bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated structure-based protein interface prediction
Authors: Walder M. , Edelstein E. , Carroll M. , Lazarev S. , Fajardo J. E. , Fiser A. , Viswanathan R. 
Published: July 2022

AbstractBackgroundIdentifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents. A variety of computational approaches have been developed for predicting a protein’s interfacial residues from its known sequence and structure. Methods using the known three-dimensional structures of proteins can be template-based or template-free. Template-based methods have limited success in predicting interfaces when homologues with known complex structures are not available to use as templates. The prediction performance of template-free methods that only rely only upon proteins’ intrinsic properties is limited by the amount of biologically relevant features that can be included in an interface prediction model.ResultsWe describe the development of an integrated method for protein interface prediction (ISPIP) to explore the hypothesis that the efficacy of a computational prediction method of protein binding sites can be enhanced by using a combination of methods that rely on orthogonal structure-based properties of a query protein, combining and balancing both template-free and template-based features. ISPIP is a method that integrates these approaches through simple linear or logistic regression models and more complex decision tree models. On a diverse test set of 156 query proteins, ISPIP outperforms each of its individual classifiers in identifying protein binding interfaces.ConclusionsThe integrated method captures the best performance of individual classifiers and delivers an improved interface prediction. The method is robust and performs well even when one of the individual classifiers performs poorly on a particular query protein. This work demonstrates that integrating orthogonal methods that depend on different structural properties of proteins performs better at interface prediction than any individual classifier alone.
Outcomes of patients admitted to the ICU for acute stroke: a retrospective cohort
Authors: Carval Thibaut , Garret Charlotte , Guillon Benoît , Lascarrou Jean-Baptiste , Martin Maëlle , Lemarié Jérémie , Dupeyrat Julien , Seguin Amélie , Zambon Olivier , Reignier Jean , Canet Emmanuel 
Published: July 2022

Abstract
Background
Although acute stroke is a leading cause of morbidity and mortality worldwide, data on outcomes of stroke patients requiring ICU admission are limited. We aimed to identify factors associated with a good neurological outcome (defined as a modified Rankin Scale score [mRS] of 0–2) 6 months after ICU admission.

Methods
We retrospectively studied consecutive patients who were admitted to the ICU of a French university-affiliated hospital between January 2014 and December 2018 and whose ICD-10 code indicated acute stroke. Patients with isolated subarachnoid hemorrhage or posttraumatic stroke were excluded.

Results
The 323 identified patients had a median age of 67 [54.5–77] years; 173 (53.6%) were male. The main reasons for ICU admission were neurological failure (87%), hemodynamic instability (28.2%), acute respiratory failure (26%), and cardiac arrest (5.3%). At ICU admission, the Glasgow Coma Scale score was 6 [4–10] and the SAPSII was 54 [35–64]. The stroke was hemorrhagic in 248 (76.8%) patients and ischemic in 75 (23.2%). Mechanical ventilation was required in 257 patients (79.6%). Six months after ICU admission, 61 (19.5%) patients had a good neurological outcome (mRS, 0–2), 50 (16%) had significant disability (mRS, 3–5), and 202 (64.5%) had died; 10 were lost to follow-up. By multivariable analysis, factors independently associated with not having an mRS of 0–2 at 6 months were older age (odds ratio, 0.93/year; 95% confidence interval, 0.89–0.96; P < 0.01) and lower Glasgow Coma Scale score at ICU admission (odds ratio, 1.23/point; 95% confidence interval, 1.07–1.40; P < 0.01).

Conclusions
Acute stroke requiring ICU admission carried a poor prognosis, with less than a fifth of patients having a good neurological outcome at 6 months. Age and depth of coma independently predicted the outcome.
Gut microbiome changes in anti-N-methyl-D-aspartate receptor encephalitis patients
Authors: Wei Jingya , Zhang Xiao , Yang Fang , Shi Xiaodan , Wang Xuan , Chen Rong , Du Fang , Shi Ming , Jiang Wen 
Published: July 2022

Abstract
Background
Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a type of autoimmune encephalitis. The underlying mechanism(s) remain largely unknown. Recent evidence has indicated that the gut microbiome may be involved in neurological immune diseases via the "gut-brain axis". This study aimed to explore the possible relationship between anti-NMDAR encephalitis and the gut microbiome.

Methods
Fecal specimens were collected from 10 patients with anti-NMDAR encephalitis and 10 healthy volunteers. The microbiome analysis was based on Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The alpha, beta, and taxonomic diversity analyses were mainly based on the QIIME2 pipeline.

Results
There were no statistical differences in epidemiology, medication, and clinical characteristics (except for those related to anti-NMDAR encephalitis) between the two groups. ASV analysis showed that Prevotella was significantly increased, while Bacteroides was reduced in the gut microbiota of the patients, compared with the controls. Alpha diversity results showed a decrease in diversity in the patients compared with the healthy controls, analyzed by the Shannon diversity, Simpson diversity, and Pielou_E uniformity based on the Kruskal–Wallis test (P = 0.0342, 0.0040, and 0.0002, respectively). Beta diversity analysis showed that the abundance and composition of the gut microbiota was significantly different between the two groups, analyzed by weighted and unweighted UniFrac distance (P = 0.005 and 0.001, respectively).

Conclusions
The abundance and evenness of bacterial distribution were significantly lower and jeopardized in patients with anti-NMDAR encephalitis than in healthy controls. Thus, our findings suggest that gut microbiome composition changes might be associated with the anti-NMDAR encephalitis. It could be a causal agent, or a consequence.
The effect of nurse practitioner (NP-led) care on health-related quality of life in people with multiple sclerosis – a randomized trial
Authors: Smyth Penelope , Watson Kaitlyn E. , Al Hamarneh Yazid N. , Tsuyuki Ross T. 
Published: July 2022

Abstract
Background
Care for People with Multiple Sclerosis (PwMS) is increasingly complex, requiring innovations in care. Canada has high rates of MS; it is challenging for general neurologists to optimally care for PwMS with busy office practices. The aim of this study was to evaluate the effects of add-on Nurse Practitioner (NP)-led care for PwMS on depression and anxiety (Hospital Anxiety and Depression Scale, HADS), compared to usual care (community neurologist, family physician).

Methods
PwMS followed by community neurologists were randomized to add-on NP-led or Usual care for 6 months. Primary outcome was the change in HADS at 3 months. Secondary outcomes were HADS (6 months), EQ5D, MSIF, CAREQOL-MS, at 3 and 6 months, and Consultant Satisfaction Survey (6 months).

Results
We recruited 248 participants; 228 completed the trial (NP-led care arm n = 120, Usual care arm n = 108). There were no significant baseline differences between groups. Study subjects were highly educated (71.05%), working full-time (41.23%), living independently (68.86%), with mean age of 47.32 (11.09), mean EDSS 2.53 (SD 2.06), mean duration since MS diagnosis 12.18 years (SD 8.82) and 85% had relapsing remitting MS. Mean change in HADS depression (3 months) was: -0.41 (SD 2.81) NP-led care group vs 1.11 (2.98) Usual care group p = 0.001, sustained at 6 months; for anxiety, − 0.32 (2.73) NP-led care group vs 0.42 (2.82) Usual care group, p = 0.059. Other secondary outcomes were not significantly different. There was no difference in satisfaction of care in the NP-led care arm (63.83 (5.63)) vs Usual care (62.82 (5.45)), p = 0.194).

Conclusion
Add-on NP-led care improved depression compared to usual neurologist care and 3 and 6 months in PwMS, and there was no difference in satisfaction with care. Further research is needed to explore how NPs could enrich care provided for PwMS in healthcare settings.

Trial registration
Retrospectively registered on clinicaltrials.gov (ClinicalTrials.gov Identifier: NCT04388592, 14/05/2020).
Optimization of programmed intermittent epidural bolus volume for different concentrations of ropivacaine in labor analgesia: a biased coin up-and-down sequential allocation trial
Authors: Ran Xin , Zhou Shuzhi , Cao Kailan , He Peng 
Published: July 2022

Abstract
Background and objectives
To date, programmed intermittent epidural bolus (PIEB) has been widely used in obstetric analgesia, while no optimal PIEB regimen has been proposed. This study aimed to assess effective analgesia in 90% of women (EV90) with different concentrations of ropivacaine (0.075% and 0.1%) combined with 0.5 µg/mL sufentanil, at an interval of 40 min using the biased coin design-up-and-down method (BCD-UDM), and to explore whether there is a difference in EV90 with the increase of ropivacaine concentration.

Methods
In total, 103 primiparous women were assigned to two groups, including group A (n = 52) and group B (n = 51). Parturients in group A were treated with 0.075% ropivacaine and 0.5 µg/mL sufentanil, while those in group B were treated with 0.1% ropivacaine and 0.5 µg/mL sufentanil. Used the biased coin up-and-down sequential allocation method to determine the EV90. The secondary outcomes were sensory block level, motor block, and adverse events (hypotension, urinary retention, and pruritus).

Results
The results revealed that EV90 was 10 mL (95% confidence interval (CI):8.03–11.54) in group A, and EV90 was 9 mL (95% CI:7.49–10.51) in group B by the isotonic regression method. The highest level of the sensory block was T8, and the lowest was T12. No case of hypotension was recorded,and only 4 parturients complained of motor block.

Conclusion
With an interval of 40 min, the optimal PIEB bolus volume of 0.075% ropivacaine and 0.5 µg/mL sufentanil was 10 mL, 0.1% ropivacaine and 0.5 µg/mL sufentanil was 9 mL. Moreover, the PIEB volume decreased along with the higher concentration of ropivacaine.

Trial registration
ChiCTR registration number: ChiCTR2000040917. Registration date: December 15, 2020.
‘Beyond the Bump’: an online wellbeing and lifestyle pilot program during COVID-19 for first year postpartum mothers: a research article
Authors: Christie Hannah E. , Roach Lauren A. , Kennedy Meredith , Beetham Kassia , Meyer Barbara J. , Schoenaker Danielle , Francois Monique 
Published: July 2022

Abstract
Background
Establishing a healthy lifestyle post-delivery is pivotal to reduce the incidence of chronic diseases. Due to COVID-19 restrictions, access to postpartum health programs has been increasingly difficult. The aim of this study was to inform, develop and evaluate Beyond the Bump (BtB); an online program to improve access to health and wellbeing education and support for physical activity in the postpartum.

Methods
A three-phase mixed-methods design of a 10-week Australia-wide online pilot program during COVID-19 with women less than 1 year postpartum and their primary care health professionals was utilised. Phase-one: needs assessment focus groups and interviews. Phase-two: BtB program implementation pre-post health measures survey, attendance and engagement with the program. Phase-three: program evaluation with feedback surveys and interviews.

Results
Women (n = 12) and health professionals (n = 16) expressed strong need for a postpartum program with access to education from experts on exercise, pelvic floor, sleep and baby nutrition. Despite BtB being developed from women’s suggestions (including time-of-day ‘morning’), attendance to all ten sessions was poor (of 162 registrations; 23% participated in the first session and 5% in the last session). Barriers to attendance included ‘too busy’,‘ forgot’ and ‘topic not relevant for age of child’. 88% of women reported the education as the most enjoyable component of the program. 100% (n = 26) of women interviewed would recommend the program to a friend.

Conclusions
There is a continuing need for postpartum support. Online programs with access to expert education and exercise were reported to be of significant interest and value. However, more research is needed to improve the uptake and value placed on mothers’ wellbeing and physical activity.
Is there any association between undesired children and health status of under-five children? Analysis of a nationally representative sample from Bangladesh
Authors: Alam Md. Zakiul , Islam Md. Syful 
Published: July 2022

Abstract
Background
Child health, especially childhood mortality, is one of the critical indicators of human development. No child mortality is desirable, but it is still high in Bangladesh. We aimed to assess the effect of the child's desired status on childhood morbidity and mortality in Bangladesh.

Methods
We used the data from the nationally representative cross-sectional Bangladesh Demographic and Health Survey (BDHS) 2017–18 and restricted the analyses to children born in the past five years preceding the survey. We estimated the undesired status (excess in boy, girl, both, and parity) by subtracting an ideal number of children from the total live birth. We measured childhood mortality (perinatal, early neonatal, neonatal, post-neonatal, infant, child, and under-five mortality), morbidity (fever, diarrhea, cough, and acute respiratory infectious-ARI), nutritional problems (stunting, wasting, underweight, and low birth weight), and treatments (postnatal care, treatment for fever, diarrhea/cough, and vitamin A supplementation). Finally, we utilized the chi-square test and multilevel mixed-effects logistic regression analyses.

Results
The prevalence of undesired children was 19.2%, 21.5%, 3.7%, and 25.4% for boys, girls, both boys and girls, and parity, respectively. Age, education, residence, division, and wealth index were significantly associated with undesired children. The prevalence of under-five mortality was 3.3% among desired children, almost double (5.4%) among undesired children. The likelihood of under-five mortality was [adjusted odds ratio (aOR): 2.05, p ≤ 0.001] higher among undesired children. Despite lower under-five mortality among higher socioeconomic status, the relative contribution of undesired children to under-fiver mortality was substantial. The undesired girl children were associated with an increased likelihood of moderately wasting (aOR: 1.28, p = 0.072), severely underweight (aOR: 1.41, p = 0.066), and low birth weight (aOR: 1.50, p ≤ 0.05). Moreover, the undesired children were 19% (p ≤ 0.05) more likely to be infected with fever. The undesired children had lower treatment for diarrhea and fever/cough and were less likely to get vitamin A supplementation (aOR: 0.71, p ≤ 0.001).

Conclusions
The share of childhood morbidity, mortality, and malnutrition were higher among undesired children. Every child should be wanted, and no unwanted pregnancies are desirable; thereby, the government should reemphasize the proper use of family planning methods to reduce child mortality and malnutrition.
The superposition effects of air pollution on government health expenditure in China— spatial evidence from GeoDetector
Authors: Xia Qi , Zhang Xiyu , Hu Yanmin , Tian Wanxin , Miao Wenqing , Wu Bing , Lai Yongqiang , Meng Jia , Fan Zhixin , Zhang Chenxi , Xin Ling , Miao Jingying , Wu Qunhong , Jiao Mingli , Shan Linghan , Wang Nianshi , Shi Baoguo , Li Ye 
Published: July 2022

Abstract
Background
As the fifth-largest global mortality risk factor, air pollution has caused nearly one-tenth of the world’s deaths, with a death toll of 5 million. 21% of China’s disease burden was related to environmental pollution, which is 8% higher than the US. Air pollution will increase the demand and utilisation of Chinese residents’ health services, thereby placing a greater economic burden on the government. This study reveals the spatial impact of socioeconomic, health, policy and population factors combined with environmental factors on government health expenditure.

Methods
Spearman’s correlation coefficient and GeoDetector were used to identify the determinants of government health expenditure. The GeoDetector consist of four detectors: factor detection, interaction detection, risk detection, and ecological detection. One hundred sixty-nine prefecture-level cities in China are studied. The data sources are the 2017 data from China’s Economic and Social Big Data Research Platform and WorldPOP gridded population datasets.

Results
It is found that industrial sulfur dioxide attributed to government health expenditure, whose q value (explanatory power of X to Y) is 0.5283. The interaction between air pollution factors and other factors will increase the impact on government health expenditure, the interaction value (explanatory power of × 1∩× 2 to Y) of GDP and industrial sulfur dioxide the largest, whose values is 0.9593. There are 96 simple high-risk areas in these 169 areas, but there are still high-risk areas affected by multiple factors.

Conclusion
First, multiple factors influence the spatial heterogeneity of government health expenditure. Second, health and socio-economic factors are still the dominant factors leading to increased government health expenditure. Third, air pollution does have an important impact on government health expenditure. As a catalytic factor, combining with other factors, it will strengthen their impact on government health expenditure. Finally, an integrated approach should be adopted to synergisticly governance the high-risk areas with multi-risk factors.
The pedagogical value of near-peer feedback in online OSCEs
Authors: Sader Julia , Cerutti Bernard , Meynard Louise , Geoffroy Frédéric , Meister Véronique , Paignon Adeline , Junod Perron Noëlle 
Published: July 2022

Abstract
Purpose of the article
During the Covid-19 pandemic, formative OSCE were transformed into online OSCE, and senior students (near peers) substituted experienced clinical teachers. The aims of the study were to evaluate quality of the feedbacks given by near peers during online OSCEs and explore the experience of near-peer feedback from both learner’s and near peer’s perspectives.

Materials and methods
All 2nd year medical students (n = 158) attended an online OSCE under the supervision of twelve senior medical students. Outcome measures were 1) students’ perception of the quality of the feedback through an online survey (Likert 1–5); 2) objective assessment of the quality of the feedback focusing on both the process and the content using a feedback scale (Likert 1–5); 3) experience of near peer feedback in two different focus groups.

Results
One hundred six medical students answered the questionnaire and had their feedback session videotaped. The mean perceived overall quality of senior students’ overall feedback was 4.75 SD 0.52. They especially valued self-evaluation (mean 4.80 SD 0.67), balanced feedback (mean 4.93 SD 0.29) and provision of simulated patient’s feedback (mean 4.97 SD 0.17). The overall objective assessment of the feedback quality was 3.73 SD 0.38: highly scored skills were subjectivity (mean 3.95 SD 1.12) and taking into account student’s self-evaluation (mean 3.71 (SD 0.87). Senior students mainly addressed history taking issues (mean items 3.53 SD 2.37) and communication skills (mean items 4.89 SD 2.43) during feedback. Participants reported that near peer feedback was less stressful and more tailored to learning needs– challenges for senior students included to remain objective and to provide negative feedback.

Conclusion
Increased involvement of near peers in teaching activities is strongly supported for formative OSCE and should be implemented in parallel even if experience teachers are again involved in such teaching activities. However, it requires training not only on feedback skills but also on the specific content of the formative OSCE.
Adapting user-centered design principles to improve communication of peer parent narratives on pediatric tracheostomy
Authors: Yan Haoyang , Kukora Stephanie K. , Pituch Kenneth , Deldin Patricia J. , Arslanian-Engoren Cynthia , Zikmund-Fisher Brian J. 
Published: July 2022

Abstract
Background
Parents who have to make tracheostomy decisions for their critically ill child may face forecasting errors and wish to learn from peer parents. We sought to develop an intervention with peer parent narratives to help parents anticipate and prepare for future challenges before making a decision.

Methods
To ensure that the intervention reflects parents’ needs (rather than experts’ opinions), we adapted a user-centered design (UCD) process to identify decision-critical information and refine the presentation format by interviewing parents who had tracheostomy decision making experience. Phase 1 (n = 10) presented 15 possible forecasting errors and asked participants to prioritize and justify the problematic ones. It also asked participants to comment on the draft narratives and preferred delivery mode and time of the intervention. Phase 2 (n = 9 additional parents and 1 previous parent) iteratively collected feedback over four waves of user interviews to guide revisions to the informational booklet.

Results
Phase 1 revealed that parents wanted information to address all forecasting errors as soon as tracheostomy becomes an option. They also highlighted diverse family situations and the importance of offering management strategies. The resulting prototype booklet contained five sections: introduction, child’s quality of life, home care, practical challenges, and resources. Feedback from Phase 2 focused on emphasizing individualized situations, personal choice, seriousness of the decision, and caregiver health as well as presenting concrete illustrations of future challenges with acknowledgement of positive outcomes and advice. We also learned that parents preferred to use the booklet with support from the care team rather than read it alone.

Conclusions
A UCD process enabled inclusion of parental perspectives that were initially overlooked and tailoring of the intervention to meet parental expectations. Similar UCD-based approaches may be valuable in the design of other types of patient communications (e.g., decision aids).