bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stigmatization, discrimination, violation of autonomy, and compromised confidentiality: A descriptive qualitative analysis of the lived experiences of people living with HIV in healthcare settings in Turkey
Authors: Senyurek Gamze , Kavas Mustafa Volkan , Ulman Yesim Isil 
Published: January 2021

Abstract
Background: Human immunodeficiency virus (HIV) infection rates have been gradually increasing in Istanbul, Turkey. Many people living with HIV (PLWH) in Turkey encounter difficulties such as adapting to a chronic disease and maintaining continuous access to healthcare services. In this study, we explored the challenges PLWH face in their daily lives and understand their perceptions of themselves, healthcare professionals, their social spheres, and healthcare services via their expressed lived experiences in the healthcare setting.Method: Individual semi-structured in-depth interviews were conducted face-to-face with 20 people living with HIV in Istanbul. All the interviews were voice-recorded and transcribed verbatim except one, upon participant request, for which the interviewer took notes. These logs and the interviewer’s filed notes were analyzed thematically using the inductive content analysis method. Thematic pattern tables showing the relations of relevant contexts, main themes, sub-themes, and codes were then formed. Results: The results highlighted the following themes: problems with patients’ autonomy, failure to protect patients’ confidentiality and privacy of personal health data, spouse/partner notification issues, the negative effect of living with HIV on their perception of themselves, stigmatizing and discriminatory attitudes intrinsic in healthcare professionals’ approaches, and their struggle to deal with such approaches. Our participants’ experiences suggest that PLWH may face multi-dimensional challenges that directly and negatively affect their lives, identities, relationships, and social status in Turkey. Conclusion: This study showed the complex and shifting nature of stigma experiences. Healthcare professionals’ discriminative or inappropriate attitudes and customs prevailing in healthcare institutions impair PLWH’s utilization of healthcare services. Additionally, structural factors such as social pressure, societal ignorance about HIV, limited access to HIV prevention, and present barriers to HIV care and support originating from current regulations contribute to these challenges. Based on these results, we argue that it is necessary to raise healthcare professionals’ and society’s knowledge and awareness concerning HIV, to train qualified community service personnel providing assistance, care, support, and education to patients, to establish a well-functioning referral system, and to develop national policies to establish appropriate partner notification services. We believe that such interventions should begin to address the social, economic, and structural factors that drive stigma.
Nonlinear ridge regression improves cell-type-specific differential expression analysis
Authors: Takeuchi Fumihiko , Kato Norihiro 
Published: January 2021

Abstract
Background: Epigenome-wide association studies (EWAS) and differential gene expression analyses are generally performed on tissue samples, which consist of multiple cell types. Cell-type-specific effects of a trait, such as disease, on the omics expression are of interest but difficult or costly to measure experimentally. By measuring omics data for the bulk tissue, cell type composition of a sample can be inferred statistically. Subsequently, cell-type-specific effects are estimated by linear regression that includes terms representing the interaction between the cell type proportions and the trait. This approach involves two issues, scaling and multicollinearity.Results: First, although cell composition is analyzed in linear scale, differential methylation/expression is analyzed suitably in the logit/log scale. To simultaneously analyze two scales, we applied nonlinear regression. Second, we show that the interaction terms are highly collinear, which is obstructive to ordinary regression. To cope with the multicollinearity, we applied ridge regularization. In simulated data, nonlinear ridge regression attained well-balanced sensitivity, specificity and precision. Marginal model attained the lowest precision and highest sensitivity and was the only algorithm to detect weak signal in real data.Conclusion: Nonlinear ridge regression performed cell-type-specific association test on bulk omics data with well-balanced performance. The omicwas package for R implements nonlinear ridge regression for cell-type-specific EWAS, differential gene expression and QTL analyses. The software is freely available from https://github.com/fumi-github/omicwas
Feasibility of Anticoagulation Using Low Molecular‑Weight Heparin During Catheter-Directed Thrombolysis for Lower Extremity Deep Venous Thrombosis
Authors: Li Yonghui , Wang Junwei , He Rongzhou , Zheng Junmeng , Chen Zhibo , Yao Chen , Huang Kai 
Published: January 2021

Abstract
Background: The optimal anticoagulant scheme during catheter-directed thrombolysis (CDT) for deep venous thrombosis (DVT) remains unknown. This study was performed to evaluate the feasibility of anticoagulation therapy using low molecular‑weight heparin (LMWH) during CDT for DVT.Methods: The clinical data of DVT patients who underwent CDT during the past six years was retrospectively collected and reviewed. Patients were divided into therapeutic-dose anticoagulation (TPDA) and sub therapeutic-dose anticoagulation (sub-TPDA) groups according to LMWH dosage.Results: A total of 61 patients involving 61 limbs were comprised. Acute and subacute DVT were identified in 39 (63.9%) and 22 (36.1%) patients, respectively. Thrombosis involving the iliac vein was identified in 34 (55.7%) patients. Inferior vena cava filter placement was performed in 38 (62.3%) patients. Intraoperatively, adjunctive balloons, stents, and thrombectomy were provided for nine (14.8%), four (6.6%), and one (1.6%) patients, respectively. Twenty (32.8%) patients accepted TPDA therapy, while 41 (67.2%) patients were administrated with sub-TPDA therapy. Median urokinase infusion rate was 2.5 (0.83 to 5) x 104 U/h. Median infusion duration time was 4 (2 to 14) days, and median urokinase dose infused was 2.4 (0.6 to 10.80) x 106 U. During CDT, five (8.2%) cases of minor bleeding were observed, and blood transfusion was not required. No major bleeding, symptomatic pulmonary embolisms, or death occurred. Complete (>90%) and partial thrombolysis (50~90%) were achieved in 56 (91.8%) patients. In comparison with sub-TPDA group, TPDA group exhibited no significant differences in baseline characteristics, clinical improvement, thrombolysis results, and complications. Conclusions: Anticoagulation therapy using low molecular‑weight heparin during CDT with low infusion rate for DVT is likely to be feasible and safe. Sub-therapeutic-dose anticoagulation and therapeutic-dose could be used for CDT with similar clinical outcome and bleeding complications.
Re-amputation in patients with diabetes -related minor amputations who underwent physical therapy during their hospitalization. A single-facility retrospective cohort study
Authors: Imaoka Shinsuke , Sato Koji , Furukawa Masahide , Okita Minoru , Higashi Toshio 
Published: January 2021

Abstract
Background：Diabetes-related foot lesions are a major cause of non-traumatic lower limb amputations and are associated with a high re-amputation rate. Lesions can cause hindrance in activities of daily living, reduce physical function, and lower a patient’s quality of life. Physical therapy is necessary to prevent these limitations. Thus far, there has been limited investigation into the re-amputation rate in patients who have undergone physical therapy. This study aimed to elucidate modifiable risk factors for re-amputation in patients with minor amputations who were treated with physical therapy during their hospitalization.Methods：This was a retrospective cohort study of 245 consecutive hospitalized patients who presented to our Wound Care Center between January 2015 and February 2018 and received physical therapy after a minor amputation. Participants were identified from admission records to surgical and physical therapy units stored in the electronic medical records. We examined re-amputations that occurred in the ipsilateral lower extremity during the 1-year post-discharge outpatient period. The maximum follow-up period was set at 1 year. We used Cox proportional hazards analysis to examine factors affecting the risk of re-amputation.Results: Of the 129 patients enrolled, 42 patients (32.5%) underwent re-amputations during an average observation period of 6.2 months (range, 2.1 to 10.9 months). The factors associated with re-amputation were a requirement for hemodialysis, ankle dorsiflexion angle, and the Functional Independence Measure (FIM) ambulation score.Conclusions: In diabetes patients with minor amputations, a requirement for hemodialysis, ankle dorsiflexion angle, and the FIM ambulation score were shown to be modifiable risk factors for re-amputation. This emphasizes that maintaining vascular endothelial function through lower limb muscle exercises for hemodialysis, improving ankle mobility, and relieving plantar pressure during walking are necessary to reduce the risk of re-amputation. Patients with these risk factors should be encouraged to participate in physical therapy.
Knowledge, attitudes and ethical and social perspectives towards fecal microbiota transplantation (FMT) among Jordanian health care providers
Authors: Al-Bakri Amal G. , Akour Amal A. , Al-Delaimy Wael K. 
Published: January 2021

Abstract
Background: Fecal microbiota transplant (FMT) is a treatment modality that involves the introduction of stool from a healthy pre-screened donor into the gastrointestinal tract of a patient. It exerts its therapeutic effects by remodeling the gut microbiota and treating microbial dysbiosis-imbalance. FMT is not regulated in Jordan, and regulatory effort for FMT therapy in Jordan, an Islamic conservative country, might be faced with unique cultural, social, religious, and ethical challenges. We aimed to assess knowledge, attitudes, and perceptions of ethical and social issues of FMT use among Jordanian healthcare professionals.Methods: An observational, cross-sectional study design was used to assess knowledge, attitudes, and perceptions of ethical and social issues of FMT among 300 Jordanian healthcare professionals. Results: A large proportion (39%) thought that the safety and efficacy of this technique are limited and 29.3% thought there is no evidence to support its use. Almost all (95%) responded that they would only perform it in certain cases, if ethically justified, and 48.3% would use it due to treatment failure of other approaches. When reporting about reasons for not using it, 40% reported that they would not perform it due to concerns about medical litigation, fear of infections (38 %), and lack of knowledge of long safety and efficacy (31.3 %). Interestingly, all practitioners said they would perform this procedure through the lower rather than upper gastrointestinal tract modality and the majority will protect the patient’s confidentiality via double-blinding (43.3%). For a subset of participants (n=100), the cultural constraints that might affect the choice of performing FMT were mainly due to donor's religion,followed by dietary intake, and alcohol consumption.Conclusion: Our health care practitioners are generally reluctant to use the FMT modality due to religious and ethical reasons but would consider it if there was a failure of other treatment and after taking into consideration many legislative, social, ethical and practice-based challenges including safety, efficacy and absence of guidelines.
Comparison of piece length and dynamics of large wood in streams covered with coniferous and broadleaf forests mapped using ortho-photographs acquired by an unmanned aerial vehicle
Authors: Tsunetaka Haruka , Mtibaa Slim , Asano Shiho , Okamoto Takashi , Kurokawa Ushio 
Published: January 2021

Abstract
As large wood (LW) supplied by landslides and debris flows is one of the main components of watershed ecosystems, the importance of quantifying the dimensions of the LW is evident. However, the low accessibility of disturbed channels after landslides and debris flows generally impedes accurate and quick LW investigations. Recent advances in photogrammetry techniques may overcome such issues. In this study, we used ortho-photographs acquired using a small unmanned aerial vehicle (UAV) to measure the lengths of LW (wood pieces > 0.2-m long and > 0.03-m diameter) entrapped mainly by closed-type check-dams. We focused on two channels that are located in coniferous and broadleaf forests and affected by two different landslides events. The measurement accuracy was analyzed by comparing the lengths derived from the UAV method with direct measurements. When the both ends of a piece LW are satisfactorily extracted from an ortho-photograph acquired via the UAV, the LW lengths of coniferous trees can be measured with an accuracy of approximately ±0.5 m. For broadleaf trees, most of the extracted lengths were shorter than the directly measured lengths, probably due to the low visibility arising from the complex structures of the root wad and tree crown. Most LW pieces were discharged from landslide scars in the broadleaf forest, whereas approximately 750 LW pieces were left in the landslide scars of the coniferous forest. The number of LW pieces in the landslide scars increased with the increase in the landslide area, suggesting that some LW pieces can be left even if large landslides occur. There were no significant changes in the lengths or locations of the entrapped LW, at either site seven months after the first UAV flight. In the coniferous forests, the rainfall that triggered landslides in 2017 exceeded the 100-year return level, which was an abnormally intense rainfall. Although the 2019 rainfall event that occurred between UAV flights did not provide enough rainfall to trigger landslides, rainfall intensities with different durations reached the second-highest value from 1976 to 2019, exceeding the 30-year return period. This suggests that most of the entrapped LW rarely migrate even under extreme rainfall.
The nexus between health status and health expenditure, energy consumption and environmental pollution: Empirical evidence from SAARC-BIMSTEC regions
Authors: Rahman Mohammad Mafizur , Alam Khosrul 
Published: January 2021

Abstract
Background: The COVID-19 pandemic has highlighted the need for the betterment of health status, while also considering health expenditure, energy, and environmental issues. This paper examines the nexus between health status and health expenditure (both public and private), energy consumption and environmental pollution in the SAARC-BIMSTEC region.Methodology: We utilized the panel autoregressive distributed lag (ARDL) model, heterogeneous panel causality test, cross sectional dependence test, cointegration test and Pesaran cross sectional dependent (CADF) unit root test for obtaining estimated results from data over 16 years (2002-2017). Results: Our results authorize the cointegration among the variables used, where energy consumption, public and private health expenditure and economic growth have positive and statistically significant effects and environmental pollution has both negative and significant effects on the health status of these regions in the long-term, but no panel wise significant impact is found in the short-term. Two-way causal relationships between health status and environmental pollution, public and private health expenditure, economic growth and sanitation facilities, and a one-way causality running from energy consumption to health status are presented. Conclusions: The improved health status in the SAARC-BIMSTEC region needs to be protected by articulating the effective policies on both public and private health expenditures, environmental pollution, energy consumption, and economic growth. The attained results are theoretically and empirically consistent, and have important policy implications in the health sector.
Polyparasitism with Schistosoma haematobium,Plasmodium and soil-transmitted helminths in school-aged children in Muyuka-Cameroon following implementation of control measures: a cross sectional study
Authors: Sumbele Irene Ule Ngole , Otia Ofon Vitalis , Bopda Orelien Sylvain Mtopi , Ebai Calvin Bisong , Kimbi Helen KuoKuo , Nkuo-Akenji Theresa 
Published: January 2021

Abstract
Background: Despite the ubiquity of polyparasitism, its health impacts have been inadequately studied. The aim of this study was to determine the prevalence and determinants of polyparasitism with Schistosoma haematobium, Plasmodium and soil-transmitted helminths (STH) following sustained control measures, as well as evaluate the outcomes and clinical correlates of infection in school-aged children (SAC) living in the schistosomiasis endemic focus of Muyuka-Cameroon.Methods: In a cross-sectional study, urine, blood and stool samples were each collected from SAC (4–14 years) selected at random between March to June 2015. Microhaematuria in urine was detected using reagent strip and S. haematobium ova by filtration/microscopy methods. Plasmodium was detected using Giemsa stained blood films and complete blood count was obtained using an auto-haematology analyser. STH in stool was detected by the Kato-Katz method. Categorical and continuous variables were compared as required, Kappa value estimated and the adjusted odds ratio (aOR) in the multivariate analysis was used to evaluate association of the risk factors with infection.Results: Out of the 638 SAC examined, single infection was prevalent in 33.4% while polyparasitism was 19.9%. Prevalence of S. haematobium + Plasmodium was 7.8%; S. haematobium + STH was 0.8%; Plasmodium + STH was 0.8% while, S. haematobium + Plasmodium + STH was 0.9%. Higher preponderance of S. haematobium + Plasmodium infection occurred in females, those from Likoko, did not use potable water, practiced bathing in stream and carried out open defecation than their equivalents. However, being female (aOR =2.38, P = 0.009) was the only significant risk factor identified. Anaemia was a common morbidity (74.3%) with a slight agreement with microscopy in predicting S. haematobium and Plasmodium infections. The sensitivity and specificity of haematuria (13.0%) in predicting S. haematobium infection was 46.5% and 100% with a moderate agreement with microscopy. Co-infection with S. haematobium and malaria parasite was significantly associated with 3-fold odds of history of fever in the last three days.Conclusions: Polyparasitism is a public health problem in Muyuka with females most at risk. Anaemia prevalence is exacerbated in co- and triple-infections and together with a history of fever are of value in predicting polyparasitism.
DNA-loop extruding SMC complexes can traverse one another in vivo
Authors: Wang Xindan , Brandão Hugo , Ren Zhongqing , Karaboja Xheni , Mirny Leonid 
Published: January 2021

Abstract
Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Via 3D polymer simulations and theory, we find that these patterns require SMC complexes to bypass each other in vivo, contrary to the common assumption that SMC complexes mutually block each other’s loop extrusion activity. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.
Halogen heterogeneity in the subcontinental lithospheric mantle revealed by I/Br ratios in kimberlites and their mantle xenoliths from South Africa, Greenland, China, Siberia, Canada, and Brazil
Authors: Toyama Chiaki , Sumino Hirochika , Okabe Nobuaki , Ishikawa Akira , Yamamoto Junji , Kaneoka Ichiro , Muramatsu Yasuyuki 
Published: January 2021

Abstract
To investigate halogen heterogeneity in the subcontinental lithospheric mantle (SCLM), we measured the concentrations of Cl, Br, and I in kimberlites and their mantle xenoliths from South Africa, Greenland, China, Siberia, Canada, and Brazil. The samples can be classified into two groups based on halogen ratios: a high-I/Br group (South Africa, Greenland, Brazil, and Canada) and a low-I/Br group (China and Siberia). The halogen compositions were examined with the indices of crustal contamination using Sr and Nd isotopes and incompatible trace elements. The results indicate that the difference between the two groups was not due to different degrees of crustal contamination but from the contributions of different mantle sources. The low-I/Br group has a similar halogen composition to seawater-influenced materials such as fluids in altered oceanic basalts and eclogites and fluids associated with halite precipitation from seawater. We conclude that the halogens of the high-I/Br group are most likely derived from a SCLM source metasomatized by a fluid derived from subducted serpentinite, whereas those of the low-I/Br group are derived from a SCLM source metasomatized by a fluid derived from seawater-altered oceanic crust. The SCLM beneath Siberia and China could be an important reservoir of subducted, seawater-derived halogens, while such role of SCLM beneath South Africa, Greenland, Canada, and Brazil seems limited.