bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of machine learning techniques to identify HIV predictors for screening in sub-Saharan Africa
Authors: Mutai Charles K. , McSharry Patrick E. , Ngaruye Innocent , Musabanganji Edouard 
Published: July 2021

Abstract
Aim
HIV prevention measures in sub-Saharan Africa are still short of attaining the UNAIDS 90–90-90 fast track targets set in 2014. Identifying predictors for HIV status may facilitate targeted screening interventions that improve health care. We aimed at identifying HIV predictors as well as predicting persons at high risk of the infection.

Method
We applied machine learning approaches for building models using population-based HIV Impact Assessment (PHIA) data for 41,939 male and 45,105 female respondents with 30 and 40 variables respectively from four countries in sub-Saharan countries. We trained and validated the algorithms on 80% of the data and tested on the remaining 20% where we rotated around the left-out country. An algorithm with the best mean f1 score was retained and trained on the most predictive variables. We used the model to identify people living with HIV and individuals with a higher likelihood of contracting the disease.

Results
Application of XGBoost algorithm appeared to significantly improve identification of HIV positivity over the other five algorithms by f1 scoring mean of 90% and 92% for males and females respectively. Amongst the eight most predictor features in both sexes were: age, relationship with family head, the highest level of education, highest grade at that school level, work for payment, avoiding pregnancy, age at the first experience of sex, and wealth quintile. Model performance using these variables increased significantly compared to having all the variables included. We identified five males and 19 females individuals that would require testing to find one HIV positive individual. We also predicted that 4·14% of males and 10.81% of females are at high risk of infection.

Conclusion
Our findings provide a potential use of the XGBoost algorithm with socio-behavioural-driven data at substantially identifying HIV predictors and predicting individuals at high risk of infection for targeted screening.
Machine learning in medicine: a practical introduction to natural language processing
Authors: Harrison Conrad J. , Sidey-Gibbons Chris J. 
Published: July 2021

Abstract
Background
Unstructured text, including medical records, patient feedback, and social media comments, can be a rich source of data for clinical research. Natural language processing (NLP) describes a set of techniques used to convert passages of written text into interpretable datasets that can be analysed by statistical and machine learning (ML) models. The purpose of this paper is to provide a practical introduction to contemporary techniques for the analysis of text-data, using freely-available software.

Methods
We performed three NLP experiments using publicly-available data obtained from medicine review websites. First, we conducted lexicon-based sentiment analysis on open-text patient reviews of four drugs: Levothyroxine, Viagra, Oseltamivir and Apixaban. Next, we used unsupervised ML (latent Dirichlet allocation, LDA) to identify similar drugs in the dataset, based solely on their reviews. Finally, we developed three supervised ML algorithms to predict whether a drug review was associated with a positive or negative rating. These algorithms were: a regularised logistic regression, a support vector machine (SVM), and an artificial neural network (ANN). We compared the performance of these algorithms in terms of classification accuracy, area under the receiver operating characteristic curve (AUC), sensitivity and specificity.

Results
Levothyroxine and Viagra were reviewed with a higher proportion of positive sentiments than Oseltamivir and Apixaban. One of the three LDA clusters clearly represented drugs used to treat mental health problems. A common theme suggested by this cluster was drugs taking weeks or months to work. Another cluster clearly represented drugs used as contraceptives. Supervised machine learning algorithms predicted positive or negative drug ratings with classification accuracies ranging from 0.664, 95% CI [0.608, 0.716] for the regularised regression to 0.720, 95% CI [0.664,0.776] for the SVM.

Conclusions
In this paper, we present a conceptual overview of common techniques used to analyse large volumes of text, and provide reproducible code that can be readily applied to other research studies using open-source software.
The survey visit as a key evaluative event in accreditation–a qualitative study of survey visit experiences among surveyors and general practice professionals
Authors: Due Tina Drud , Thorsen Thorkil , Kousgaard Marius Brostrøm 
Published: July 2021

Abstract
Background
Accreditation is a widely employed quality assurance concept in health care and the survey visit is the central method for assessing participating organisations’ compliance with accreditation standards. Despite this, research on the survey visit as a method for assessing compliance is scarce. In Denmark a mandatory accreditation programme was introduced for general practice clinics in 2016. We performed a qualitative, explorative study of the reflections and actions of surveyors and general practice professionals (GPs and staff) concerning the production of information about compliance with the accreditation standards in relation to the survey visit.

Methods
We conducted qualitative interviews with GPs and staff from general practices in two Danish regions before and after their survey visit. We also interviewed the surveyors. We observed survey visits to qualify the interviews and analysis. All interviews were audio recorded, transcribed, and analysed using an integrative approach.

Results
The surveyors combined documents, questioning of the professionals, and visual impressions of the clinic to assess compliance. They sought to de-dramatise the survey visit and to generate a natural conversation with attention to workflows. Trust in the professionals’ statements was fundamental to the surveyors’ approach, and they were confident in their ability to assess compliance. Their level of scrutiny was influenced by their observations and the quality of documents. The general practice professionals had generally sought to comply with the standards and to give an authentic portrait of the clinic. The few cases of misrepresention concerned standards that the professionals found too excessive.

Conclusion
The validity of the survey visit as a method to assess compliance was highly dependent on the professionals’ willingness to convey a realistic picture of their practice. Since they were generally willing to do so, the trust-based approach seemed suitable for identifying cases of non-compliance caused by insufficient understanding of the standards. However, it can be difficult for the surveyors to detect when the professionals engage in misrepresentation due to disagreements with the standards. Thus, when adopting a trust-based approach to the survey visit, it seems particularly important to ensure that the professionals view the standards as meaningful and manageable.
Gap between desired and self-determined roles of general practitioners: a multicentre questionnaire study in Japan
Authors: Chinen Takashi , Sasabuchi Yusuke , Kotani Kazuhiko , Yamaguchi Hironori 
Published: July 2021

Abstract
Background
Primary care physicians have diverse responsibilities. To collaborate with cancer specialists efficiently, they should prioritise roles desired by other collaborators rather than roles based on their own beliefs. No previous studies have reported the priority of roles such clinic-based general practitioners are expected to fulfil across the cancer care continuum. This study clarified the desired roles of clinic-based general practitioners to maximise person-centred cancer care.

Methods
A web-based multicentre questionnaire in Japan was distributed to physicians in 2019. Physician roles within the cancer care continuum were divided into 12 categories, including prevention, diagnosis, surgery, follow-up with cancer survivors, chemotherapy, and palliative care. Responses were evaluated by the proportion of three high-priority items to determine the expected roles of clinic-based general practitioners according to responding physicians in similarly designated roles.

Results
Seventy-eight departments (25% of those recruited) from 49 institutions returned questionnaires. Results revealed that some physicians had lower expectations for clinic-based general practitioners to diagnose cancer, and instead expected them to provide palliative care. However, some physicians expected clinic-based general practitioners to be involved in some treatment and survivorship care, though the clinic-based general practitioners did not report the same priority.

Conclusion
Clinic-based general practitioners prioritised involvement in prevention, diagnoses, and palliative care across the cancer continuum, although lower expectations were placed on them than they thought. Some additional expectations of their involvement in cancer treatment and survivorship care were unanticipated by them. These gaps represent issues that should be addressed.
Comorbid early esophageal cancer and Gongylonema pulchrum infection: a case report
Authors: Zhou Qiaozhi , Wei Yongqiu , Zhai Huihong , Li Shaogang , Xu Rui , Li Peng 
Published: July 2021

Abstract
Background
Gongylonema pulchrum is a zoonotic parasite rarely found in humans. To date, there have been no reports on the carcinogenic properties of G. pulchrum, and there are few reports overall on the relationship between esophageal cancer and parasites.

Case presentation
This report describes the first case of esophageal gongylonemiasis coexisting with early esophageal cancer. The patient had no high-risk factors for esophageal cancer, such as smoking, flushing after drinking, or tumor history. We speculate the existence of unknown links between esophageal cancer and parasitic infection in this patient.

Discussion and conclusions
We report the first case of a human presenting both esophageal G. pulchrum infection and esophageal squamous cell carcinoma with the hope that it may provide evidence for a new hypothesis of tumorigenesis.
Cecal retroflexion is infrequently performed in routine practice and the retroflexed view is of poor quality
Authors: Keswani Rajesh N. , Kahi Charles J. , Benson Mark , Gawron Andrew J. , Kaltenbach Tonya R. , Yadlapati Rena H. , Gregory Dyanna L. , Duloy Anna 
Published: July 2021

Abstract
Background
As right colon polyps are challenging to detect, a retroflexed view of right colon (RV) may be useful. However, cecal retroflexion (CR) without a RV to the hepatic flexure (HF) is inadequate. We aimed to determine the frequency of CR and quality of the RV in routine practice.

Methods
This prospective observational study performed at an academic medical center assessed colonoscopy inspection technique of endoscopists who had performed ≥ 100 annual screening colonoscopies. We video recorded ≥ 28 screening/surveillance colonoscopies per endoscopist and randomly evaluated 7 videos per endoscopist. Six gastroenterologists blindly reviewed the videos to determine if CR was performed and HF withdrawal time (cecum to HF time, excluding ileal/polypectomy time).

Results
Reviewers assessed 119 colonoscopies performed by 17 endoscopists. The median HF withdrawal time was 3 min and 46 s. CR was performed in 31% of colonoscopies. CR frequency varied between endoscopists with 9 never performing CR and 2 performing CR in all colonoscopies. When performed, nearly half (43%) of RVs did not extend to the HF with median RV duration of 16 s (IQR 9–30 s). Three polyps were identified in the RV (polyp detection rate of 8.1%), all identified prior to a forward view.

Conclusions
CR is performed infrequently in routine practice. When CR is performed, the RV is of low quality with a very short inspection duration and insufficient ascending colon examination. Further education is required to educate endoscopists in optimal technique to improve overall colonoscopy quality.
Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis—a prospective multicentre translational study
Authors: Ammer-Herrmenau C. , Asendorf T. , Beyer G. , Buchholz S. M. , Cameron S. , Damm M. , Frost F. , Henker R. , Jaster R. , Phillip V. , Placzek M. , Ratei C. , Sirtl S. , van den Berg T. , Weingarten M. J. , Woitalla J. , Mayerle J. , Ellenrieder V. , Neesse A. 
Published: July 2021

Abstract
Background
Acute pancreatitis (AP) is an inflammatory disorder that causes a considerable economic health burden. While the overall mortality is low, around 20% of patients have a complicated course of disease resulting in increased morbidity and mortality. There is an emerging body of evidence that the microbiome exerts a crucial impact on the pathophysiology and course of AP. For several decades multiple clinical and laboratory parameters have been evaluated, and complex scoring systems were developed to predict the clinical course of AP upon admission. However, the majority of scoring systems are determined after several days and achieve a sensitivity around 70% for early prediction of severe AP. Thus, continued efforts are required to investigate reliable biomarkers for the early prediction of severity in order to guide early clinical management of AP patients.

Methods
We designed a multi-center, prospective clinical-translational study to test whether the orointestinal microbiome may serve as novel early predictor of the course, severity and outcome of patients with AP. We will recruit 400 AP patients and obtain buccal and rectal swabs within 72 h of admission to the hospital. Following DNA extraction, microbiome analysis will be performed using 3rd generation sequencing Oxford Nanopore Technologies (ONT) for 16S rRNA and metagenomic sequencing. Alpha- and beta-diversity will be determined and correlated to the revised Atlanta classification and additional clinical outcome parameters such as the length of hospital stay, number and type of complications, number of interventions and 30-day mortality.

Discussion
If AP patients show a distinct orointestinal microbiome dependent on the severity and course of the disease, microbiome sequencing could rapidly be implemented in the early clinical management of AP patients in the future.
Trial registration: ClinicalTrials.gov Identifier: NCT04777812
Subarachnoid hemorrhage secondary to Brucella-induced cerebral aneurysm: a case report
Authors: Guan Yanyan , Xu Nannan , Yao Yongyuan , Zheng Feng , Chen Fengzhe , Wang Wei , Dong Xiaomeng , Wang Gang 
Published: July 2021

Abstract
Background
Brucellosis is a common zoonotic disease that is prevalent in many areas worldwide. This infectious disease can occasionally affect the central nervous system but intracranial arteries are rarely involved.

Case presentation
A 17-year-old female who had a history of recurrent fever for 1 month was admitted for subarachnoid hemorrhage due to cerebral aneurysm rupture. Surgery was performed to fix the aneurysm, but the patient had persistent fever after the surgery. Cerebrospinal fluid testing showed a high white blood cell count and elevated protein level but no pathogen was identified in the first two tests. Brucella melitensis was identified in the third cerebrospinal fluid culture, and a diagnosis of brucellosis was finally rendered. The patient was subsequently treated with anti-Brucella medications and her symptoms improved significantly at the last follow-up.

Conclusion
Although extremely rare, Brucella-induced cerebral aneurysms can occur and this should be considered in the differential diagnosis of cerebrovascular accidents, especially in Brucella epidemic areas.
Fatal hemorrhagic pneumonia in patients with hematologic diseases and Stenotrophomonas maltophilia bacteremia: a retrospective study
Authors: Zhu Lixia , Wang Lulu , Zhang Yuping , Chen Rongrong , Li Xueying , Sun Jianai , Zhou De , Zhu Mingyu , Zheng Xiaolong , Li Li , Zhu Jingjing , Xie Mixue , Yang Xiudi , Yu Wenjuan , Tong Hongyan , Zhu Honghu , Xie Wanzhuo , Jin Jie , Ye Xiujin 
Published: July 2021

Abstract
Background
Fatal hemorrhagic pneumonia is one of the most severe manifestations of Stenotrophomonas maltophilia (SM) infections. Here, we aimed to investigate the clinical characteristics of SM bacteremia and to identify the risk factors of hemorrhagic pneumonia caused by SM in patients with hematologic diseases.

Methods
The clinical records of 55 patients diagnosed with hematologic diseases and SM bacteremia were retrospectively reviewed. We compared patients’ clinical characteristics and outcomes between the hemorrhagic pneumonia group and non-hemorrhagic pneumonia group.

Results
Twenty-seven (49.1%) patients developed hemorrhagic pneumonia. The overall mortality rate of SM bacteremia was 67.3%. Hemorrhagic pneumonia (adjusted HR 2.316, 95% CI 1.140–4.705; P = 0.020) was an independent risk factor of 30-day mortality in hematological patients with SM bacteremia. Compared with the non-hemorrhagic pneumonia group, patients in the hemorrhagic pneumonia group were older and showed clinical manifestations as higher proportions of isolated SM in sputum culture, neutropenia and elevated procalcitonin (PCT). Multivariate analysis showed that neutropenia, high levels of PCT, prior tigecycline therapy within 1 month were independent risk factors associated with hemorrhagic pneumonia.

Conclusions
Neutropenia, high level of PCT and prior tigecycline therapy within 1 month were significant independent predictors of hemorrhagic pneumonia in hematologic patients with SM bacteremia. Due to no effective antibiotics to prevent hemorrhagic pneumonia, prophylaxis of SM infection and its progression to hemorrhagic pneumonia is particularly important.
A clinical scoring system for pediatric hand-foot-mouth disease
Authors: Huang Hui , Deng Li , Jia Liping , Zhu Runan 
Published: July 2021

Abstract
Background
The aim of the present study was to develop a clinical scoring system for the diagnosis of hand-foot-mouth disease (HFMD) with improved accuracy.

Methods
A retrospective analysis was performed on standardized patient history and clinical examination data obtained from 1435 pediatric patients under the age of three years who presented with acute rash illness and underwent enterovirus nucleic acid detection. Patients were then divided into the HFMD (1094 patients) group or non-HFMD (341 patients) group based on a positive or a negative result from the assay, respectively. We then divided the data into a training set (1004 cases, 70%) and a test set (431 cases, 30%) using a random number method. Multivariate logistic regression was performed on 15 clinical variables (e.g. age, exposure history, number of rash spots in a single body region) to identify variables highly predictive of a positive diagnosis in the training set. Using the variables with high impact on the diagnostic accuracy, we generated a scoring system for predicting HFMD and subsequently evaluated this system in the test set by receiver operating characteristic curve (ROC curve).

Results
Using the logistic model, we identified seven clinical variables (age, exposure history, and rash density at specific regions of the body) to be included into the scoring system. The final scores ranged from − 5 to 24 (higher scores positively predicted HFMD diagnosis). Through our training set, a cutoff score of 7 resulted in a sensitivity of 0.76 and specificity of 0.68. The area under the receiver operating characteristic curve (AUC) was 0.804 (95% confidence interval [CI]: 0.773–0.835) (P < 0.001). Using the test set, we obtained an AUC of 0.76 (95% CI: 0.710–0.810) with a sensitivity of 0.76 and a specificity of 0.62. These results from the test set were consistent with those from the training set.

Conclusions
This study establishes an objective scoring system for the diagnosis of typical and atypical HFMD using measures accessible through routine clinical encounters. Due to the accuracy and sensitivity achieved by this scoring system, it can be employed as a rapid, low-cost method for establishing diagnoses in children with acute rash illness.
COVID-19 and its effects on endothelium in HIV-positive patients in sub-Saharan Africa: Cardiometabolic risk, thrombosis and vascular function (ENDOCOVID STUDY)
Authors: Goswami Nandu , Fredriksen Per Morten , Lundin Knut E. A. , Agu Chidozie , Elias Simiat Olanike , Motaung Keolebogile Shirley , Brix Bianca , Cvirn Gerhard , Sourij Harald , Stelzl Evelyn , Kessler Harald H. , Saloň Adam , Nkeh-Chungag Benedicta 
Published: July 2021

Abstract
Background
COVID-19 has affected almost every country in the world, especially in terms of health system capacity and economic burden. People from sub-Saharan Africa (SSA) often face interaction between human immunodeficiency virus (HIV) infection and non-communicable diseases such as cardiovascular disease. Role of HIV infection and anti-retroviral treatment (ART) in altered cardiovascular risk is questionable and there is still need to further carry out research in this field. However, thus far it is unclear, what impact the COVID-19 co-infection in people living with HIV (PLHIV), with or without therapy will have. The ENDOCOVID project aims to investigate whether and how HIV-infection in COVID-19 patients modulates the time course of the disease, alters cardiovascular risk, and changes vascular endothelial function and coagulation parameters/ thrombosis risk.

Methods
A total of 1026 patients will be included into this study. Cardiovascular research PLHIV with (n = 114 in each of the three recruiting centers) - or without - ART (n = 114 in each of the three recruiting centers) with COVID-19 and HIV-negative with COVID-19 (n = 114 in each of the three recruiting centers) will be carried out via clinical and biochemical measurements for cardiovascular risk factors and biomarkers of cardiovascular disease (CVD). Vascular and endothelial function will be measured by brachial artery flow-mediated dilatation (FMD), carotid intima-media thickness (IMT) assessments, and retinal blood vessel analyses, along with vascular endothelial biomarkers and cogualation markers. The correlation between HIV-infection in COVID-19 PLHIV with or without ART and its role in enhancement of cardiovascular risk and endothelial dysfunction will be assessed at admission, weekly, at discharge and, 4 weeks post-discharge (if possible).

Impact of project
The ENDOCOVID project aims to evaluate in the long-term the cardiovascular risk and vascular endothelial function in PLHIV thus revealing an important transitional cardiovascular phenotype in COVID-19. The study was registered under clinicaltrials.gov (NCT04709302).