bluuebunny/crossref_metadata_2025_split huggingface dataset:
llperm: a permutation of regressor residuals test for microbiome data
Authors: Viljanen Markus , Boshuizen Hendriek 
Published: December 2022

Abstract
Background
Differential abundance testing is an important aspect of microbiome data analysis, where each taxa is fitted with a statistical test or a regression model. However, many models do not provide a good fit to real microbiome data. This has been shown to result in high false positive rates. Permutation tests are a good alternative, but a regression approach is desired for small data sets with many covariates, where stratification is not an option.

Results
We implement an R package ‘llperm’ where the The Permutation of Regressor Residuals (PRR) test can be applied to any likelihood based model, not only generalized linear models. This enables distributions with zero-inflation and overdispersion, making the test suitable for count regression models popular in microbiome data analysis. Simulations based on a real data set show that the PRR-test approach is able to maintain the correct nominal false positive rate expected from the null hypothesis, while having equal or greater power to detect the true positives as models based on likelihood at a given false positive rate.

Conclusions
Standard count regression models can have a shockingly high false positive rate in microbiome data sets. As they may lead to false conclusions, the guaranteed nominal false positive rate gained from the PRR-test can be viewed as a major benefit.
Healthcare professionals’ knowledge of the systematic ABCDE approach: a cross-sectional study
Authors: Schoeber Nino H. C. , Linders Marjolein , Binkhorst Mathijs , De Boode Willem-Pieter , Draaisma Jos M. T. , Morsink Marlies , Nusmeier Anneliese , Pas Martijn , van Riessen Christine , Turner Nigel M. , Verhage Rutger , Fluit Cornelia R. M. G. , Hogeveen Marije 
Published: December 2022

Abstract
Background
The Airway, Breathing, Circulation, Disability and Exposure (ABCDE) approach is a universal, priority-based approach for the assessment and treatment of critically ill patients. Although the ABCDE approach is widely recommended, adherence in practice appears to be suboptimal. The cause of this non-compliance is unknown. As knowledge is a prerequisite for adherence, the aim of this study was to assess healthcare professionals’ knowledge of the ABCDE approach.

Methods
A cross-sectional study was conducted at the Radboud University Medical Center, the Netherlands. A digital multiple-choice assessment tool of the ABCDE approach was developed by an expert panel through a mini-Delphi method and validated by performing test item statistics and an expert-novice comparison. The validated test was sent to healthcare professionals (nurses, residents and medical specialists) of the participating departments: Anaesthesiology, Paediatrics, Emergency Department and the Neonatal, Paediatric and Adult Intensive Care Units. Primary outcome was the test score, reflecting individual level of knowledge. Descriptive statistics, regression analysis and ANOVA were used.

Results
Test validation showed a Cronbach’s alpha of 0.71 and an expert-novice comparison of 91.9% (standard deviation (SD) 9.1) and 72.4% (15.2) respectively (p < 0.001). Of 954 eligible participants, 240 filled out the questionnaire. The mean (SD) test score (% of correct answers) was 80.1% (12.2). Nurses had significantly lower scores (74.9% (10.9)) than residents (92.3% (7.5)) and medical specialists (88.0% (8.6)) (p < 0.001). The Neonatal Intensive Care Unit (75.9% (12.6)) and Adult Intensive Care Unit (77.4% (11.2)) had significantly lower scores than Paediatric Intensive Care Unit (85.6% (10.6)), Emergency Department (85.5% (10.4)) and Anaesthesiology (85.3% (10.6)) (p < 0.05). Younger participants scored higher than older participants (−0.30% (-0.46;-0.15) in test score/year increase in age).

Conclusion
Scores of a validated knowledge test regarding the ABCDE approach vary among healthcare professionals caring for critically ill patients. Type of department, profession category and age had a significant influence on the test score. Further research should relate theoretical knowledge level to clinical practice. Tailored interventions to increase ABCDE-related knowledge are recommended.
Normal spirometry prediction equations for the Iranian population
Authors: Sahebi Leyla , Rahimi Besharat , Shariat Mamak , Mousavy Seyyed Hosein , Hosseini Mohsen 
Published: December 2022

Abstract
Background
This study aimed to establish normative spirometric equations in a healthy population of Iranian children and adults, and compare these equations with those developed by the Caucasian Global Lung Initiative (GLI) for the first time.

Methods
Spirometric data from healthy Iranian aged 4–82 years sampled in 2019 were used to derive reference equations using the generalized additive model for location (mu), shape (lambda), and scale (sigma).

Results
A total of 418 females and 204 males were included in the study. Applying the GLI standards for the Iranian population resulted from the Z scores of FEV1, FVC, FEV1/FVC, and FEF25−75% was not different from zero. Based on the newly calculated LLN, eleven individuals showed significant values below the LLN for FEV1/FVC. In all age groups, this frequency was less than 5%, except for men over 70 years of age, which was 12.5%. There are significant differences between new data and GLI for Caucasian data.

Conclusion
It is recommended that the values and equations generated from this study should be used by physicians and technicians in their routine practice for the diagnosis and assessment of pulmonary disorders.
Stepwise reduction of bone mineral density increases the risk of cage subsidence in oblique lumbar interbody fusion patients biomechanically: an in-silico study
Authors: Yang Zhi-Qiang , Cai Ping , Li Jing-Chi , Wang Xian-Di , Xie Tian-Hang , Pu Xing-Xiao , Lin Run , Zeng Jian-Cheng , Song Yue-Ming 
Published: December 2022

Abstract
Background
Cage subsidence causes poor prognoses in patients treated by oblique lumbar interbody fusion (OLIF). Deterioration of the biomechanical environment initially triggers cage subsidence, and patients with low bone mineral density (BMD) suffer a higher risk of cage subsidence. However, whether low BMD increases the risk of cage subsidence by deteriorating the local biomechanical environment has not been clearly identified.

Methods
OLIF without additional fixation (stand-alone, S-A) and with different additional fixation devices (AFDs), including anterolateral single rod screws (ALSRs) and bilateral pedicle screws (BPSs) fixation, was simulated in the L4-L5 segment of a well-validated finite element model. The biomechanical effects of different BMDs were investigated by adjusting the material properties of bony structures. Biomechanical indicators related to cage subsidence were computed and recorded under different directional moments.

Results
Overall, low BMD triggers stress concentration in surgical segment, the highest equivalent stress can be observed in osteoporosis models under most loading conditions. Compared with the flexion-extension loading condition, this variation tendency was more pronounced under bending and rotation loading conditions. In addition, AFDs obviously reduced the stress concentration on both bony endplates and the OLIF cage, and the maximum stress on ALSRs was evidently higher than that on BPSs under almost all loading conditions.

Conclusions
Stepwise reduction of BMD increases the risk of a poor local biomechanical environment in OLIF patients, and regular anti-osteoporosis therapy should be considered an effective method to biomechanically optimize the prognosis of OLIF patients.
Daily dose evaluation based on corrected CBCTs for breast cancer patients: accuracy of dose and complication risk assessment
Authors: Hamming Vincent C. , Andersson Sebastian , Maduro John H. , Langendijk Johannes A. , Both Stefan , Sijtsema Nanna M. 
Published: December 2022

Abstract
Objectives
The goal of this study is to validate different CBCT correction methods to select the superior method that can be used for dose evaluation in breast cancer patients with large anatomical changes treated with photon irradiation.

Materials and method
Seventy-six breast cancer patients treated with a partial VMAT photon technique (70% conformal, 30% VMAT) were included in this study. All patients showed at least a 5 mm variation (swelling or shrinkage) of the breast on the CBCT compared to the planning-CT (pCT) and had a repeat-CT (rCT) for dose evaluation acquired within 3 days of this CBCT. The original CBCT was corrected using four methods: (1) HU-override correction (CBCTHU), (2) analytical correction and conversion (CBCTCC), (3) deep learning (DL) correction (CTDL) and (4) virtual correction (CTV). Image quality evaluation consisted of calculating the mean absolute error (MAE) and mean error (ME) within the whole breast clinical target volume (CTV) and the field of view of the CBCT minus 2 cm (CBCT-ROI) with respect to the rCT. The dose was calculated on all image sets using the clinical treatment plan for dose and gamma passing rate analysis.

Results
The MAE of the CBCT-ROI was below 66 HU for all corrected CBCTs, except for the CBCTHU with a MAE of 142 HU. No significant dose differences were observed in the CTV regions in the CBCTCC, CTDL and CTv. Only the CBCTHU deviated significantly (p < 0.01) resulting in 1.7% (± 1.1%) average dose deviation. Gamma passing rates were > 95% for 2%/2 mm for all corrected CBCTs.

Conclusion
The analytical correction and conversion, deep learning correction and virtual correction methods can be applied for an accurate CBCT correction that can be used for dose evaluation during the course of photon radiotherapy of breast cancer patients.
Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes
Authors: Boekhorst Jos , Venlet Naomi , Procházková Nicola , Hansen Mathias L. , Lieberoth Christian B. , Bahl Martin I. , Lauritzen Lotte , Pedersen Oluf , Licht Tine Rask , Kleerebezem Michiel , Roager Henrik M. 
Published: December 2022

Abstract
Background
It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures and determinants of microbiota-dependent energy harvest is lacking.

Results
Here, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and overall structure stratified as enterotypes. We hypothesised that a slower intestinal transit would allow for more energy extraction. However, opposite of what we expected, the stool energy density was positively associated with intestinal transit time. Stratifications into enterotypes showed that individuals with a Bacteroides enterotype (B-type) had significantly lower stool energy density, shorter intestinal transit times, and lower alpha-diversity compared to individuals with a Ruminococcaceae enterotype (R-type). The Prevotella (P-type) individuals appeared in between the B- and R-type. The differences in stool energy density between enterotypes were not explained by differences in habitual diet, intake of dietary fibre or faecal bacterial cell counts. However, the R-type individuals showed higher urinary and faecal levels of microbial-derived proteolytic metabolites compared to the B-type, suggesting increased colonic proteolysis in the R-type individuals. This could imply a less effective colonic energy extraction in the R-type individuals compared to the B-type individuals. Notably, the R-type had significantly lower body weight compared to the B-type.

Conclusions
Our findings suggest that gut microbial energy harvest is diversified among individuals by intestinal transit time and associated gut microbiome ecosystem variations. A better understanding of these associations could support the development of personalised nutrition and improved weight-loss strategies.
Multivariate moment-matching for model order reduction of quadratic-bilinear systems using error bounds
Authors: Khattak Muhammad Altaf , Ahmad Mian Ilyas , Feng Lihong , Benner Peter 
Published: December 2022

AbstractWe propose an adaptive moment-matching framework for model order reduction of quadratic-bilinear systems. In this framework, an important issue is the selection of those shift frequencies where moment-matching is to be achieved. So far, the choice often has been random or linked to the linear part of the nonlinear system. In this paper, we extend the use of an existing a posteriori error bound for general linear time invariant systems to quadratic-bilinear systems and develop a greedy-type framework to select a good choice of interpolation points for the construction of the projection matrices. The results are compared with standard quadratic-bilinear projection methods and we observe that the approximations obtained by the proposed method yield high accuracy.
Japanese version of the Brief Sense of Community Scale: construct validity and reliability
Authors: Yu Kyung-Ran , Asai Keigo , Hiraizumi Taku , Wakashima Koubun 
Published: December 2022

Abstract
Background
The Brief Sense of Community Scale is a widely accepted eight-item scale that measures the four dimensions of sense of community; however, the factor structure of the Japanese version of this scale has never been confirmed. In this study, we demonstrated the reliability and validity of the Japanese version of the Brief Sense of Community Scale.

Methods
After completing the back translation of the scale, a sample of 993 Japanese individuals completed the Japanese version of the Brief Sense of Community Scale.

Results
The results indicate that the Japanese version of the Brief Sense of Community Scale is comparable to the original scale and demonstrated adequate goodness-of-fit for both the four-factor and second-order models, which demonstrates its validity. Nonetheless, it remains necessary to consider possible cross-national cultural concerns when utilizing the scale.

Conclusions
The Japanese version of the Brief Sense of Community Scale will contribute toward the creation of a community in which all members feel comfortable.
Improving L2 learners’ IELTS task 2 writing: the role of model essays and noticing hypothesis
Authors: Nguyen Long Quoc , Le Ha Van 
Published: December 2022

AbstractAchieving a sufficient IELTS band score for academic purposes has been a major goal of many L2 learners around the world, especially those in Asia. However, IELTS writing scores were consistently reported to be the lowest when compared to the scores in speaking, reading, and listening. Despite a growing body of research in IELTS writing, little focused on the role of model essays and noticing hypotheses. The present study aimed to fill in this gap by examining whether or not the implementation of both noticing hypothesis and model essays had a discernible influence on learners’ IELTS task 2 writing. To reach this goal, a quasi-experimental design including a pretest and a posttest was conducted with the voluntary participation of 52 undergraduates. These participants were divided into two groups: control group (CG,n= 25), learning in the conventional method (peer feedback and teacher feedback), and experimental group (EG,n= 27), using the noticing-model essays method. Following this, semi-structured interviews were performed to gain insights into the quantitative data. The results from this mixed-methods approach showed that there were significant gains in the overall performance and in the lexical resources subscale in the EG while no considerable changes were observed in the CG. Additionally, the other subscales (task response, grammatical range and accuracy, and cohesion-coherence) did not witness any significant differences between the two groups. Several pedagogical implications and recommendations for future research, especially in the Asian context, were also discussed.
The 50 most cited studies on posterior tibial slope in joint preserving knee surgery
Authors: Vieider Romed P. , Berthold Daniel P. , Runer Armin , Winkler Philipp W. , Schulz Phillip , Rupp Marco-Christopher , Siebenlist Sebastian , Muench Lukas N. 
Published: December 2022

AbstractPurposeTo determine the 50 most cited studies on posterior tibial slope (PTS) in joint preserving knee surgery and assess their level of evidence, objective study quality scores as well as to examine whether the study quality correlated with the citation count and citation density in the top 50 list.MethodsA literature search on Web of Science was performed to determine the 50 most cited studies on the topic of PTS in joint preserving knee surgery between 1990 and 2022. The studies were evaluated for their bibliographic parameters, level of evidence rating (LOE), citation counts, the Modified Coleman Methodological Score (MCMS), the Methodological Index for Non-Randomized Studies (MINORS), and the Radiologic Methodology and Quality Scale (MQCSRE).ResultsOf the top 50 list, 16 studies were published in theAmerican Journal of Sports Medicine. A total of 23studies were produced in the United States (46%). Of 10 different study types, case control studies (n = 16, 32%) and cadaveric studies (n = 10, 20%) were most common. 15 studies (30%) were purely radiological studies. 6 studies were level II (12%), 23 level III (46%), 15 level IV (30%), and 6 level V studies (12%), respectively. The number of citations ranged from 42 to 447 (mean 105.6 ± 79.2 citations) and showed a mean citation density of 10.3 ± 5.2, composed of the decades 1994 – 2000 (8.3 ± 4.1), 2001 – 2010 (11.1 ± 5.9), 2011 – 2019 (10.1 ± 5.1). Mean quality scores were 55.9 ± 13.0 for MCMS (n= 18), 14.5 ± 3.2 for MINORS (n = 18) and 18.1 ± 3.7 for MQCSRE (n = 20), respectively. High citation counts did not correlate with higher study quality scores (p > 0.05). Radiological studies were not significantly cited more often than non-radiological studies (mean 116.9 ± 88.3 vs. 100.8 ± 75.8 citations;p > 0.05).ConclusionIn joint preserving knee surgery, the 50 most cited studies on PTS did not represent a ranking of the highest methodological quality scores. Citation counts and citation density over the past three decades did not significantly differ, even though the number of articles in the presented list multiplied over the same period. This list can serve as a reference tool for orthopedic surgeons aiming to review PTS literature.
Investigating the feasibility and acceptability of using Instagram to engage post-graduate students in a mass communication social media-based health intervention, #WeeStepsToHealth
Authors: O’Kane Niamh , McKinley Michelle C. , Gough Aisling , Hunter Ruth F. 
Published: December 2022

Abstract

Background
Instagram’s popularity among young adults continues to rise, and previous work has identified diffusion of unhealthy messages and misinformation throughout the platform. However, we know little about how to use Instagram to promote health messages. This study aims to assess the feasibility and acceptability of using Instagram to engage post-graduate students in a mass communication social media (SM)-based health intervention.

Methods
A 4-week intervention targeting post-graduate students with physical activity (PA), nutrition, and general wellbeing messages was conducted via Instagram. Feasibility and acceptability were assessed using SM metrics (likes, comments, and shares), pre- and post-intervention online surveys (knowledge, attitude, and behavioural outcomes), and a focus group conducted with a sample of individuals in the target population (to assess intervention recall, feedback on message framing, and acceptability of Instagram).

Results
The two independent samples captured by online surveys (pre-intervention, n = 43, post-intervention, n = 41, representing 12.3% and 11.7% of Instagram followers, respectively) were predominantly female (88.4%, 80.5%) aged 18–34 (95.4%, 95.1%). Respondents in the second survey reported higher weekly PA levels (+ 13.7%) and more frequent nutritional behaviours including consumption of five or more fruits and vegetables (+ 23.3%) and looking at nutritional labels (+ 10.3%). However, respondents in the second survey also reported less frequent meal preparation (− 18.0%) and a small increase in fast food consumption (+ 2.8% consuming fast food 3–4 days a week). A total of 247 ‘likes’ were collected from 28 Instagram posts (mean 8.8 likes per post). Humorous posts achieved a moderately higher level of engagement than non-humorous posts (median 10 and 8 likes, respectively). Focus group participants liked the campaign content and trusted the information source.

Conclusions
Findings indicate that Instagram could be a feasible and acceptable platform for engaging post-graduate students in a SM-based mass communication health intervention, and that humour may have the potential to encourage further engagement.
Transcranial Doppler assessment of patients with cerebral small vessel disease
Authors: Tawfik Mohamed M. , Ebrahim Alaa , Hamed Salma , Haroun Mahmoud 
Published: December 2022

Abstract
Background
Cerebral small vessel disease (SVD) is associated with acute events such as lacunar and hemorrhagic strokes, or chronic events such as cognitive deficit in the form of subcortical dementia, mood deficit in the form of late onset depression, sphincteric affection, and gait apraxia. Under conditions of moderate blood flow deficit, the inability of sclerotic vessels to dilate due to impairment of the cerebral autoregulation, renders the periventricular white matter seriously ischemic. Therefore, it is important to detect the implications of cerebral large artery disease on the severity of SVD, and the ability of transcranial duplex (TCD) to evaluate it in people at risk.

Methods
Fifty lacunar stroke patients were recruited, and evaluated using MRI brain to assess SVD score, carotid duplex and TCD to assess extracranial and intracranial stenoses, respectively.

Results
Both intracranial and extracranial stenoses showed significant relation to the severity of cerebral SVD. Moreover, there were significant relation between intracranial stenosis and presence of lacuna and EPVS.

Conclusion
Cerebral large artery disease contributes to the pathogenesis and severity of cerebral SVD. Therefore, TCD may be a useful tool for the prediction of occurrence of cerebral SVD in high-risk individuals, especially hypertensives.
Achilles Tendon Injuries Requiring Surgical Treatment in the Pediatric and Adolescent Population: A Case Series
Authors: Chen Daniel L. , Beran Matthew C. , Duncan Molly , Young Julie A. , Napolitano Jonathan T. , MacDonald James 
Published: December 2022

AbstractPediatric Achilles tendon injuries requiring surgical treatment are considered rare and have not been well described. A retrospective chart review was conducted from 2010 to 2020 to identify cases of acute Achilles tendon rupture or laceration that required surgical repair in individuals 19 years or younger. A total of 24 individuals with acute Achilles tendon ruptures (n= 8) and lacerations (n= 16) were identified. All spontaneous ruptures occurred in skeletally mature individuals during sports. One subject was on minocycline at the time of injury, while two had a body mass index (BMI) ≥ 99% for age. Another had a history of clubfoot surgery on the injured side. Patients with lacerations were younger (9.9 ± 3.3 vs 16.3 ± 1.6 years) and had lower BMI (17.3 ± 3.8 vs. 28.0 ± 9.4) than those with spontaneous ruptures. The majority of cases had good outcomes with no postoperative complications.