18-month follow up program as part of the primary health care, did not improve maintenance of motor function for stroke survivors. In this study we evaluated whether the follow-up program could lead to a reduction in the use of health care compared to standard care. Furthermore, we analyse to what extent differences in health care costs for stroke patients could be explained by individual need factors (such as physical disability, cognitive impairment, age, gender and marital status), and we tested whether a generic health related quality of life (HRQoL) is able to predict the utilisation of health care services for patients post-stroke as well as more disease specific indexes.

Methods
The Last study was a multicentre, pragmatic, single-blinded, randomized controlled trial. Adults (age ≥ 18 years) with first-ever or recurrent stroke, community dwelling, with modified Rankin Scale < 5. The study included 380 persons recruited 10 to 16 weeks post-stroke, randomly assigned to individualized coaching for 18 months (n = 186) or standard care (n = 194). Individual need was measured by the Motor assessment scale (MAS), Barthel Index, Hospital Anxiety and Depression Scale (HADS), modified Rankin Scale (mRS) and Gait speed. HRQoL was measured by EQ-5D-5 L. Health care costs were estimated for each person based on individual information of health care use. Multivariate regression analysis was used to analyse cost differences between the groups and the relationship between individual costs and determinants of health care utilisation.

Results
There were higher total costs in the intervention group. MAS, Gait speed, HADS and mRS were significant identifiers of costs post-stroke, as was EQ-5D-5 L.

Conclusion
Long term, regular individualized coaching did not reduce health care costs compared to standard care. We found that MAS, Gait speed, HADS and mRS were significant predictors for future health care use. The generic EQ-5D-5 L performed equally well as the more detailed battery of outcome measures, suggesting that HRQoL measures may be a simple and efficient way of identifying patients in need of health care after stroke and targeting groups for interventions.

Trial registration
https://www.clinicaltrials.govNCT01467206. The trial was retrospectively registered after the first 6 participants were included.