bluuebunny/crossref_metadata_2025_split huggingface dataset:
Access to and Quality of Primary Healthcare: a Multi-Country Qualitative Case Study in West and East Africa
Authors: Ameh Soter , Akeem Bolarinwa Oladimeji , Ochimana Caleb , Oluwasanu Abayomi Olabayo , Mohamed Shukri F , Okello Samson , Muhihi Alfa , Danaei Goodarz 
Published: August 2020

Abstract
Background: Universal health coverage is one of the Sustainable Development Goal targets known to improve population health and reduce financial burden. There is little qualitative data on access to and quality of primary healthcare in West and East Africa. We elicited in-depth viewpoints of healthcare users and providers, and other stakeholders regarding access to and quality of healthcare.Methods: A qualitative case study was conducted in four communities in Nigeria, and one community each in Kenya, Uganda and Tanzania in 2018. Purposive sampling was used to recruit 155 participants for 24 focus group discussions, 24 in-depth interviews, and 12 key informant interviews. The conceptual framework in this study combined elements of the Health Belief Model, Health Care Utilisation Model, four ‘As’ of access to care, and pathway model to better understand health-seeking behaviours of the study participants. The data were analysed with MAXQDA 2018 qualitative software to identify three themes identified a priori and one emerging theme.Results: Access to primary healthcare in the seven communities was limited. Quality of care was perceived to be unacceptable in public facilities whereas cost of care was unaffordable in private facilities. Patients and health providers and stakeholders highlighted shortage of equipment, frequent drug stock-outs and long waiting times as major issues, but had varying opinions on satisfaction with care. Use of herbal medicines and other traditional treatments delayed or deterred seeking modern healthcare in Nigerian sites. Conclusions: There was a substantial gap in primary healthcare coverage and quality in the selected communities in rural and urban East and West Africa. Alternative models of healthcare delivery should be used to fill this gap and facilitate achieving universal health coverage.
Fidelity Evaluation of the Compared Procedures for Conducting the PREDIAPS Implementation Strategy to Optimize Diabetes Prevention in Primary Care
Authors: Sánchez Alvaro , Rogers Heather Lynn , Pablo Susana , García Esther , Rodríguez Inmaculada , Flores Mª Antonia , Galarza Olga , Gaztañaga Ana B. , Martínez Pedro A. , Alberdi Eider , Resines Elena , Llarena Ana I. , Grandes Gonzalo , Group PREDIAPS 
Published: August 2020

Abstract
Background: Assessing the fidelity of an implementation strategy is important to understand why and how the strategy influences the uptake of evidence-based interventions. The present study aims to assess the fidelity of the two procedures for engaging primary care (PC) professionals and for the deployment of an implementation strategy for optimizing type 2 diabetes prevention in routine PC within the PREDIAPS randomized cluster implementation trial. Method: We conducted an observational descriptive fidelity evaluation study of the PREDIAPS implementation strategy. Nine PC centers from the Basque Health Service (Osakidetza) were allocated to two different procedures to engage physicians and nurses and deploy a implementation strategy to model and adapt the clinical intervention and its implementation to their specific contexts: a Global procedure, promoting the cooperation of all healthcare professionals from the beginning; or a Sequential procedure, centered first on nurses who then pursued the pragmatic cooperation of physicians. Process indicators of the delivery and receipt of implementation strategy actions among centers and groups compared and the comparison of documented modifications to the planned implementation strategy were used to assess the following components of fidelity: adherence, dose, quality of delivery, professionals’ responsiveness and program differentiation. Results: Generally, the procedures compared for professionals engagement and deployment of the implementation strategy were carried out with the planned differentiation. Nonetheless, some unexpected between-group differences were observed, the initial rate of collaboration of nurses being higher in the Sequential (93%) than in the Global (67%) groups. Exposure rate to the programed implementation actions (% of hours received out of those delivered) were similar in both groups by professional category, with nurses (86%) having a higher rate of exposure than physicians (75%). Professionals identified half of the planned discrete strategies and their rating of strategies’ perceived usefulness was overwhelmingly positive, with few differences between Sequential and Global centers. Conslusions: The PREDIAPS implementation strategy has been implemented with high fidelity and minor unplanned reactive modifications. Professionals’ exposure to the implementation strategy was high in both groups. The centers’ organizational context (i.e., work overload) led to small mismatches between groups in participation and exposure of professionals to implementation actions.Trial Registration: Clinicaltrials.gov identifier: NCT03254979. Registered 16 August 2017, https://www.clinicaltrials.gov/ct2/show/NCT03254979
Chromatin Loop Anchors Are Core Structural Components of the Gene Expression Machinery in Maize
Authors: Deschamps Stephane , Crow John A , Chaidir Nadia , Peterson-Burch Brooke , Kumar Sunil , Lin Haining , Zastrow-Hayes Gina , May Gregory D. 
Published: August 2020

Abstract
Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with transcriptional activity. Chromatin loops, made of two “anchors” flanking a loop “interior”, overlap with up to 90% of high-resolution interaction domains from a previous public maize interactome dataset. A majority of all anchors are shared between multiple loops, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analysis indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Up to 63% of all unique variants derived from a prior public maize eQTL datasets overlap with Hi-C loop anchors. Anchor annotation suggests that <7% of all loops detected from one Hi-C library are potentially devoid of any genes or regulatory elements. The overall conservation and organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions A majority of expressed genes and open chromatin regions co-locate with a conserved set of chromatin loop anchors. The results presented here will be a useful reference to further investigate the function of chromatin loop anchors and of the formation of interaction regions in the regulation of gene expression in maize.
Endoscopic Submucosal Dissection for Gastric Tube Carcinoma After Esophagectomy Contributes to Long-Term Outcomes: A Retrospective Case Series
Authors: Hashimoto Satoru , Sato Hiroki , Mizuno Ken-ichi , Takahashi Kazuya , Takatsuna Masafumi , Yokoyama Junji , Ichikawa Hiroshi , Takeuchi Manabu , Kobayashi Masaaki , Terai Shuji 
Published: August 2020

Abstract
Background: Gastric tube carcinoma (GTC) after esophagectomy has been observed increasingly in recent years after advanced treatment of esophageal carcinoma. Surgical removal of the reconstructed gastric tube is not usually preferred; however, endoscopic submucosal dissection (ESD) is greatly anticipated to be a promising option. This study investigated the efficacy and safety of ESD for GTC. Methods: This study was designed based on a retrospective survey performed at our single center between 2003 and 2018. Patients with GTC were treated with ESD and followed-up according to the policy of our institution. The curability of ESD was evaluated histologically according to the Japanese gastric cancer treatment guidelines. Patient characteristics, outcomes of ESD procedures, and long-term outcomes were analyzed. Results: A total of 31 patients (2 females; median age, 73 years) with 45 GTC cases were treated with ESD. The mean period from esophagectomy to the diagnosis of GTC was 10.6 years. The only adverse event due to ESD was bleeding (2 patients: 4.4%). No fatal events, such as perforation, occurred. The rates of complete resections and curative resections were 86.7% and 60.0%, respectively. The 3-year and 5-year overall survival rates were 67.6% and 47.7%, respectively. The 3-year and 5-year disease-specific survival rates were 100% and 92.9%, respectively. One patient died of GTC and 14 patients died of other diseases, including five primary carcinomas. Conclusions: ESD for GTC can be a safe treatment and contribute to positive long-term outcomes. Long-term regular gastroscopy is required for early detection. Screening should be performed before ESD and follow-up should be performed after ESD to prolong overall survival.
High-density lipoprotein cholesterol is a predictor of survival in cirrhotic patients with acute gastrointestinal bleeding: a retrospective study
Authors: Cheng Ran , Tan Ning , Kang Qian , Luo Hao , Chen Hongyu , Pan Jiali , Han Yifan , Yang Yuqing , Xu Xiaoyuan 
Published: August 2020

Abstract
Background: Lipid profiles are declined in patients with viral liver cirrhosis and correlated with severity of liver disease. Hepatitis B virus (HBV) is the leading cause of liver cirrhosis in China. Our primary aim was to investigate whether serum lipids and lipoproteins associate with survival in patients with HBV-related cirrhosis and acute gastrointestinal bleeding, and develop a 6-week mortality risk score that incorporates it.Methods: From January 2008 to December 2015, consecutive cirrhotic patients with acute gastrointestinal bleeding admitted to our hospital were evaluated and divided into the derivation (n=593) and validation (n=350) cohorts. A logistic regression model was established to confirm the association between lipoprotein cholesterol and mortality. Accuracy to predict mortality were assessed by area under the receiver operating characteristic curves (AUROCs) and compared using the Hanley and McNeil test.Results: Among study subjects, the 6-week mortality rate was 10.6%. High-density lipoprotein cholesterol (HDL-C) level was found to correlate most strongly with prognostic scores. On ROC analysis, HDL-C showed excellent diagnostic accuracy for 6-week mortality. Logistic regression analysis provided a simple algorithm based on the combined use of 4 variables (serum sodium (Na), HDL-C, presence of hepatocellular carcinoma (HCC) and QT interval prolongation), allowing accurate early discrimination of 3 distinct prognostic subgroups with 1.7% (low risk), 10.6% (intermediate risk), and 55.6% (high risk) mortality. Its accuracy was similar to the D’Amico score and significantly better than that of Child–Pugh, the model of end-stage liver disease (MELD), albumin-bilirubin (ALBI), and Augustin score. Baseline HDL-C values ≤ 0.57mmol/L were associated with markedly lower 6-week survival. Comparable results were found in the validation set. Conclusion: HDL-C is a potential indicator for the prognosis of patients with cirrhosis and acute gastrointestinal bleeding. The new algorithm based on HDL-C allowed an accurate predictive assessment of 6-week mortality after bleeding attack.
Differential Ketogenic Diet-Induced Shift in CSF Lipid/Carbohydrate Metabolome of Pediatric Epilepsy Patients With Optimal Vs. No Anticonvulsant Response
Authors: Masino Susan A. , Ruskin David N. , Freedgood Nathalie R. , Lindefeldt Marie , Dahlin Maria 
Published: August 2020

Abstract
Background: The low carbohydrate, high fat ketogenic diet can be an effective anticonvulsant treatment in some pediatric patients with pharmacoresistant epilepsy. Its mechanism(s) of action, however, remain uncertain. Direct sampling of cerebrospinal fluid before and after metabolic therapy may reveal key changes associated with differential clinical outcomes. Methods: We performed metabolomic analysis of cerebrospinal fluid samples taken before and during ketogenic diet treatment in patients with optimal response (100% seizure remission) and patients with no response (no seizure improvement) to search for differential diet effects in hallmark metabolic compounds in these two groups. Optimal responders and non-responders were similar in age range and included males and females. Seizure types and the etiologies or syndromes of epilepsy varied but did not appear to differ systematically between responders and non-responders. Results: Principal component analysis showed a strong effect of ketogenic diet treatment on the cerebrospinal fluid metabolome. Longitudinal and between-subjects analyses revealed that many lipids and carbohydrates were changed significantly by ketogenic diet, with changes typically being of larger magnitude in responders. Notably, responders had more robust changes in glucose and the ketone bodies b-hydroxybutyrate and acetoacetate than non-responders; conversely, non-responders had significant increases in fructose and sorbose, which did not occur in responders. Conclusions: The data suggest that a differential and stronger metabolic response to the ketogenic diet may predict a better anticonvulsant response, and such variability is likely due to inherent biological factors of individual patients. Strategies to boost the metabolic response may be beneficial.
COPD patients prescribed inhaled corticosteroid in primary care – Time for re-assessment based on exacerbation rate and blood eosinophils?
Authors: Savran Osman , Godtfredsen Nina Skavlan , Sørensen Torben , Jensen Christian , Ulrik Charlotte 
Published: August 2020

Abstract
Background and objective Inhaled corticosteroid (ICS) therapy for COPD should be guided by exacerbations and blood eosinophils according to the GOLD 2020 strategy document. In the present study, we applied these recent recommendations in a large cohort of COPD patients recruited from general practice. Methods The participating general practitioners (n = 144) recruited patients with a diagnosis of COPD currently prescribed ICS and reported data on exacerbation history and blood-eosinophils. Clinical variables were compared using multinomial logistic regression. Results The study cohort comprised 1,567 COPD patients (44% males and mean age 73 years). In the past 12 months, 849 (54%) of the COPD patients currently prescribed ICS had had no exacerbation, whereas 383 (24%) and 328 (21%) patients, respectively, had a history of one exacerbation and two or more exacerbations. Compared to patients with one or no exacerbation, patients with ≥2 exacerbations (21%) per year reported more respiratory symptoms (p<0.001). Among patients with no and at least one exacerbation within the preceding 12 months, 30% and 27%, respectively, had a blood-eosinophil count ≥ 0.3 x 10 9 /L. In patients with two or more exacerbations within the last 12 months, 77% had a blood-eosinophil count of ≥ 0.1 x 10 9 /L. Furthermore, 166 patients (11%) had at least one hospital admission due to COPD exacerbation, and a blood-eosinophil count of ≥ 0.1 x 10 9 /L. Conclusion This study of a large cohort of COPD patients currently prescribed inhaled corticosteroids suggest the need for re-evaluating the management strategy to increase benefit and reduce adverse effects of ICS treatment in COPD patients managed in primary care.
Prognostic Factors on Low-Birth-Weight Infants of Atresia and/or Tracheoesophageal Fistula: a Cohort Study
Authors: Xu Xiaonan , Zhang Ni , Li Binde , Huang Li 
Published: August 2020

Abstract
Background: Low-birth-weight is the main factor affecting the survival rate of esophageal atresia (EA)/ tracheoesophageal fistula (TEF). The study aims to summarize the factors influencing the prognosis of EA/TEF, which is expected to be helpful for clinical diagnosis and treatment. Methods: A retrospective data analysis was performed in our hospital underwent TEF/EA repair between January 2012 and January 2015. The incidence of preoperative, intraoperative critical events and postoperative complications and overall survival (OS) were compared between two groups of infants: 81 patients with EA/TEF, 24 low-birth-weight patients (<2500 g) with EA/TEF and 57 patients (>2500 g). The morbidity was compared between patients with stress hyperglycemia and euglycemia postoperatively. Results: The overall incidence of preoperative, intraoperative critical events and postoperative complications in low-birth-weight patients was significantly higher (P=0.002, P=0.001, P=0.001), but OS was lower (75.9% vs 92.3%, p=0.027). OS of patients with stress hyperglycemia postoperatively was lower than that of euglycemia (81.0% vs 93.6%, p=0.03).Conclusions: Low-birth-weight still was the main factor that impacted on the prognosis of EA/TEF. The lower the birth weight was, the higher the mortality was. Postoperative stress hyperglycemia was one of the important factors that influenced survival rate.
Modeling Plasmodium falciparum Diagnostic Test Sensitivity using Machine Learning with Histidine-Rich Protein 2 Variants
Authors: Ford Colby T , Alemayehu Gezahegn , Blackburn Kayla , Lopez Karen , Dieng Cheikh Cambel , Golassa Lemu , Lo Eugenia , Janies Daniel 
Published: August 2020

Abstract
Malaria, predominantly caused by Plasmodium falciparum , poses one of largest and most durable health threats in the world. Previously, simplistic regression-based models have been created to characterize malaria rapid diagnostic test performance, though these models often only include a couple genetic factors. Specifically, the Baker et al., 2005 model uses two types of particular repeats in histidine-rich protein 2 (PfHRP2) to describe a P. falciparum infection, though the efficacy of this model has waned over recent years due to genetic mutations in the parasite.
In this work, we use a dataset of 102 P. falciparum PfHRP2 genetic sequences collected in Ethiopia and derived a larger set of motif repeat matches for use in generating a series of diagnostic machine learning models. Here we show that the usage of additional and different motif repeats proves effective in predicting infection. Furthermore, we use machine learning model explanability methods to highlight which of the repeat types are most important, thereby showcasing a novel methodology for identifying potential targets for future versions of rapid diagnostic tests.
Real-world Experience of Nintedanib Therapy in Idiopathic-inflammatory-myopathy-related Interstitial Lung Disease: Efficacy and Tolerability
Authors: Liang Junyu , Cao Heng , Yang Yang , Ke Yini , Sun Chuanyin , Yue Lihuan , Lin Jin 
Published: August 2020

Abstract
Background

Interstitial lung disease (ILD) is a common and frequently fatal extra-muscular complication in patients with idiopathic inflammatory myopathy (IIM), and is refractory to the conventional immunosuppressive medications. Nintedanib has previously been proven to be effective and tolerable in idiopathic pulmonary fibrosis, systemic-sclerosis-related ILD, etc. However, the efficacy and safety of nintedanib in idiopathic-inflammatory-myopathy-related ILD (IIM-ILD) remain unknown. The purpose of this study was to initially explore the efficacy and tolerability of nintedanib in IIM-ILD patients.
Methods

A real-world analysis was conducted to explore the efficacy and tolerability of nintedanib in IIM-ILD patients who regularly received outpatient visit or hospitalization from January 2018 to October 2019 in one medical center. The primary end point was occurrence of rapid progression of interstitial lung disease (RP-ILD) in the follow-up. And time to death from any cause, complication of pulmonary infection and difference in immunosuppressive regimen were taken as secondary end points in this study. Adverse events were descriptively recorded.
Results

22 patients receiving nintedanib therapy and 82 patients under conventional medications were included. After propensity score matching, the primary comparison revealed that better survival (P = 0.036) and prominently less RP-ILD (P = 0.031) in patients with nintedanib therapy. Logistic regression analysis identified that disease activity (P = 0.032), anti-PM-Scl75 antibody (P = 0.027) and nintedanib therapy (P = 0.023, OR value = 0.063) were significantly correlated with RP-ILD. Cox proportional hazards regression analysis demonstrated that disease activity (P = 0.007), anti-MDA5 antibody (P = 0.004) and nintedanib therapy (P = 0.027, HR value = 0.190) were significantly associated with survival of IIM-ILD patients. Similar results can also be seen in analyses before propensity score matching. In the 22 patients with nintedanib therapy, diarrhea was the most common adverse event (54.5%) and hepatic insufficiency contributed to most dosage reduction (50%) or therapy discontinuation (50%).
Conclusion

Nintedanib therapy might reduce incidence of RP-ILD and improve survival in IIM-ILD patients. Anti-PM-Scl75 and anti-MDA5 antibodies could predict RP-ILD and survival respectively. In addition to the most frequent diarrhea, hepatic insufficiency was closely related to dosage reduction or therapy discontinuation.
Trial registration:

ISRCTN.com, ISRCTN 10507540. Retrospectively registered.
The extended stability of cervical swabs in careHPV™ Collection Medium
Authors: Tan Cheng-Siang 
Published: August 2020

Abstract
Background:

The careHPV™ Test is a US FDA approved, CE mark, and WHO prequalified in vitro diagnostic test that is designed to screen for 14 HRHPV genotypes. The careHPV™ Test is the only commercial HPV tests validated to be used in the low resource settings, boasting the economy of processing a maximum of 90 samples per batch and a near point-of-care turnaround time of 3 hours. Cervical swabs stored in the careHPV™ Collection Medium are stable for 30 days when stored between 2–8 °C according to the manufacturer. However, we often had difficulty to consolidate enough samples for a full batch-test within 30 days, especially when screening women living in the low-density villages in the rural Sarawak, Malaysian Borneo.
Objectives:

The aim of this study is to determine the stability and repeatability of cervical swabs preserved in careHPV™ Collection Medium stored at 4 °C over the recommended 30 days using the careHPV™ Test.
Methods:

Two groups of confirmed HRHPV positive and HRHPV negative cervical swab samples in careHPV™ Collection Medium consisting of 4 samples each were maintained at 4 °C and tested using careHPV™ Test at day-38, -123, -131, -223 and − 395.
Results:

All cervical swabs in careHPV™ Collection Medium stored at 4 °C remained stable for testing and demonstrated 100% repeatability for at least 395 days from the day of collection.
Conclusion:

The careHPV™ Test can be successfully performed on cervical swabs preserved in the careHPV Collection Medium, which are stored at 4 °C for at least 395 days.