bluuebunny/crossref_metadata_2025_split huggingface dataset:
What makes a ‘successful’ collaborative research project between public health practitioners and academics? A mixed-methods review of funding applications submitted to a local intervention evaluation scheme
Authors: van der Graaf Peter , Blank Lindsay , Holding Eleanor , Goyder Elizabeth 
Published: January 2021

Abstract
Background
The national Public Health Practice Evaluation Scheme (PHPES) is a response-mode funded evaluation programme operated by the National Institute for Health Research School for Public Health Research (NIHR SPHR). The scheme enables public health professionals to work in partnership with SPHR researchers to conduct rigorous evaluations of their interventions. Our evaluation reviewed the learning from the first five years of PHPES (2013–2017) and how this was used to implement a revised scheme within the School.

Methods
We conducted a rapid review of applications and reports from 81 PHPES projects and sampled eight projects (including unfunded) to interview one researcher and one practitioner involved in each sampled project (n = 16) in order to identify factors that influence success of applications and effective delivery and dissemination of evaluations. Findings from the review and interviews were tested in an online survey with practitioners (applicants), researchers (principal investigators [PIs]) and PHPES panel members (n = 19) to explore the relative importance of these factors. Findings from the survey were synthesised and discussed for implications at a national workshop with wider stakeholders, including public members (n = 20).

Results
Strengths: PHPES provides much needed resources for evaluation which often are not available locally, and produces useful evidence to understand where a programme is not delivering, which can be used to formatively develop interventions. Weaknesses: Objectives of PHPES were too narrowly focused on (cost-)effectiveness of interventions, while practitioners also valued implementation studies and process evaluations. Opportunities: PHPES provided opportunities for novel/promising but less developed ideas. More funded time to develop a protocol and ensure feasibility of the intervention prior to application could increase intervention delivery success rates. Threats: There can be tensions between researchers and practitioners, for example, on the need to show the 'success’ of the intervention, on the use of existing research evidence, and the importance of generalisability of findings and of generating peer-reviewed publications.

Conclusions
The success of collaborative research projects between public health practitioners (PHP) and researchers can be improved by funders being mindful of tensions related to (1) the scope of collaborations, (2) local versus national impact, and (3) increasing inequalities in access to funding. Our study and comparisons with related funding schemes demonstrate how these tensions can be successfully resolved.
Challenges in the abortion supply chain: a call to action for evaluation research
Authors: Samandari Ghazaleh , Kapp Nathalie , Hamon Christopher , Campbell Allison 
Published: January 2021

Abstract
Background
Reducing the burden of unsafe abortion rests considerably on women’s ability to access appropriate and timely treatment or services. A critical component of that care relies on a functional supply chain to ensure availability of abortion drugs and supplies within the health system. Disruptions in the supply of medical abortion drugs delay provision of abortion services and can increase the risks to a woman’s health. We examine the ways in which supply chain management (SCM) affects women’s ability to access safe and timely abortion to meet their reproductive health needs and highlight the gap in evaluation research on which SCM interventions best improve access to safe abortion care.
SCM comprises a critical component of efficient and sustainable abortion service provision and is a requisite for expansion of services. Furthermore, governments are responsible for safeguarding links in the abortion supply chain, from registration to distribution of abortion drugs and supplies. Strategic public–private partnerships and use of innovative local or community-based distribution mechanisms can strengthen supply chain systems. Finally, alternatives to the pull-based models of distribution could alleviate bottlenecks in the final steps of abortion supply chains. Programs aimed at increasing access to safe and comprehensive abortion care must include SCM as a foundational component of service provision. Without access to a sustainable and affordable supply of abortion drugs and equipment, any attempt at providing abortion services will be critically limited. More implementation research is needed to identify the most effective interventions for improving SCM.
Delivery strategies for optimizing uptake of contraceptives among adolescents aged 15–19 years in Nsanje District, Malawi
Authors: Makwinja Andrew Kondaine , Maida Zione Mchikaya , Nyondo-Mipando Alinane Linda 
Published: January 2021

Abstract
Background
Despite documented benefits of contraceptives, uptake among young people aged 20–24 years is high compared to adolescents aged 15–19 years in Malawi. As the world’s population of 15–19-year-olds continues to grow the need to meet the increasing demand for contraceptive services and information that address adolescent-specific needs cannot be underestimated. To inform Sexual and Reproductive health services for the youth, we explored strategies for optimizing uptake of contraceptives among this age group.

Methods
An exploratory qualitative cross-sectional study was conducted at Nsanje District Hospital and Nyamadzere Community Day Secondary School guided by Social-Ecological Framework to understand strategies that may optimize the uptake of contraceptives among adolescents aged 15–19. Nsanje district was purposively selected based on the reason that it is the second district in Malawi with the highest rate of adolescent childbearing of girls aged 15–19 years. We conducted a Focus Group Discussion (FGD) with 9 traditional leaders, 11 Key Informant Interviews (KIIs) with health workers, 20 In-depth Interviews (IDIs) with 12 adolescents, 4 teachers, and 4 parents. All data were digitally recorded, transcribed verbatim into English. The data was analyzed and managed using deductive thematic analysis guided by Social-Ecological Framework.

Results
Adolescents suggested accessing contraceptives from local drug stores, pharmacies and hospitals at a health system level and through Youth Centres, clubs, and corners at a Community level. There is a need to ensure a continuous supply of various kinds of contraceptives and the presence of youth-friendly health care workers in the specified areas.

Conclusion
There is no one way of delivering contraceptives to adolescents. Multiple avenues existent at the health facility and community could be leveraged to optimize delivery and uptake of contraceptives in a manner that is not intimidating to an adolescent while involving key stakeholders.
Apparent diffusion coefficient for the prediction of tumor response to neoadjuvant chemo-radiotherapy in locally advanced rectal cancer
Authors: Zhao Mengjing , Zhao Lihao , Yang Han , Duan Yuxia , Li Gang 
Published: January 2021

Abstract
Background
Patients with locally advanced rectal cancer generally have different response rates to preoperative neoadjuvant chemo-radiotherapy. This study investigated the value of the apparent diffusion coefficient (ADC) as a predictor to forecast the response to neoadjuvant chemo-radiotherapy in patients with locally advanced rectal cancer.

Methods
Ninety-one locally advanced rectal cancer patients who underwent neoadjuvant chemo-radiotherapy between 2015 and 2018 were enrolled. Diffusion-weighted magnetic resonance imaging was performed before treatment and within 4 weeks after the completion of neoadjuvant chemo-radiotherapy. Mean ADC values of regions of interest were evaluated by two radiologists. The tumor response was evaluated according to RESCIST 1.1. The cut-off value for the mean ADC and increasing percentage (ΔADC%) after neoadjuvant chemo-radiotherapy was calculated using the receiver operating characteristic curve. The response rate of pre-ADC and ΔADC% above/below the cut-off values was determined using the chi-square test, respectively. Primary tumor progression-free survival (PFS) was analyzed using the Kaplan–Meier method, based on the pre-ADC and ΔADC% cut-off values.

Results
The cut-off value of mean pre-ADC and ΔADC% was 0.94 × 10–3 mm2/s (80.36% sensitivity, 74.29% specificity) and 26.0% (73.21% sensitivity, 77.14% specificity), respectively. Lower mean pre-ADC values were related to a better response rate (83.3% vs 29.7%, P < 0.001) and PFS (26.12 vs 17.70 months, P = 0.004). ΔADC% above the cut-off value was also related to a better response rate (83.7% vs 35.7%, P < 0.001) and PFS (26.93 vs 15.65 months, P = 0.034).

Conclusions
The mean ADC pre-treatment value and ΔADC% were potential predictors for the tumor response in locally advanced rectal cancer patients treated with neoadjuvant chemo-radiotherapy.
Case series and finite element analysis of PFNA combined with cerclage wire for treatment of subtrochanteric fracture of femur
Authors: Huang Xiaowei , Zhang Fangxue , Zhang Yong 
Published: January 2021

Abstract
Objective
To retrospectively analyze the clinical efficacy of PFNA combined with a cerclage wire in the treatment of 52 patients with unstable subtrochanteric fracture of the femur and to analyze the biomechanical effect of ligature on a fracture model.

Methods
In this study, 52 patients with unstable subtrochanteric fractures were treated in our orthopedic trauma center from June 2013 to July 2018. The Seinsheimer type IV fracture model was established using the patient’s CT data, and the joint surface of the distal femoral condyle and the external condyle were restrained. The femoral head was used as the loading point, and a force of 500 N was applied vertically along the long axis of the femoral shaft.

Results
All 52 patients were followed up for 12 to 37 months, with an average of 18.07 ± 4.38 months. According to the Sanders hip function score, 28 cases were excellent (55–60 points), 22 cases were good (45–54 points), and 2 cases were poor (35–44 points), with an excellent and good rate of 96.15%. Postoperative deep vein thrombosis occurred in 3 cases, and fracture nonunion occurred in 1 case. No infection, loose fracture of internal fixation or hip varus deformity occurred. The finite element analysis indicated that the displacement of the whole model decreased slightly and the relative sliding of the fracture block decreased, but the maximum stress of the femur increased after the addition of the cerclage wire.

Conclusion
The treatment of unstable subtrochanteric fracture of the femur with PFNA combined with cerclage wire has the advantages of simple operation, satisfactory reduction of fracture, stable fixation, and good recovery of limb function. The finite element analysis suggested that the biomechanical strength fixation was enhanced after the addition of cerclage wire. However, the local stress concentration of the tie may increase the risk of failure.
Pancreatic involvement in patients with inborn errors of metabolism
Authors: Hwang Woo Jin , Lim Han Hyuk , Kim Yoo-Mi , Chang Mea Young , Kil Hong Ryang , Kim Jae Young , Song Wung Joo , Levy Harvey L. , Kim Sook-Za 
Published: January 2021

AbstractBackgroundRepeated inflammation of the pancreas can cause pancreatitis or diabetes. It is well recognized that the organic acidemias may be complicated by pancreatitis but less recognized are other metabolic disorders in which pancreatitis can occur. This study shows that long-term follow-up of patients with various metabolic disorders in Korea revealed several with episodes of isolated pancreatitis or diabetes concomitantly with pancreatitis.Results and discussionIn this study, two patients with methylmalonic aciduria (MMA), two with propionic acidemia (PPA), one with fatty acid oxidation disorder (FAOD), and one with hyperornithinemia, gyrate atrophy, and juvenile onset diabetes mellitus (DM) were clinically followed for up to 10 – 21 years. Two Korean siblings with MMA showed recurrent pancreatitis from the age of 15 and 19, respectively. The frequency of admission due to pancreatitis was up to 11 times. One patient with MMA developed diabetes mellitus at the age of 20. The other patient with MMA developed recurrent pancreatitis at 4 years and diabetes at 8 years of age. One of the patients with PPA presented with diabetic ketoacidosis. The other PPA patient died of cardiac arrest at age 10. The patient with FAOD presented with pancreatitis at 10 years and died at the age of 15 years due to cardiac arrest. A 35-year-old woman with hyperornithinemia/gyrate atrophy was diagnosed with juvenile onset diabetes at the age of 7 years. No pancreatitis occurred during the follow-up period.ConclusionsWe conclude that various metabolic disorders can trigger acute or chronic pancreatitis. Proper and prompt multidisciplinary management of metabolic derangement is crucial for preventing pancreatic damage. Further clinical and investigational studies are required to elucidate the pathogenesis of pancreatitis and diabetes mellitus in patients with inborn errors in metabolism.
An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features
Authors: An Ji-Yong , Meng Fan-Rong , Yan Zi-Ji 
Published: January 2021

Abstract
Background
Prediction of novel Drug–Target interactions (DTIs) plays an important role in discovering new drug candidates and finding new proteins to target. In consideration of the time-consuming and expensive of experimental methods. Therefore, it is a challenging task that how to develop efficient computational approaches for the accurate predicting potential associations between drug and target.

Results
In the paper, we proposed a novel computational method called WELM-SURF based on drug fingerprints and protein evolutionary information for identifying DTIs. More specifically, for exploiting protein sequence feature, Position Specific Scoring Matrix (PSSM) is applied to capturing protein evolutionary information and Speed up robot features (SURF) is employed to extract sequence key feature from PSSM. For drug fingerprints, the chemical structure of molecular substructure fingerprints was used to represent drug as feature vector. Take account of the advantage that the Weighted Extreme Learning Machine (WELM) has short training time, good generalization ability, and most importantly ability to efficiently execute classification by optimizing the loss function of weight matrix. Therefore, the WELM classifier is used to carry out classification based on extracted features for predicting DTIs. The performance of the WELM-SURF model was evaluated by experimental validations on enzyme, ion channel, GPCRs and nuclear receptor datasets by using fivefold cross-validation test. The WELM-SURF obtained average accuracies of 93.54, 90.58, 85.43 and 77.45% on enzyme, ion channels, GPCRs and nuclear receptor dataset respectively. We also compared our performance with the Extreme Learning Machine (ELM), the state-of-the-art Support Vector Machine (SVM) on enzyme and ion channels dataset and other exiting methods on four datasets. By comparing with experimental results, the performance of WELM-SURF is significantly better than that of ELM, SVM and other previous methods in the domain.

Conclusion
The results demonstrated that the proposed WELM-SURF model is competent for predicting DTIs with high accuracy and robustness. It is anticipated that the WELM-SURF method is a useful computational tool to facilitate widely bioinformatics studies related to DTIs prediction.
Association analysis of repetitive elements and R-loop formation across species
Authors: Zeng Chao , Onoguchi Masahiro , Hamada Michiaki 
Published: January 2021

Abstract
Background
Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation.

Results
We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeat retrotransposons (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells.

Conclusions
Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.
Impact of Polyvalent Mechanical Bacterial Lysate on lymphocyte number and activity in asthmatic children: a randomized controlled trial
Authors: Bartkowiak-Emeryk Małgorzata , Emeryk Andrzej , Roliński Jacek , Wawryk-Gawda Ewelina , Markut-Miotła Ewa 
Published: January 2021

Abstract
Background
Polyvalent Mechanical Bacterial Lysate (PMBL®) contains antigens of bacteria responsible for respiratory infections. PMBL® has been proven to reduce the number of respiratory infections, and in its use, immunological benefits have been seen in allergic patients. PMBL® activates both innate and specific immune responses. The lysate induces dendritic cells, T and B lymphocytes and IgA secretion, as well as the production of antibodies directed against administered bacterial antigens. Moreover, it increases the response against other bacteria and viruses. The immunologic mechanism of lysate’s action is not yet clearly determined. The objective of this study was to assess the effect of PMBL® on T cells in children with allergic asthma.

Methods
This study was a part of the EOLIA study. Herein, 49 children with allergic asthma and house dust mites allergy were included: 21 in PMBL® and 28 in the Placebo group, both, drug and placebo were administered sublingually. The tests were done at baseline and 12 weeks after the last tablet intake. The lymphocytes CD45+, lymphocytes T CD3+, CD3+CD25+, CD3+CD69+, Th CD3+CD4+, CD4+CD25+, CD4+CD25+ high, CD4+CD69+, Treg CD4+CD25+FOXP3, Tc CD3+CD8+, CD8+CD25+, CD8+CD69+, NK-like T CD3+CD16+CD56+ and NK cells CD3−CD16+CD56+ were described.

Results
At baseline, no significant differences between groups relative to blood count cells were observed, except for eosinophils. After 12 weeks, we observed an increase of T lymphocytes count. In addition, CD4+CD25+FOXP3+, CD8+ and CD3−CD16+CD56+ and (insignificantly) Th count increased. However, CD69+ and CD25+ subset of CD3+ significantly decreased.

Conclusions
The EOLIA study demonstrated that PMBL® administration 10 days per month for 3 months changed the panel of T lymphocytes.
Trial registration Clinical Trial Registration: This study was a part of the EOLIA (Efficacy Of mechanical bacterial Lysate In Allergic children), a clinical study NCT02541331. Frederic Durmont, MD Lallemand Pharma International AG. Date of registration 09/08/2013. URL of trial registry record: https://clinicaltrials.gov/ct2/show/study/NCT02541331.
Sero- and apx-typing of German Actinobacillus pleuropneumoniae field isolates from 2010 to 2019 reveals a predominance of serovar 2 with regular apx-profile
Authors: Schuwerk Lukas , Hoeltig Doris , Waldmann Karl-Heinz , Valentin-Weigand Peter , Rohde Judith 
Published: January 2021

AbstractSerotyping is the most common method to characterize field isolates of Actinobacillus (A.) pleuropneumoniae, the etiological agent of porcine pleuropneumonia. Based on serology, many farms seem to be infected and antibodies against a wide variety of serovars are detectable, but, so far it is unknown to what degree respective serovars contribute to outbreaks of clinical manifest disease. In this study, 213 German A. pleuropneumoniae field isolates retrieved for diagnostic purposes from outbreaks of porcine pleuropneumonia between 2010 and 2019 were genetically serotyped and analyzed regarding their apx-toxin gene profile using molecular methods. Serotyping revealed a prominent role of serovar 2 in clinical cases (64% of all isolates) and an increase in the detection of this serovar since 2010 in German isolates. Serovar 9/11 followed as the second most frequent serovar with about 15% of the isolates. Furthermore, very recently described serovars 16 (n = 2) and 18 (n = 8) were detected. Most isolates (93.4%) showed apx-profiles typical for the respective serovar. However, this does not hold true for isolates of serovar 18, as 75% (n = 6) of all isolates of this serovar deviated uniformly from the “typical” apx-gene profile of the reference strain 7311555. Notably, isolates from systemic lesions such as joints or meninges did not harbor the complete apxICABD operon which is considered typical for highly virulent strains. Furthermore, the extremely low occurrence (n = 1) of NAD independent (biovar II) isolates in German A. pleuropneumoniae was evident in our collection of clinical isolates.
WISE: a computer system performance index scoring framework
Authors: Luciano Lorenzo , Kiss Imre , Beardshear Peter William , Kadosh Esther , Hamza A. Ben 
Published: January 2021

AbstractThe performance levels of a computing machine running a given workload configuration are crucial for both users and providers of computing resources. Knowing how well a computing machine is running with a given workload configuration is critical to making proper computing resource allocation decisions. In this paper, we introduce a novel framework for deriving computing machine and computing resource performance indicators for a given workload configuration. We propose a workload/machine index score (WISE) framework for computing a fitness score for a workload/machine combination. The WISE score indicates how well a computing machine is running with a specific workload configuration by addressing the issue of whether resources are being stressed or sitting idle wasting precious resources. In addition to encompassing any number of computing resources, the WISE score is determined by considering how far from target levels the machine resources are operating at without maxing out. Experimental results demonstrate the efficacy of the proposed WISE framework on two distinct workload configurations.