bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species
Authors: Chiang Tai-Wei , Mai Te-Lun , Chuang Trees-Juen 
Published: May 2022

Abstract
Background
Circular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activities. While numerous databases have collected a large amount of predicted circRNA candidates and provided the corresponding circRNA-regulated interactions, a stand-alone package for constructing circRNA-miRNA-mRNA interactions based on user-identified circRNAs across species is lacking.

Results
We present CircMiMi (circRNA-miRNA-mRNA interactions), a modular, Python-based software to identify circRNA-miRNA-mRNA interactions across 18 species (including 16 animals and 2 plants) with the given coordinates of circRNA junctions. The CircMiMi-constructed circRNA-miRNA-mRNA interactions are derived from circRNA-miRNA and miRNA-mRNA axes with the support of computational predictions and/or experimental data. CircMiMi also allows users to examine alignment ambiguity of back-splice junctions for checking circRNA reliability and examine reverse complementary sequences residing in the sequences flanking the circularized exons for investigating circRNA formation. We further employ CircMiMi to identify circRNA-miRNA-mRNA interactions based on the circRNAs collected in NeuroCirc, a large-scale database of circRNAs in the human brain. We construct circRNA-miRNA-mRNA interactions comprising differentially expressed circRNAs, and miRNAs in autism spectrum disorder (ASD) and cross-species analyze the relevance of the targets to ASD. We thus provide a rich set of ASD-associated circRNA-miRNA-mRNA axes and a useful starting point for investigation of regulatory mechanisms in ASD pathophysiology.

Conclusions
CircMiMi allows users to identify circRNA-mediated interactions in multiple species, shedding light on regulatory roles of circRNAs. The software package and web interface are freely available at https://github.com/TreesLab/CircMiMi and http://circmimi.genomics.sinica.edu.tw/, respectively.
SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks
Authors: Paci Paola , Fiscon Giulia 
Published: May 2022

Abstract
Background
Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions. This methodology has aroused a broad acknowledgment within the scientific community thanks to the encouraging results achieved when applied to breast invasive carcinoma, leading to the identification of PVT1, a long non-coding RNA functioning as ceRNA for the miR-200 family. The main shortcoming of the model is that it is no freely available and implemented in MATLAB®, a proprietary programming platform requiring a paid license for installing, operating, manipulating, and running the software.

Results
Breaking through these model limitations demands to distribute it in an open-source, freely accessible environment, such as R, designed for an ordinary audience of users that are not able to afford a proprietary solution. Here, we present SPINNAKER (SPongeINteractionNetworkmAKER), the open-source version of our widely established mathematical model for predicting ceRNAs crosstalk, that is released as an exhaustive collection of R functions. SPINNAKER has been even designed for providing many additional features that facilitate its usability, make it more efficient in terms of further implementation and extension, and less intense in terms of computational execution time.

Conclusions
SPINNAKER source code is freely available at https://github.com/sportingCode/SPINNAKER.git together with a thoroughgoing PPT-based guideline. In order to help users get the key points more conveniently, also a practical R-styled plain-text guideline is provided. Finally, a short movie is available to help the user to set the own directory, properly.
A predictive ambulance dispatch algorithm to the scene of a motor vehicle crash: the search for optimal over and under triage rates
Authors: Ceklic Ellen , Tohira Hideo , Ball Stephen , Brown Elizabeth , Brink Deon , Bailey Paul , Brits Rudolph , Finn Judith 
Published: May 2022

Abstract
Background
Calls for emergency medical assistance at the scene of a motor vehicle crash (MVC) substantially contribute to the demand on ambulance services. Triage by emergency medical dispatch systems is therefore important, to ensure the right care is provided to the right patient, in the right amount of time. A lights and sirens (L&S) response is the highest priority ambulance response, also known as a priority one or hot response. In this context, over triage is defined as dispatching an ambulance with lights and sirens (L&S) to a low acuity MVC and under triage is not dispatching an ambulance with L&S to those who require urgent medical care. We explored the potential for crash characteristics to be used during emergency ambulance calls to identify those MVCs that required a L&S response.

Methods
We conducted a retrospective cohort study using ambulance and police data from 2014 to 2016. The predictor variables were crash characteristics (e.g. road surface), and Medical Priority Dispatch System (MPDS) dispatch codes. The outcome variable was the need for a L&S ambulance response. A Chi-square Automatic Interaction Detector technique was used to develop decision trees, with over/under triage rates determined for each tree. The model with an under/over triage rate closest to that prescribed by the American College of Surgeons Committee on Trauma (ACS COT) will be deemed to be the best model (under triage rate of ≤ 5% and over triage rate of between 25–35%.

Results
The decision tree with a 2.7% under triage rate was closest to that specified by the ACS COT, had as predictors—MPDS codes, trapped, vulnerable road user, anyone aged 75 + , day of the week, single versus multiple vehicles, airbag deployment, atmosphere, surface, lighting and accident type. This model had an over triage rate of 84.8%.

Conclusions
We were able to derive a model with a reasonable under triage rate, however this model also had a high over triage rate. Individual EMS may apply the findings here to their own jurisdictions when dispatching to the scene of a MVC.
Workplace violence against emergency health care workers: What Strategies do Workers use?
Authors: Spelten Evelien , van Vuuren Julia , O’Meara Peter , Thomas Brodie , Grenier Mathieu , Ferron Richard , Helmer Jennie , Agarwal Gina 
Published: May 2022

Abstract
Background
Workplace violence by patients and bystanders against health care workers, is a major problem, for workers, organizations, patients, and society. It is estimated to affect up to 95% of health care workers. Emergency health care workers experience very high levels of workplace violence, with one study finding that paramedics had nearly triple the odds of experiencing physical and verbal violence.
Many interventions have been developed, ranging from zero-tolerance approaches to engaging with the violent perpetrator. Unfortunately, as a recent Cochrane review showed, there is no evidence that any of these interventions work in reducing or minimizing violence.
To design better interventions to prevent and minimize workplace violence, more information is needed on those strategies emergency health care workers currently use to prevent or minimize violence.
The objective of the study was to identify and discuss strategies used by prehospital emergency health care workers, in response to violence and aggression from patients and bystanders. Mapping the strategies used and their perceived usefulness will inform the development of tailored interventions to reduce the risk of serious harm to health care workers.
In this study the following research questions were addressed: (1) What strategies do prehospital emergency health care workers utilize against workplace violence from patients or bystanders? (2) What is their experience with these strategies?

Methods
Five focus groups with paramedics and dispatchers were held at different urban and rural locations in Canada. The focus group responses were transcribed verbatim and analyzed using thematic analysis.

Results
It became apparent that emergency healthcare workers use a variety of strategies when dealing with violent patients or bystanders. Most strategies, other than generic de-escalation techniques, reflect a reliance on the systems the workers work with and within.

Conclusion
The study results support the move away from focusing on the individual worker, who is the victim, to a systems-based approach to help reduce and minimize violence against health care workers. For this to be effective, system-based strategies need to be implemented and supported in healthcare organizations and legitimized through professional bodies, unions, public policies, and regulations.
Assessing research self-efficacy among primary health care physicians: a snapshot from Qatar
Authors: Bougmiza Iheb , Naja Sarah , Alchawa Mohamad , Alah Muna Abed , Al Kaabi Noora , Al Kubaisi Noora , Selim Nagah 
Published: May 2022

Abstract
Background
Research self-efficacy is one of the crucial predictors of productively engaging in research activities emphasized by the Qatar National Vision 2030. Nevertheless, studies typically focus on research self-efficacy among students, neglecting physicians, despite the importance of research as competency in continuous professional development. Therefore, the objective of our study is to understand the level of research self-efficacy among physicians and its determinants.

Methods
An analytical cross-sectional design was employed. We utilized an open survey through DACIMA Software that included questions related to Self-Efficacy in Research Measure (SERM) and possible determinants. One-hundred-twenty-two completed answers, and the response rate was 19.2%. Following descriptive analyses, a chi-square test was used to uncover the associations among variables, with significance set to p ≤ 0.05. Next, a logistic regression model was conducted to identify the predictors of a low research self-efficacy level. Finally, reliability and principal component analysis were applied on the SERM scale.

Results
Three-quarters of the sample reported insufficient research self-efficacy. The sociodemographic and professional factors did not significantly associate with insufficient research self-efficacy. However, participation in clinical guidelines proved to be a determinant of sufficient research self-efficacy.

Conclusions
Physicians must be encouraged to participate in clinical guidelines to improve their research self-efficacy level.
Study protocol for ‘the effects of multimodal training of cognitive and/or physical functions on cognition and physical fitness of older adults: a cluster randomized controlled trial’
Authors: Chow Bik-Chu , Jiao Jiao , Man David , Lippke Sonia 
Published: May 2022

Abstract
Background
The elderly population worldwide is increasing exponentially which will be associated with more people suffering from cognition and fitness declines. The well-established benefits of exercise training for the elderly’s cognitive and physical functioning have been observed. However, the amalgamated effect of combining cognitive and physical exercises on the older adults’ cognitive functions, physical fitness, or psycho-related health remains unclear. Thus, this study protocol was planned to conduct different combinations of cognitive and/or physical training interventions to community-dwelling older adults and expected to see the multifaceted effects of the varied combination of training on their health.

Methods
This study is a cluster randomized controlled trial (CRCT). A total of 285 older adults (age ≥ 60) from twenty elderly centres as clusters will be randomly selected and assigned to intervention groups (IGs, n = 16) or control groups (CGs, n = 4). Each IG will be randomly assigned to one of the four combinations of three training modes that include cognitive (A), physical (B), and combined cognitive and physical training (CCPT, i.e. C), namely Mixed ABC, A + B, C + A, B + C. The intervention will last for 4 months in which the training is conducted for 16 sessions, 2 sessions per week, and 60 min per session. Four repeated assessments (pre-test, two post-training tests after 2 months and 4 months, and a follow-up test) will be conducted. The CG will only receive the four repeated assessments but no intervention. The outcome measures include cognitive tests (tests of execution, memory, and psych-social status), physical fitness, and dynamic balance tests.

Discussion
This study will provide substantial evidence that the integrated format of cognitive and physical exercises training will have higher cognition and fitness impact than the single training modes, and all these mixed modalities will have greater positive outcomes than the control condition. If the effectiveness is proven, the intervention can be further explored and extended to the nation so that many more elderly would be benefited.

Trial registration
The trial has been registered in the ClinicalTrials.gov in U.S. NIH (ID: NCT04727450, date: January 27, 2021).
Visual impairment as a predictor for deterioration in functioning: the Leiden 85-plus Study
Authors: Verbeek ERJ , Drewes YM , Gussekloo J 
Published: May 2022

Abstract
Background
Visual impairment frequently occurs amongst older people. Therefore, the aim of this study was to investigate the predictive value of visual impairment on functioning, quality of life and mortality in people aged 85 years.

Methods
From the Leiden 85-plus Study, 548 people aged 85 years were eligible for this study. Visual acuity was measured at baseline by Early Treatment Diabetic Retinopathy Study charts (ETDRS). According to the visual acuity (VA) three groups were made, defined as no (VA > 0.7), moderate (0.5 ≤ VA ≤ 0.7) or severe visual impairment (VA < 0.5). Quality of life, physical, cognitive, psychological and social functioning were measured annually for 5 years. For mortality, participants were followed until the age of 95.

Results
At baseline, participants with visual impairment scored lower on physical, cognitive, psychological and social functioning and quality of life (p < 0.001). Compared to participants with no visual impairment, participants with moderate and severe visual impairment had an accelerated deterioration in basic activities of daily living (respectively 0.27-point (p = 0.017) and 0.35 point (p = 0.018)). In addition, compared to participants with no visual impairment, the mortality risk was 1.83 (95% CI 1.43, 2.35) for participants with severe visual impairment.

Discussion
In very older adults, visual impairment predicts accelerated deterioration in physical functioning. In addition, severely visually impaired adults had an increased mortality risk. A pro-active attitude, focussing on preventing and treating visual impairment could possibly contribute to the improvement of physical independence, wellbeing and successful aging in very old age.
Associations between socioeconomic status and physical activity among older adults: cross-sectional results from the OUTDOOR ACTIVE study
Authors: Stalling Imke , Albrecht Birte Marie , Foettinger Linda , Recke Carina , Bammann Karin 
Published: May 2022

Abstract
Background
Regular physical activity (PA) is an important strategy for healthy ageing. Socioeconomic status was found to be a key determinant of PA, however, evidence on associations between socioeconomic status and PA among older adults is limited. The aim of this study was to contribute to research on the associations of socioeconomic status and PA among older adults by including self-reported and objectively measured PA data. Furthermore, we examined the self-reported PA data more closely by looking at the activities separately.

Methods
Cross-sectional data of 1507 participants (52.5% female) of the OUTDOOR ACTIVE study between 65 and 75 years, residing in Bremen, Germany, were included in the analyses. Self-reported PA was assessed via questionnaire and comprised all organised and non-organised activities. For analyses, mean hours per week of total and moderate to vigorous PA, and mean metabolic equivalents per week were used. Objectively measured PA was assessed using accelerometers over seven consecutive days. Socioeconomic status was included as an additive social class index containing education, income, and occupation. To test for associations between PA and socioeconomic status, linear regressions were carried out.

Results
Self-reported PA showed significant negative associations with socioeconomic status for both men and women. Objectively measured PA was positively associated with socioeconomic status, which was significant in men but not in women. When examining physical activities separately, time spent on housework, gardening, biking, and walking decreased with increasing socioeconomic status. Women in the second SES quintile and men in the third quintile reported the most, and women in the first quintile and men in the fifth quintile the least hours per week spent on exercise.

Conclusions
The results of this study contributed to the existing research gap on the associations of socioeconomic status and PA among older adults. Moreover, we provided information on both self-reported and objectively measured PA, and showed the discrepancies in the two methods’ results. These findings can help to develop PA promotion interventions targeting specific socioeconomic status groups and to develop accurate, valid, and reliable self-reported and objective measurements of PA for older adults.
Characteristics of step responses following varying magnitudes of unexpected lateral perturbations during standing among older people – a cross-sectional laboratory-based study
Authors: Batcir Shani , Shani Guy , Shapiro Amir , Melzer Itshak 
Published: May 2022

Abstract
Introduction
The inability to recover from unexpected lateral loss of balance may be particularly relevant to the problem of falling.

Aim
We aimed to explore whether different kinematic patterns and strategies occur in the first recovery step in single-step trials in which a single step was required to recover from a fall, and in multiple-step trials in which more than one step was required to recover from a fall. In addition, in the multiple-step trials, we examined kinematic patterns of balance recovery where extra steps were needed to recover balance.

Methods
Eighty-four older adults (79.3 ± 5.2 years) were exposed to unannounced right/left perturbations in standing that were gradually increased to trigger a recovery stepping response. We performed a kinematic analysis of the first recovery step of all single-step and multiple-step trials for each participant and of total balance recovery in the multiple-step trial.

Results
Kinematic patterns and strategies of the first recovery step in the single-step trials were significantly dependent on the perturbation magnitude. It took a small, yet significantly longer time to initiate a recovery step and a significantly longer time to complete the recovery step as the magnitude increased. However, the first recovery step in the multiple-step trials showed no significant differences between different perturbation magnitudes; while, in total balance recovery of these trials, we observed a small, yet significant difference as the magnitude increased.

Conclusions
At relatively low perturbation magnitudes, i.e., single-step trials, older adults selected different first stepping strategies and kinematics as perturbation magnitudes increased, suggesting that this population activated pre-planned programs based on the perturbation magnitude. However, in the first recovery step of the multiple-step trials, i.e., high perturbation magnitudes, similar kinematic movement patterns were used at different magnitudes, suggesting a more rigid, automatic behavior, while the extra-steps were scaled to the perturbation magnitude. This suggest that older adults activate pre-planned programs based on the magnitude of the perturbation, even before the first step is completed..
Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea
Authors: Bainomugisa Arnold , Lavu Evelyn , Pandey Sushil , Majumdar Suman , Banamu Jennifer , Coulter Chris , Marais Ben , Coin Lachlan , Graham Stephen M. , du Cros Philipp 
Published: May 2022

Abstract
Background
Molecular mechanisms determining the transmission and prevalence of drug resistant tuberculosis (DR-TB) in Papua New Guinea (PNG) are poorly understood. We used genomic and drug susceptibility data to explore the evolutionary history, temporal acquisition of resistance and transmission dynamics of DR-TB across PNG.

Methods
We performed whole genome sequencing on isolates from Central Public Health Laboratory, PNG, collected 2017–2019. Data analysis was done on a composite dataset that also included 100 genomes previously sequenced from Daru, PNG (2012–2015).

Results
Sampled isolates represented 14 of the 22 PNG provinces, the majority (66/94; 70%) came from the National Capital District (NCD). In the composite dataset, 91% of strains were Beijing 2.2.1.1, identified in 13 provinces. Phylogenetic tree of Beijing strains revealed two clades, Daru dominant clade (A) and NCD dominant clade (B). Multi-drug resistance (MDR) was repeatedly and independently acquired, with the first MDR cases in both clades noted to have emerged in the early 1990s, while fluoroquinolone resistance emerged in 2009 (95% highest posterior density 2000–2016). We identified the presence of a frameshift mutation within Rv0678 (p.Asp47fs) which has been suggested to confer resistance to bedaquiline, despite no known exposure to the drug. Overall genomic clustering was significantly associated with rpoC compensatory and inhA promoter mutations (p < 0.001), with high percentage of most genomic clusters (12/14) identified in NCD, reflecting its role as a potential national amplifier.

Conclusions
The acquisition and evolution of drug resistance among the major clades of Beijing strain threaten the success of DR-TB treatment in PNG. With continued transmission of this strain in PNG, genotypic drug resistance surveillance using whole genome sequencing is essential for improved public health response to outbreaks. With occurrence of resistance to newer drugs such as bedaquiline, knowledge of full drug resistance profiles will be important for optimal treatment selection.