bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experience of a tertiary-level urology center in the clinical urological events of rare and very rare incidence. IV. Urological surprises: 2. Clinically visible giant hydronephrosis in adults: Is there a significant function?
Authors: Gadelkareem Rabea Ahmed , Abdelhafez Mohamed Farouk , Moeen Ahmed Mohamed , Shahat Ahmed Abdelhamid , Gadelmoula Mohamed Mahmoud , Osman Mahmoud Mohammed , Abdelgawad Amr Mostafa , Elgammal Mohammed Abdallah , Abdel-Moniem Ahmed Mohamed 
Published: March 2020

AbstractBackgroundGiant hydronephrosis is rare with a controversy about the complete loss of renal functions. Our objective is to present our center’s experience with the management of cases of clinically visible giant hydronephrosis considering the potential residual functions. Our study is a retrospective case series of clinically visible giant hydronephrosis which was managed during the period July 2001–June 2016. Demographic and clinical variables were studied with specific considerations to the potential residual functions.ResultsOf more than 82,000 urological interventions, only 47 cases (0.057%) were operated upon for clinically visible giant hydronephrosis. Group 1 included 21 patients (mean age = 50.43 ± 13.71 years) who were treated initially by nephrostomy tube, and group 2 included 26 patients (mean age = 42.96 ± 15.16 years) who were treated primarily by nephrectomy. The main clinical presentation was abdominal distention (61.7%), while 13 patients (27.7%) were unaware of the swellings. The commonest underlying causes of hydronephrosis were urolithiasis (68.1%) and bilharzial ureteral strictures (23.4%). The contralateral kidney was diseased in 22 cases (46.8%) including the bilateral clinically visible hydronephrosis in 7 cases (15%). Indications of placement of a nephrostomy tube included uremia, infections, and evaluation of renal functions, where 5 cases of group 1 regained significant split function ranged 14–33%.ConclusionsClinically visible giant hydronephrosis is an extreme form of renal dilatation with different etiologies such as urolithiasis and bilharziasis. Initial placement of a nephrostomy tube may save significant residual functions in these kidneys.
Fast tree aggregation for consensus hierarchical clustering
Authors: Hulot Audrey , Chiquet Julien , Jaffrézic Florence , Rigaill Guillem 
Published: March 2020

Abstract
Background
In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering methods have been developed in the past decade. When a single source of data is at play, hierarchical clustering (HC) is extremely popular, as a tree structure is highly interpretable and arguably more informative than just a partition of the data. However, applying blindly HC to multiple sources of data raises computational and interpretation issues.

Results
We propose mergeTrees, a method that aggregates a set of trees with the same leaves to create a consensus tree. In our consensus tree, a cluster at height h contains the individuals that are in the same cluster for all the trees at height h. The method is exact and proven to be $\mathcal {O}(nq\log (n))$O(nqlog(n)), n being the individuals and q being the number of trees to aggregate. Our implementation is extremely effective on simulations, allowing us to process many large trees at a time. We also rely on mergeTrees to perform the cluster analysis of two real -omics data sets, introducing a spectral variant as an efficient and robust by-product.

Conclusions
Our tree aggregation method can be used in conjunction with hierarchical clustering to perform efficient cluster analysis. This approach was found to be robust to the absence of clustering information in some of the data sets as well as an increased variability within true clusters. The method is implemented in / and available as an package named , which makes it easy to integrate in existing or new pipelines in several research areas.
Brachial pulse pressure is associated with the presence and extent of coronary artery disease in stable angina patients: a cross-sectional study
Authors: Li Jin , Peng Yangpei , Ji Kangting 
Published: March 2020

Abstract
Background
Previous epidemiological evidence has identified many risk factors for coronary artery disease (CAD). Pulse pressure (PP) was reported to be associated with CAD. However, more attention was paid to aortic PP than to brachial PP. This cross-sectional study aimed to investigate the direct relationship between brachial PP and the presence and extent of CAD in stable angina patients.

Methods
We recruited a total of 1118 consecutive patients with stable chest pain suspected of CAD. After screening with exclusion criteria, 654 patients were finally included in our study. Every patient underwent both blood pressure measurement and selective coronary angiography. Univariate and multivariate analysis were performed to analyze the association between PP and the presence and extent of CAD.

Results
This study revealed that brachial PP was an independent correlate of multivessel CAD. In multivariate generalized linear regression model, increasing brachial PP (per 1 mmHg) were associated with the increased number of diseased vessels (β = 0.01, SE = 0.00, P < 0.0001). Binary logistic regression analysis further confirmed this association. The risk of multivessel CAD increased significantly in patients with brachial PP ≥ 60 mmHg (OR = 1.69, 95% CI = 1.14–2.48, P = 0.0084) and as per 1 mmHg increased in brachial PP (OR = 1.02, 95% CI = 1.01–1.03, P = 0.0002), independent of age, gender, body mass index (BMI), smoking, diabetes, hypercholesterolemia and creatinine (Cr). This association was still of statistical significance in subgroup analysis of hypertension and diabetes.

Conclusion
Increasing brachial PP was significantly and independently associated with increased risk of multivessel coronary disease in stable angina patients. The association of brachial PP with CAD was more pronounced in hypertension group than in non-hypertension one.
Non-communicable diseases research output in the Eastern Mediterranean region: an overview of systematic reviews
Authors: Akkawi Alaa , Khabsa Joanne , Noubani Aya , Jamali Sarah , Sibai Abla M. , Lotfi Tamara 
Published: March 2020

Abstract
Background
Rates of non-communicable diseases (NCDs) are rapidly rising in the Eastern Mediterranean Region (EMR). Systematic reviews satisfy the demand from practitioners and policy makers for prompt comprehensive evidence. The aim of this study is to review trends in NCD systematic reviews research output and quality by time and place, describe design and focus, and examine gaps in knowledge produced.

Methods
Using the Montori et al. systematic reviews filter, MeSH and keywords were applied to search Medline Ovid, Cochrane Central and Epistemonikos for publications from 1996 until 2015 in the 22 countries of the EMR. The ‘Measurement Tool to Assess Systematic Reviews’, AMSTAR, was used to assess the methodological quality of the papers.

Results
Our search yielded 2439 papers for abstract and title screening, and 89 papers for full text screening. A total of 39 (43.8%) studies included meta-analysis. Most of the papers were judged as being of low AMSTAR quality (83.2%), and only one paper was judged as being of high AMSTAR quality. Whilst annual number of papers increased over the years, the growth was mainly attributed to an increase in low-quality publications approaching in 2015 over four times the number of medium-quality publications. Reviews were significantly more likely to be characterized by higher AMSTAR scores (±SD) when meta-analysis was performed compared to when meta-analysis was not performed (3.4 ± 1.5 vs 2.6 ± 2.0; p-value = 0.034); and when critical appraisal of the included studies was conducted (4.3 ± 2.3 vs 2.5 ± 1.5; p-value = 0.004). Most of the reviews focused on cancer and diabetes as an outcome (25.8% and 24.7%, respectively), and on smoking, dietary habits and physical activity as exposures (15.7%, 12.4%, 9.0%, respectively). There was a blatant deficit in reviews examining associations between behaviors and physiologic factors, notably metabolic conditions.

Conclusions
Systematic reviews research in the EMR region are overwhelmingly of low quality, with gaps in the literature for studies on cardiovascular disease and on associations between behavioral factors and intermediary physiologic parameters. This study raises awareness of the need for high-quality evidence guided by locally driven research agenda responsive to emerging needs in countries of the EMR.
Assessing the effect of genetic markers on drug immunogenicity from a mechanistic model-based approach
Authors:   on behalf of the ABIRISK Consortium, Duhazé Julianne , Caubet Miguel , Hässler Signe , Bachelet Delphine , Allez Matthieu , Deisenhammer Florian , Fogdell-Hahn Anna , Gleizes Aude , Hacein-Bey-Abina Salima , Mariette Xavier , Pallardy Marc , Broët Philippe 
Published: March 2020

Abstract
Background
With the growth in use of biotherapic drugs in various medical fields, the occurrence of anti-drug antibodies represents nowadays a serious issue. This immune response against a drug can be due either to pre-existing antibodies or to the novel production of antibodies from B-cell clones by a fraction of the exposed subjects. Identifying genetic markers associated with the immunogenicity of biotherapeutic drugs may provide new opportunities for risk stratification before the introduction of the drug. However, real-world investigations should take into account that the population under study is a mixture of pre-immune, immune-reactive and immune-tolerant subjects.

Method
In this work, we propose a novel test for assessing the effect of genetic markers on drug immunogenicity taking into account that the population under study is a mixed one. This test statistic is derived from a novel two-part semiparametric improper survival model which relies on immunological mechanistic considerations.

Results
Simulation results show the good behavior of the proposed statistic as compared to a two-part logrank test. In a study on drug immunogenicity, our results highlighted findings that would have been discarded when considering classical tests.

Conclusion
We propose a novel test that can be used for analyzing drug immunogenicity and is easy to implement with standard softwares. This test is also applicable for situations where one wants to test the equality of improper survival distributions of semi-continuous outcomes between two or more independent groups.
Use of adenosine deaminase (ADA) to diagnose suspected peritoneal tuberculosis in Rwanda: a cross-sectional study
Authors: Ntwari Jules , Dusabejambo Vincent , Page Cameron 
Published: March 2020

Abstract
Background
Peritoneal tuberculosis is the most common cause of low albumin gradient ascites in developing countries, but it can be easily confused with other causes of ascites. Peritoneal tuberculosis requires early recognition of symptoms and signs in order to make a quick diagnosis for appropriate treatment. Measurement of adenosine deaminase (ADA) level > 39 in ascites fluid is an established test to diagnose peritoneal tuberculosis. Many low-income countries do not currently test for adenosine deaminase in ascites fluid, including Rwanda.

Method
Cross-sectional, descriptive study conducted through the Internal Medicine Department of three university teaching hospitals in Rwanda. Participants were patients older than 16 years presenting to tertiary referral hospitals with ascites of unknown cause.

Results
Of 103 ascites fluid samples collected, 52 of them (50.5%) had an elevated ADA, consistent with a presumptive diagnosis of peritoneal TB. Among those 52 subjects diagnosed with peritoneal TB, 39 out of 52 (75%) did not receive anti-TB medications. Among the 17 subjects who were treated with anti-TB medications, 4 of 17 (23.6%) did not have peritoneal TB based on ADA level. Samples with low-albumin gradient ascites were more likely to have high ADA ≥39 IU/L (p = 0.039).

Conclusion
Our findings suggest that 3out of 4 patients with PTB in Rwanda are not getting TB treatment and 1 in 4 patients who are taking TB medications do not need it. Even if the true number of Rwandans who are being undertreated and overtreated is less than our study suggests, these results should prompt a larger study of peritoneal tuberculosis. Adding adenosine deaminase (ADA) to the diagnostic tools available to clinicians could help achieve the goal of correctly putting every Rwandan with tuberculosis on treatment, while avoiding unnecessary tuberculosis medications in those who do not have the disease.
High levels of viral repression, malnutrition and second-line ART use in adolescents living with HIV: a mixed methods study from Myanmar
Authors: Murray Jillian , Whitehouse Katherine , Ousley Janet , Bermudez Elkin , Soe Theint Thida , Hilbig Adelene , Soe Kyi Pyar , Mon Phyu Ei , Tun Kyaw Tint , Ei Win Le Shwe Sin , Cyr Joanne , Deglise Carole , Ciglenecki Iza 
Published: March 2020

Abstract
Background
Adolescents living with HIV/AIDS (ALHIV) are a particularly vulnerable but often overlooked group in the HIV response despite additional disease management challenges.

Methods
All ALHIV (10–19 years), on ART for ≥6 months, presenting to care at a Médecins Sans Frontières (MSF) clinic in Myanmar from January–April 2016 were eligible for the quantitative study component (clinical history, medical examination, laboratory investigation). A subset of these respondents were invited to participate in qualitative interviews. Interviews and focus groups were also conducted with other key informants (care givers, clinicians).

Results
Of 177 ALHIV, 56% (100) were aged 9–13 years and 77 (44%) were 14–19. 49% (86) had been orphaned by one parent, and 19% (33) by both. 59% (104) were severely underweight (BMI < 16). 47% presented with advanced HIV (WHO stage III/IV). 93% were virally supressed (< 250 copies/mL). 38 (21%) of ALHIV were on a second-line ART after first-line virological failure. Qualitative interviewing highlighted factors limiting adherence and the central role that HIV counsellors play for both ALHIV patients and caregivers.

Conclusions
Our study shows good clinical, immunological, and virological outcomes for a cohort of Myanmar adolescents living with HIV, despite a majority being severely underweight, presenting with Stage III or IV illness, and the prevalence of comorbid infections (TB). Many treatment and adherence challenges were articulated in qualitative interviewing but emphasized the importance of actively engaging adolescents in their treatment. Comprehensive HIV care for this population must include routine viral load testing and social support programs.
Influenza in the school-aged population in Mexico: burden of disease and cost-effectiveness of vaccination in children
Authors: Falcón-Lezama Jorge Abelardo , Saucedo-Martínez Rodrigo , Betancourt-Cravioto Miguel , Alfaro-Cortes Myrna María , Bahena-González Roberto Isaac , Tapia-Conyer Roberto 
Published: March 2020

Abstract
Background
The current national influenza vaccination schedule in Mexico does not recommend vaccination in the school-aged population (5–11 years). Currently, there are limited data from middle-income countries analysing the cost-effectiveness of influenza vaccination in this population. We explored the clinical effects and economic benefits of expanding the current national influenza vaccination schedule in Mexico to include the school-aged population.

Methods
A static 1-year model incorporating herd effect was used to assess the cost-effectiveness of expanding the current national influenza vaccination schedule of Mexico to include the school-aged population. We performed a cross-sectional epidemiological study using influenza records (2009–2018), death records (2010–2015), and discharge and hospitalisation records (2010–2016), from the databases of Mexico’s Influenza Surveillance System (SISVEFLU), the National Mortality Epidemiological and Statistical System (SEED), and the Automated Hospital Discharge System (SAEH), respectively. Cost estimates for influenza cases were based on 7 scenarios using data analysed from SISVEFLU; assumptions for clinical management of cases were defined according to Mexico’s national clinical guidelines. The primary health outcome for this study was the number of influenza cases avoided. A sensitivity analysis was performed using conservative and optimistic parameters (vaccination coverage: 30% / 70%, Vaccine effectiveness: 19% / 68%).

Results
It was estimated that expanding the influenza immunisation programme to cover school-aged population in Mexico over the 2018–2019 influenza season would result in 671,461 cases of influenza avoided (50% coverage and 50% effectiveness assumed). Associated with this were 262,800 fewer outpatient consultations; 154,100 fewer emergency room consultations; 97,600 fewer hospitalisations, and 15 fewer deaths. Analysis of cases avoided by age-group showed that 55.4% of them were in the school-aged population, and the decrease in outpatient consultations was largest in this population. There was an overall decrease in the economic burden for the Mexican health care system of 111.9 million US dollars; the immunization programme was determined to be cost-saving in the base, conservative and optimistic scenarios.

Conclusions
Vaccinating school-aged population in Mexico would be cost-effective; expansion of the current national vaccination schedule to this age group is supported.
Two novel mutations in ADAMTS13 in a Chinese boy with congenital thrombocytopenic purpura: a case report
Authors: Hou Ling , Du Yue 
Published: March 2020

Abstract
Background
Mutations in the ADAMTS13 gene family have been reported to cause congenital thrombotic thrombocytopenic purpura (cTTP), a rare disease characterized by thrombocytopenia and hemolytic anemia. Nearly 150 causative mutations in ADAMTS13 have been identified; however, only a few of them were detected in Chinese patients.

Case presentation
A 5-year-old Chinese boy presented with history of thrombocytopenic purpura, hemolytic anemia, and renal injury since the neonatal period. Gene analysis revealed two novel mutations in ADAMTS13: a missense mutation 332G > A (p:Gly111Glu) in exon4 and a nonsense mutation 3121C > T (p:Gln1041stop) in exon 24. Genetic analysis of his parents confirmed the heterozygous nature of the mutations.

Conclusion
We report two novel mutations in ADAMTS13 (332G > A, 3121C > T) in a Chinese boy. These two mutations may lead to early onset of cTTP and severe symptoms.
MicroRNAs associated to single drug components of R-CHOP identifies diffuse large B-cell lymphoma patients with poor outcome and adds prognostic value to the international prognostic index
Authors: Due Hanne , Brøndum Rasmus Froberg , Young Ken H. , Bøgsted Martin , Dybkær Karen 
Published: March 2020

Abstract
Background
Treatment resistance is a major clinical challenge of diffuse large B-cell lymphoma (DLBCL) where approximately 40% of the patients have refractory disease or relapse. Since DLBCL is characterized by great clinical and molecular heterogeneity, the purpose of the present study was to investigate whether miRNAs associated to single drug components of R-CHOP can improve robustness of individual markers and serve as a prognostic classifier.

Methods
Fifteen DLBCL cell lines were tested for sensitivity towards single drug compounds of the standard treatment R-CHOP: rituximab (R), cyclophosphamide (C), doxorubicin (H), and vincristine (O). For each drug, cell lines were ranked using the area under the dose-response curve and grouped as either sensitive, intermediate or resistant. Baseline miRNA expression data were obtained for each cell line in untreated condition, and differential miRNA expression analysis between sensitive and resistant cell lines identified 43 miRNAs associated to growth response after exposure towards single drugs of R-CHOP. Using the Affymetrix HG-U133 platform, expression levels of miRNA precursors were assessed in 701 diagnostic DLBCL biopsies, and miRNA-panel classifiers predicting disease progression were build using multiple Cox regression or random survival forest. Classifiers were validated and ranked by repeated cross-validation.

Results
Prognostic accuracies were assessed by Brier Scores and time-varying area under the ROC curves, which revealed better performance of multivariate Cox models compared to random survival forest models. The Cox model including miR-146a, miR-155, miR-21, miR-34a, and miR-23a~miR-27a~miR-24-2 cluster performed the best and successfully stratified GCB-DLBCL patients into high- and low-risk of disease progression. In addition, combination of the Cox miRNA-panel and IPI substantially increased prognostic performance in GCB classified patients.

Conclusion
As a proof of concept, we found that expression data of drug associated miRNAs display prognostic utility and adding these to IPI improves prognostic stratification of GCB-DLBCL patients treated with R-CHOP.
The impact of socioeconomic factors on the healthcare costs of people living with HIV in Turkey
Authors: Özdemir Hülya Özkan , Tosun Selma , Kabadurmuş Fatma Nur Karaman , Özdemir Durmuş 
Published: March 2020

AbstractBackgroundThis study addresses an important field within HIV research, the impact of socioeconomic factors on the healthcare costs of people living with HIV/AIDS (PLHIV). We aimed to understand how different socioeconomic factors could create diverse healthcare costs for PLHIV in Turkey.MethodsData were collected between January 2017 and December 2017. HIV-positive people attending the clinic who had been referred to the national ART programme from January 1992 until December 2017 were surveyed. The questionnaire collected socioeconomic data. The cost data for the same patients was taken from the electronic database Probel Hospital Information Management System (PHIMS) for the same period. The PHIMS data include costs for medication (highly active antiretroviral therapy or HAART), laboratory, pathology, radiology, polyclinic, examination and consultation, hospitalisation, surgery and intervention, blood and blood products, supplies and other costs. Data were analysed using STATA 14.2 to estimate the generalised linear model (GLM).ResultsThe findings of our GLM indicate that age, gender, marital and parental status, time since diagnosis, employment, wealth status, illicit drug use and CD4 cell count are the factors significantly related to the healthcare cost of patients. We found that compared with people who have AIDS (CD4 cells < 200 cells/mm3), people who have a normal range of CD4 cells (≥ 500 cells/mm3) have $1046 less in expenditures on average. Compared to younger people (19–39 years), older people (≥ 55) have $1934 higher expenditures on average. Costs are $644 higher on average for married people and $401 higher on average for people who have children. Healthcare costs are $518 and $651 higher on average for patients who are addicted to drugs and who use psychiatric drug(s), respectively. Compared to people who were recently diagnosed with HIV, people who were diagnosed ≥10 years ago have $743 lower expenditures on average.ConclusionOur results suggest that in addition to immunological status, socioeconomic factors play a substantial role in the healthcare costs of PLHIV. The key factors influencing the healthcare costs of PLHIV are also critical for public policy makers, healthcare workers, health ministries and employment community programs.