bluuebunny/crossref_metadata_2025_split huggingface dataset:
“The talking bit of medicine, that’s the most important bit”: doctors and Aboriginal interpreters collaborate to transform culturally competent hospital care
Authors: Kerrigan Vicki , McGrath Stuart Yiwarr , Majoni Sandawana William , Walker Michelle , Ahmat Mandy , Lee Bilawara , Cass Alan , Hefler Marita , Ralph Anna P. 
Published: July 2021

Abstract
Background
In hospitals globally, patient centred communication is difficult to practice, and interpreters are underused. Low uptake of interpreters is commonly attributed to limited interpreter availability, time constraints and that interpreter-medicated communication in healthcare is an aberration. In Australia’s Northern Territory at Royal Darwin Hospital, it is estimated around 50% of Aboriginal patients would benefit from an interpreter, yet approximately 17% get access. Recognising this contributes to a culturally unsafe system, Royal Darwin Hospital and the NT Aboriginal Interpreter Service embedded interpreters in a renal team during medical ward rounds for 4 weeks in 2019. This paper explores the attitudinal and behavioural changes that occurred amongst non-Indigenous doctors and Aboriginal language interpreters during the pilot.

Methods
This pilot was part of a larger Participatory Action Research study examining strategies to achieve culturally safe communication at Royal Darwin Hospital. Two Yolŋu and two Tiwi language interpreters were embedded in a team of renal doctors. Data sources included interviews with doctors, interpreters, and an interpreter trainer; reflective journals by doctors; and researcher field notes. Inductive thematic analysis, guided by critical theory, was conducted.

Results
Before the pilot, frustrated doctors unable to communicate effectively with Aboriginal language speaking patients acknowledged their personal limitations and criticised hospital systems that prioritized perceived efficiency over interpreter access. During the pilot, knowledge of Aboriginal cultures improved and doctors adapted their work routines including lengthening the duration of bed side consults. Furthermore, attitudes towards culturally safe communication in the hospital changed: doctors recognised the limitations of clinically focussed communication and began prioritising patient needs and interpreters who previously felt unwelcome within the hospital reported feeling valued as skilled professionals. Despite these benefits, resistance to interpreter use remained amongst some members of the multi-disciplinary team.

Conclusions
Embedding Aboriginal interpreters in a hospital renal team which services predominantly Aboriginal peoples resulted in the delivery of culturally competent care. By working with interpreters, non-Indigenous doctors were prompted to reflect on their attitudes which deepened their critical consciousness resulting in behaviour change. Scale up of learnings from this pilot to broader implementation in the health service is the current focus of ongoing implementation research.
A urine extracellular vesicle circRNA classifier for detection of high-grade prostate cancer in patients with prostate-specific antigen 2–10 ng/mL at initial biopsy
Authors: He Ya-Di , Tao Wen , He Tao , Wang Bang-Yu , Tang Xiu-Mei , Zhang Liang-Ming , Wu Zhen-Quan , Deng Wei-Ming , Zhang Ling-Xiao , Shao Chun-Kui , Zhou Jing , Rong Li-Min , Gao Xin , Li Liao-Yuan 
Published: July 2021

AbstractThe aim of this study was to identify a urine extracellular vesicle circular RNA (circRNA) classifier that could detect high-grade prostate cancer (PCa) of Grade Group (GG) 2 or greater. For this purpose, we used RNA sequencing to identify candidate circRNAs from urinary extracellular vesicles from 11 patients with high-grade PCa and 11 case-matched patients with benign prostatic hyperplasia. Using ddPCR in a training cohort (n = 263), we built a urine extracellular vesicle circRNA classifier (Ccirc, containing circPDLIM5, circSCAF8, circPLXDC2, circSCAMP1, and circCCNT2), which was evaluated in two independent cohorts (n = 497, n = 505). Ccirc showed higher accuracy than two standard of care risk calculators (RCs) (PCPT-RC 2.0 and ERSPC-RC) in both the training cohort and the validation cohorts. In all three cohorts, this novel urine extracellular vesicle circRNA classifier plus RCs was statistically more predictive than RCs alone for predicting ≥ GG2 PCa. This assay, which does not require precollection digital rectal examination nor special handling, is repeatable, noninvasive, and can be easily implemented as part of the basic clinical workflow.
Genotyping of non-polio enteroviruses associated with acute flaccid paralysis in Thailand in 2013 and 2014
Authors: Onvimala Napa , Kosoltanapiwat Nathamon , Pumirat Pornpan , Vanaporn Muthita , Nimmanitya Suchitra , Tacharoenmuang Ratana , Guntapong Ratigorn , Leaungwutiwong Pornsawan 
Published: July 2021

Abstract
Background
Acute flaccid paralysis (AFP) surveillance was conducted as part of the World Health Organization’s strategy for completely eradicating poliomyelitis and leaving non-polio enteroviruses NPEVs as one of the main potential causes of AFP. We aimed to detect NPEV in association with AFP.

Methods
We used 459 isolates reported to be Negative Polio and some NPEVs by the World Health Organization Polio Regional Reference Laboratory (Thailand), which had been obtained during polio surveillance programmes conducted in Thailand in 2013–2014. Of 459 isolates, 35 belonged to the genus Enterovirus by RT-PCR and genotyping by DNA sequencing.

Results
This study found 17 NPEV genotypes, with 3, 13 and 1 belonging to enterovirus (EV) species A (EV-A), EV-B, and EV-C, respectively. The EV-A types identified included coxsackievirus A2 (CA2), CA4, and EV71, typically associated with hand, foot and mouth diseases. EV-B is the most prevalent cause of AFP in Thailand, while CA21 was the only type of EV-C detected. The EV-B species (13/35; 76.5%) constituted the largest proportion of isolates, followed by EV-A (3/35; 17.6%) and EV-C (1/35; 5.9%). For the EV-B species, Echovirus (E) 30 and CVB were the most frequent isolates. E30, CVB, E14, and E6 were considered endemic strains.

Conclusion
NPEVs, e.g. CA4, are reported for the first time in Thailand. Despite some limitations to this study, this is the first report on the circulation patterns of NPEVs associated with AFP in Thailand. AFP surveillance has unearthed many unknown NPEVs and, the cases of death due to AFP occur annually. Therefore, it is important to study NPEVs in the wake of the eradication of poliovirus in the context of the continued incidence of paralysis.
DNA–protein interaction studies: a historical and comparative analysis
Authors: Ferraz Ricardo André Campos , Lopes Ana Lúcia Gonçalves , da Silva Jessy Ariana Faria , Moreira Diana Filipa Viana , Ferreira Maria João Nogueira , de Almeida Coimbra Sílvia Vieira 
Published: July 2021

Abstract
DNA–protein interactions are essential for several molecular and cellular mechanisms, such as transcription, transcriptional regulation, DNA modifications, among others. For many decades scientists tried to unravel how DNA links to proteins, forming complex and vital interactions. However, the high number of techniques developed for the study of these interactions made the choice of the appropriate technique a difficult task. This review intends to provide a historical context and compile the methods that describe DNA–protein interactions according to the purpose of each approach, summarise the respective advantages and disadvantages and give some examples of recent uses for each technique. The final aim of this work is to help in deciding which technique to perform according to the objectives and capacities of each research team. Considering the DNA–binding proteins characterisation, filter binding assay and EMSA are easy in vitro methods that rapidly identify nucleic acid-protein binding interactions. To find DNA-binding sites, DNA-footprinting is indeed an easier, faster and reliable approach, however, techniques involving base analogues and base-site selection are more precise. Concerning binding kinetics and affinities, filter binding assay and EMSA are useful and easy methods, although SPR and spectroscopy techniques are more sensitive. Finally, relatively to genome-wide studies, ChIP–seq is the desired method, given the coverage and resolution of the technique. In conclusion, although some experiments are easier and faster than others, when designing a DNA–protein interaction study several concerns should be taken and different techniques may need to be considered, since different methods confer different precisions and accuracies.
Impact of a restrictive antibiotic policy on the acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in an endemic region: a before-and-after, propensity-matched cohort study in a Caribbean intensive care unit
Authors: Le Terrier Christophe , Vinetti Marco , Bonjean Paul , Richard Régine , Jarrige Bruno , Pons Bertrand , Madeux Benjamin , Piednoir Pascale , Ardisson Fanny , Elie Elain , Martino Frédéric , Valette Marc , Ollier Edouard , Breurec Sébastien , Carles Michel , Thiéry Guillaume 
Published: July 2021

Abstract
Background
High-level antibiotic consumption plays a critical role in the selection and spread of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in the ICU. Implementation of a stewardship program including a restrictive antibiotic policy was evaluated with respect to ESBL-E acquisition (carriage and infection).

Methods
We implemented a 2-year, before-and-after intervention study including all consecutive adult patients admitted for > 48 h in the medical-surgical 26-bed ICU of Guadeloupe University Hospital (French West Indies). A conventional strategy period (CSP) including a broad-spectrum antibiotic as initial empirical treatment, followed by de-escalation (period before), was compared to a restrictive strategy period (RSP) limiting broad-spectrum antibiotics and shortening their duration. Antibiotic therapy was delayed and initiated only after microbiological identification, except for septic shock, severe acute respiratory distress syndrome and meningitis (period after). A multivariate Cox proportional hazard regression model adjusted on propensity score values was performed. The main outcome was the median time of being ESBL-E-free in the ICU. Secondary outcome included all-cause ICU mortality.

Results
The study included 1541 patients: 738 in the CSP and 803 in the RSP. During the RSP, less patients were treated with antibiotics (46.8% vs. 57.9%; p < 0.01), treatment duration was shorter (5 vs. 6 days; p < 0.01), and administration of antibiotics targeting anaerobic pathogens significantly decreased (65.3% vs. 33.5%; p < 0.01) compared to the CSP. The incidence of ICU-acquired ESBL-E was lower (12.1% vs. 19%; p < 0.01) during the RSP. The median time of being ESBL-E-free was 22 days (95% CI 16-NA) in the RSP and 18 days (95% CI 16–21) in the CSP. After propensity score weighting and adjusted analysis, the median time of being ESBL-E-free was independently associated with the RSP (hazard ratio, 0.746 [95% CI 0.575–0.968]; p = 0.02, and hazard ratio 0.751 [95% CI 0.578–0.977]; p = 0.03, respectively). All-cause ICU mortality was lower in the RSP than in the CSP (22.5% vs. 28.6%; p < 0.01).

Conclusions
Implementation of a program including a restrictive antibiotic strategy is feasible and is associated with less ESBL-E acquisition in the ICU without any worsening of patient outcome.
MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits
Authors: Runcie Daniel E. , Qu Jiayi , Cheng Hao , Crawford Lorin 
Published: July 2021

AbstractLarge-scale phenotype data can enhance the power of genomic prediction in plant and animal breeding, as well as human genetics. However, the statistical foundation of multi-trait genomic prediction is based on the multivariate linear mixed effect model, a tool notorious for its fragility when applied to more than a handful of traits. We present , a statistical framework and associated software package for mixed model analyses of a virtually unlimited number of traits. Using three examples with real plant data, we show that can leverage thousands of traits at once to significantly improve genetic value prediction accuracy.
STRONG: metagenomics strain resolution on assembly graphs
Authors: Quince Christopher , Nurk Sergey , Raguideau Sebastien , James Robert , Soyer Orkun S. , Summers J. Kimberly , Limasset Antoine , Eren A. Murat , Chikhi Rayan , Darling Aaron E. 
Published: July 2021

AbstractWe introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
The Chinese herbal formula Huoxiang Zhengqi for diarrhea-predominant irritable bowel syndrome (CHAIRS): a study protocol for a double-blinded randomized controlled trial
Authors: Guo Xiaohui , Xuan Meiling , Zheng Huan , Qin Shumin , Wu Haomeng , Huang Shaogang , Wen Zehuai 
Published: July 2021

Abstract
Background
Diarrhea-predominant irritable bowel syndrome (IBS-D) is a common chronic digestive disease. Recent observational studies have reported that the Chinese herbal formula Huoxiang Zhengqi (HXZQ) can relieve IBS-D symptoms, but no high-level evidence is presented. Therefore, we want to evaluate the efficacy and safety of HXZQ for IBS-D patients.

Methods
This is a double-blind, randomized, placebo-controlled trial. The 212 eligible patients with IBS-D will be randomly assigned to receive either HXZQ oral liquid or a placebo, at a 1:1 ratio, for 4 weeks with a 4-week follow-up period. Adequate relief will be the primary outcome measures. IBS symptom severity score, IBS quality-of-life questionnaire, EQ-5D-5L, and Chinese medicine symptom questionnaire will be the secondary outcome measures.

Discussion
This trial aims to demonstrate the efficacy and safety of HXZQ for IBS-D, which is expected to be an effective IBS-D treatment.

Trial registration
The trial was registered with the Chinese Clinical Trial Registry, ChiCTR1900026837. Registered on 24 October 2019.
Placebo response and effect in randomized clinical trials: meta-research with focus on contextual effects
Authors: Hafliðadóttir Sigurlaug H. , Juhl Carsten B. , Nielsen Sabrina M. , Henriksen Marius , Harris Ian A. , Bliddal Henning , Christensen Robin 
Published: July 2021

AbstractBackgroundContextual effects (i.e., placeboresponse) refer to all health changes resulting from administering an apparently inactive treatment. In a randomized clinical trial (RCT), the overall treatment effect (i.e., the post-treatment effect in the intervention group) can be regarded as the true effect of the intervention plus the impact of contextual effects. This meta-research was conducted to examine the average proportion of the overall treatment effect attributable to contextual effects in RCTs across clinical conditions and treatments and explore whether it varies with trial contextual factors.MethodsData was extracted from trials included in the main meta-analysis from the latest update of the Cochrane review on “Placebo interventions for all clinical conditions”(searched from 1966 to March 2008). Only RCTs reported in English having an experimental intervention group, a placebo comparator group, and a no-treatment control group were eligible.ResultsIn total, 186 trials (16,655 patients) were included. On average, 54% (0.54, 95%CI 0.46 to 0.64) of the overall treatment effect was attributable to contextual effects. The contextual effects were higher for trials with blinded outcome assessor and concealed allocation. The contextual effects appeared to increase proportional to the placebo effect, lower mean age, and proportion of females.ConclusionApproximately half of the overall treatment effect in RCTs seems attributable to contextual effects rather than to the specific effect of treatments. As the study did not include all important contextual factors (e.g., patient-provider interaction), the true proportion of contextual effects could differ from the study’s results. However, contextual effects should be considered when assessing treatment effects in clinical practice.Trial registrationPROSPEROCRD42019130257. Registered on April 19, 2019.
Metabolic control and hypoglycaemia in people with type 1 diabetes: insulin pump therapy vs. intensified insulin therapy in an unselected cohort in routine care
Authors: Kramer Guido , Kloos Christof , Müller Ulrich A. , Wolf Gunter , Kuniss Nadine 
Published: July 2021

Abstract
Aims
The aim of this study was to compare individuals with type 1 diabetes with continuous subcutaneous insulin infusion (CSII) and intensified insulin therapy (ICT) in routine care regarding metabolic control and treatment satisfaction.

Methods
Individuals with type 1 diabetes (CSII n = 74; ICT n = 163) were analysed regarding metabolic control, frequency of hypoglycaemia and treatment satisfaction (DTSQs range 0–36).

Results
Individuals with CSII (duration of CSII: 14.1 ± 7.2 years) were younger (51.1 ± 15.8 vs. 56.2 ± 16.2 years, p = 0.023), had longer diabetes duration (28.7 ± 12.4 vs. 24.6 ± 14.3 years, p = 0.033), lower insulin dosage (0.6 ± 0.2 vs. 0.7 ± 0.4 IU/kg, p = 0.004), used more frequently short-acting analogue insulin (90.5% vs. 48.5%, p < 0.001) and flash/continuous glucose monitoring (50.0% vs. 31.9%, p = 0.009) than people with ICT. HbA1c was similar between CSII and ICT (7.1 ± 0.8%/54.4 ± 9.1 mmol/mol vs. 7.2 ± 1.0%/55.7 ± 10.9 mmol/mol, p = 0.353). Individuals with CSII had higher frequency of non-severe hypoglycaemia per week (in people with blood glucose monitoring: 1.9 ± 1.7 vs. 1.2 ± 1.6, p = 0.014; in people with flash/continuous glucose monitoring: 3.3 ± 2.2 vs. 2.1 ± 2.0, p = 0.006). Prevalence of polyneuropathy (18.9% vs. 38.0%, p = 0.004) and systolic blood pressure (138.0 ± 16.4 vs. 143.9 ± 17.1 mmHg, p = 0.014) was lower in CSII. Satisfaction with diabetes treatment (26.7 ± 7.3 vs. 26.0 ± 6.8, p = 0.600) did not differ between CSII and ICT.

Conclusions
CSII and ICT yielded comparable metabolic control and treatment satisfaction but CSII was associated with higher incidence of non-severe hypoglycaemia and lower insulin dosage.
Software engineering techniques for statically analyzing mobile apps: research trends, characteristics, and potential for industrial adoption
Authors: Autili Marco , Malavolta Ivano , Perucci Alexander , Scoccia Gian Luca , Verdecchia Roberto 
Published: July 2021

AbstractMobile platforms are rapidly and continuously changing, with support for new sensors, APIs, and programming abstractions. Static analysis is gaining a growing interest, allowing developers to predict properties about the run-time behavior of mobile apps without executing them. Over the years, literally hundreds of static analysis techniques have been proposed, ranging from structural and control-flow analysis to state-based analysis.In this paper, we present a systematic mapping study aimed at identifying, evaluating and classifying characteristics, trends and potential for industrial adoption of existing research in static analysis of mobile apps. Starting from over 12,000 potentially relevant studies, we applied a rigorous selection procedure resulting in 261 primary studies along a time span of 9 years. We analyzed each primary study according to a rigorously-defined classification framework. The results of this study give a solid foundation for assessing existing and future approaches for static analysis of mobile apps, especially in terms of their industrial adoptability.Researchers and practitioners can use the results of this study to (i) identify existing research/technical gaps to target, (ii) understand how approaches developed in academia can be successfully transferred to industry, and (iii) better position their (past and future) approaches for static analysis of mobile apps.
Changes to the identity of EndoC-βH1 beta cells may be mediated by stress-induced depletion of HNRNPD
Authors: Jeffery Nicola , Chambers David , Invergo Brandon M. , Ames Ryan M. , Harries Lorna W. 
Published: July 2021

Abstract
Background
Beta cell identity changes occur in the islets of donors with diabetes, but the molecular basis of this remains unclear. Protecting residual functional beta cells from cell identity changes may be beneficial for patients with diabetes.

Results
A somatostatin-positive cell population was induced in stressed clonal human EndoC-βH1 beta cells and was isolated using FACS. A transcriptomic characterisation of somatostatin-positive cells was then carried out. Gain of somatostatin-positivity was associated with marked dysregulation of the non-coding genome. Very few coding genes were differentially expressed. Potential candidate effector genes were assessed by targeted gene knockdown. Targeted knockdown of the HNRNPD gene induced the emergence of a somatostatin-positive cell population in clonal EndoC-βH1 beta cells comparable with that we have previously reported in stressed cells.

Conclusions
We report here a role for the HNRNPD gene in determination of beta cell identity in response to cellular stress. These findings widen our understanding of the role of RNA binding proteins and RNA biology in determining cell identity and may be important for protecting remaining beta cell reserve in diabetes.
Simulation of gymnastics performance based on MEMS sensor
Authors: Chen Bingxin , Kuang Lifei , He Wei 
Published: July 2021

AbstractThe development and progress of multi-sensor data fusion theory and methods have also laid the foundation for the research of human body posture tracking system based on inertial sensing. The main research in this paper is the simulation of gymnastics performance based on MEMS sensors. In the preprocessing to reduce noise interference, this paper mainly uses median filtering to remove signal glitches. This article uses virtual character models for gymnastics performances. The computer receives sensor data from the sink node of the motion capture device through a Bluetooth communication module. The unit calculates the quaternion output from the dynamic link library of sensor data processing, calculates the rotation amount and coordinate offset of each sensor node’s limb, and uses the character model to realize the real-time rendering of the virtual character model. At the same time, it controls the storage of sensor data, the drive of the model, and the display of the graphical interface. When a gesture action is about to occur, a trigger signal is given to the system to mark the beginning of the action, so as to obtain the initial data of each axis signal of the MEMS sensor. When the gesture action is completed, give the system a signal to end the action. Mark the end of the action, so that you can capture the original signal data during the beginning and end of the gesture action. In order to ensure the normal communication between PS and PL, it is necessary to test the key interfaces involved. Because the data received by the SPI acquisition module is irregular, it is impossible to verify whether the data is wrong, so the SPI acquisition module is replaced with a module that automatically increments data, and the IP core is generated, and a test platform is built for testing. The data shows that the average measurement error of X-axis displacement of the space tracking system is 8.17%, the average measurement error of Y-axis displacement is 7.51%, the average measurement error of Z-axis displacement is 9.72%, and the average error of three-dimensional space measurement is 8.7%. The results show that the MEMS sensor can accurately recognize the action with high accuracy.