bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing a neural unreliability account of auditory sensory processing atypicalities in Rett Syndrome
Authors: Brima Tufikameni , Beker Shlomit , Prinsloo Kevin D. , Butler John S. , Djukic Aleksandra , Freedman Edward G. , Molholm Sophie , Foxe John J. 
Published: June 2024

Abstract
Background
In the search for objective tools to quantify neural function in Rett Syndrome (RTT), which are crucial in the evaluation of therapeutic efficacy in clinical trials, recordings of sensory-perceptual functioning using event-related potential (ERP) approaches have emerged as potentially powerful tools. Considerable work points to highly anomalous auditory evoked potentials (AEPs) in RTT. However, an assumption of the typical signal-averaging method used to derive these measures is “stationarity” of the underlying responses – i.e. neural responses to each input are highly stereotyped. An alternate possibility is that responses to repeated stimuli are highly variable in RTT. If so, this will significantly impact the validity of assumptions about underlying neural dysfunction, and likely lead to overestimation of underlying neuropathology. To assess this possibility, analyses at the single-trial level assessing signal-to-noise ratios (SNR), inter-trial variability (ITV) and inter-trial phase coherence (ITPC) are necessary.

Methods
AEPs were recorded to simple 100 Hz tones from 18 RTT and 27 age-matched controls (Ages: 6–22 years). We applied standard AEP averaging, as well as measures of neuronal reliability at the single-trial level (i.e. SNR, ITV, ITPC). To separate signal-carrying components from non-neural noise sources, we also applied a denoising source separation (DSS) algorithm and then repeated the reliability measures.

Results
Substantially increased ITV, lower SNRs, and reduced ITPC were observed in auditory responses of RTT participants, supporting a “neural unreliability” account. Application of the DSS technique made it clear that non-neural noise sources contribute to overestimation of the extent of processing deficits in RTT. Post-DSS, ITV measures were substantially reduced, so much so that pre-DSS ITV differences between RTT and TD populations were no longer detected. In the case of SNR and ITPC, DSS substantially improved these estimates in the RTT population, but robust differences between RTT and TD were still fully evident.

Conclusions
To accurately represent the degree of neural dysfunction in RTT using the ERP technique, a consideration of response reliability at the single-trial level is highly advised. Non-neural sources of noise lead to overestimation of the degree of pathological processing in RTT, and denoising source separation techniques during signal processing substantially ameliorate this issue.
Developmentally dynamic changes in DNA methylation in the human pancreas
Authors: MacCalman Ailsa , De Franco Elisa , Franklin Alice , Flaxman Christine S. , Richardson Sarah J. , Murrall Kathryn , Burrage Joe ,   Barts Pancreas Tissue Bank (BPTB), Walker Emma M. , Morgan Noel G. , Hattersley Andrew T. , Dempster Emma L. , Hannon Eilis , Jeffries Aaron R. , Owens Nick D. L. , Mill Jonathan 
Published: June 2024

AbstractDevelopment of the human pancreas requires the precise temporal control of gene expression via epigenetic mechanisms and the binding of key transcription factors. We quantified genome-wide patterns of DNA methylation in human fetal pancreatic samples from donors aged 6 to 21 post-conception weeks. We found dramatic changes in DNA methylation across pancreas development, with > 21% of sites characterized as developmental differentially methylated positions (dDMPs) including many annotated to genes associated with monogenic diabetes. An analysis of DNA methylation in postnatal pancreas tissue showed that the dramatic temporal changes in DNA methylation occurring in the developing pancreas are largely limited to the prenatal period. Significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small proportion of sites showing sex-specific DNA methylation trajectories across pancreas development. Pancreas dDMPs were not distributed equally across the genome and were depleted in regulatory domains characterized by open chromatin and the binding of known pancreatic development transcription factors. Finally, we compared our pancreas dDMPs to previous findings from the human brain, identifying evidence for tissue-specific developmental changes in DNA methylation. This study represents the first systematic exploration of DNA methylation patterns during human fetal pancreas development and confirms the prenatal period as a time of major epigenomic plasticity.
Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality
Authors: Wang Bin , Bu Yuanpeng , Zhang Guwen , Liu Na , Feng Zhijuan , Gong Yaming 
Published: June 2024

Abstract
Background
Vegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean.

Results
In this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes.

Conclusions
Herein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.
Comparison of two propensity score-based methods for balancing covariates: the overlap weighting and fine stratification methods in real-world claims data
Authors: Wan Wen , Murugesan Manoradhan , Nocon Robert S. , Bolton Joshua , Konetzka R. Tamara , Chin Marshall H. , Huang Elbert S. 
Published: June 2024

Abstract
Background
Two propensity score (PS) based balancing covariate methods, the overlap weighting method (OW) and the fine stratification method (FS), produce superb covariate balance. OW has been compared with various weighting methods while FS has been compared with the traditional stratification method and various matching methods. However, no study has yet compared OW and FS. In addition, OW has not yet been evaluated in large claims data with low prevalence exposure and with low frequency outcomes, a context in which optimal use of balancing methods is critical. In the study, we aimed to compare OW and FS using real-world data and simulations with low prevalence exposure and with low frequency outcomes.

Methods
We used the Texas State Medicaid claims data on adult beneficiaries with diabetes in 2012 as an empirical example (N = 42,628). Based on its real-world research question, we estimated an average treatment effect of health center vs. non-health center attendance in the total population. We also performed simulations to evaluate their relative performance. To preserve associations between covariates, we used the plasmode approach to simulate outcomes and/or exposures with N = 4,000. We simulated both homogeneous and heterogeneous treatment effects with various outcome risks (1-30% or observed: 27.75%) and/or exposure prevalence (2.5-30% or observed:10.55%). We used a weighted generalized linear model to estimate the exposure effect and the cluster-robust standard error (SE) method to estimate its SE.

Results
In the empirical example, we found that OW had smaller standardized mean differences in all covariates (range: OW: 0.0–0.02 vs. FS: 0.22–3.26) and Mahalanobis balance distance (MB) (< 0.001 vs. > 0.049) than FS. In simulations, OW also achieved smaller MB (homogeneity: <0.04 vs. > 0.04; heterogeneity: 0.0-0.11 vs. 0.07–0.29), relative bias (homogeneity: 4.04–56.20 vs. 20–61.63; heterogeneity: 7.85–57.6 vs. 15.0-60.4), square root of mean squared error (homogeneity: 0.332–1.308 vs. 0.385–1.365; heterogeneity: 0.263-0.526 vs 0.313-0.620), and coverage probability (homogeneity: 0.0–80.4% vs. 0.0-69.8%; heterogeneity: 0.0-97.6% vs. 0.0-92.8%), than FS, in most cases.

Conclusions
These findings suggest that OW can yield nearly perfect covariate balance and therefore enhance the accuracy of average treatment effect estimation in the total population.
Frailty identification and management among Brazilian healthcare professionals: a survey
Authors: Azevedo Paula Schmidt , de Melo Ruth Caldeira , de Souza Juli Thomaz , Frost Rachael , Gavin James P. , Robinson Katie , Boas Paulo José Fortes Villas , Minicucci Marcos Ferreira , Aprahamian Ivan , Wachholz Patrick Alexander , Hinslif-Smith Kathryn , Gordon Adam Lee 
Published: June 2024

Abstract
Background
National and international guidelines on frailty assessment and management recommend frailty screening in older people. This study aimed to determine how Brazilian healthcare professionals (HCPs) identify and manage frailty in practice.

Methods
An anonymous online survey on the assessment and management of frailty was circulated virtually through HCPs across Brazil.

Results
Most of the respondants used non-specific criteria such as gait speed (45%), handgrip strength (37.6%), and comprehensive geriatric assessment (33.2%). The use of frailty-specific criteria was lower than 50%. The most frequently used criteria were the Frailty Index (19.1%), Frailty Phenotype (13.2%), and FRAIL (12.5%). Only 43.5% felt confident, and 40% had a plan to manage frailty. In the multivariate-adjusted models, training was the most crucial factor associated with assessing frailty, confidence, and having a management plan (p < 0.001 for all). Those with fewer years of experience were more likely to evaluate frailty (p = 0.009). Being a doctor increased the chance of using a specific tool; the opposite was true for dietitians (p = 0.03). Those who assisted more older people had a higher likelihood of having a plan (p = 0.011).

Conclusion
Frailty assessment was heterogeneous among healthcare professions groups, predominantly using non-specific criteria. Training contributed to frailty assessment, use of specific criteria, confidence, and having a management plan. This data informs the need for standardized screening criteria and management plans for frailty, in association with increasing training at the national level for all the HCPs who assist older people.
The assessment and detection rate of intrinsic capacity deficits among older adults: a systematic review and meta-analysis
Authors: Tan Fangqin , Wei Xiaoxia , Zhang Ji , Zhao Yihao , Tong Xunliang , Michel Jean-Pierre , Shao Ruitai , Gong Enying 
Published: June 2024

Abstract
Background
Assessing and monitoring intrinsic capacity (IC) is an effective strategy to promote healthy ageing by intervening early in high-risk populations. This review systematically analyzed the global detection rates of IC deficits and explored variations across diverse populations and data collection methods.

Methods
This study was preregistered with PROSPERO, CRD42023477315. In this systematic review and meta-analysis, we systematically searched ten databases from January 2015 to October 2023, for peer-reviewed, observational studies or baseline survey of trials that assessed IC deficits among older adults aged 50 and above globally following the condition, context and population approach. The main outcome was intrinsic capacity deficits which could be assessed by any tools. Meta-analyses were performed by a random-effect model to pool the detection rates across studies and subgroup analyses were conducted by populations and data collection methods.

Results
Fifty-six studies conducted in 13 countries were included in the review and 44 studies with detection rates of IC were included in the meta-analysis. The pooled detection rate of IC deficits was 72.0% (65.2%-78.8%) and deficits were most detected in sensory (49.3%), followed by locomotion (40.0%), cognition (33.1%), psychology (21.9%), and vitality (20.1%). Variations in detection rates of IC deficits were observed across studies, with higher rates observed in low- and middle-income countries (74.0%) and hyper-aged societies (85.0%). Study population and measurement tools also explained the high heterogeneity across studies.

Conclusion
IC deficits are common among older adults, while heterogeneity exists across populations and by measurement. Early monitoring with standardized tools and early intervention on specific subdomains of IC deficits are greatly needed for effective strategies to promote healthy ageing.
Risk factors for postoperative urinary retention in fragility hip fracture patients: a prospective study
Authors: Tantigate Direk , Jansatjawan Nathanan , Adulkasem Nath , Ramart Patkawat , Riansuwan Kongkhet 
Published: June 2024

Abstract
Background
Postoperative urinary retention (POUR) among older patients with hip fractures is common and may result in delayed ambulation, prolonged hospital stays, and urinary tract infections. Although preoperative urinary catheter indwelling and early postoperative removal can prevent perioperative urinary retention, this condition may occur in some patients after catheter removal, which requires urinary catheter re-indwelling or intermittent catheterization. Therefore, this study aims to identify risk factors and develop a screening tool for postoperative urinary retention in patients who have undergone operative treatment for fragility hip fractures subsequent to urinary catheter removal.

Methods
A prospective cohort study of 145 fragility hip fracture in older patients who were operatively treated between September 2020 and May 2022 was conducted. All patients were evaluated for urine retention after urinary catheter removal using a bladder scan. In addition, factors related to urinary retention were collected and utilized for screening tool development.

Results
Of the included patients, 22 (15.2%) were diagnosed with POUR. A multivariable logistic regression model using a stepwise backward elimination algorithm identified the current use of drugs with anticholinergic effect (OR = 11.9, p = 0.012), international prostate symptom score (IPSS) ≥ 8 (OR = 9.3, p < 0.001), and inability to independently get out of bed within 24 h postoperatively (OR = 6.5, p = 0.051) as risk factors of POUR. The screening tool that has been developed revealed an excellent performance (AuROC = 0.85, 95%CI 0.75 to 0.91) with good calibration and minimal optimism.

Conclusions
Current use of drugs with anticholinergic effects, IPSS ≥ 8, and inability to independently get out of bed within 24 h postoperatively are significant variables of POUR. For additional external validation, a proposed scoring system for POUR screening was developed.

Trial registration
The study protocol was retrospectively registered in The Thai Clinical Trials Registry (TCTR20220502001: 2 May 2022).
Prevalence of the CRISPR-cas system and its association with antibiotic resistance in clinical Klebsiella pneumoniae isolates
Authors: Kadkhoda Hiva , Gholizadeh Pourya , Ghotaslou Reza , Pirzadeh Tahereh , Ahangarzadeh Rezaee Mohammad , Nabizadeh Edris , Feizi Hadi , Samadi Kafil Hossein , Aghazadeh Mohammad 
Published: June 2024

Abstract
Background and objective(s)
CRISPR-Cas is a prokaryotic adaptive immune system that protects bacteria and archaea against mobile genetic elements (MGEs) such as bacteriophages plasmids, and transposons. In this study, we aimed to assess the prevalence of the CRISPR-Cas systems and their association with antibiotic resistance in one of the most challenging bacterial pathogens, Klebsiella pneumoniae.

Materials and methods
A total of 105 K. pneumoniae isolates were collected from various clinical infections. Extended-spectrum β-lactamases (ESBLs) phenotypically were detected and the presence of ESBL, aminoglycoside-modifying enzymes (AME), and CRISPR-Cas system subtype genes were identified using PCR. Moreover, the diversity of the isolates was determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR.

Results
Phenotypically, 41.9% (44/105) of the isolates were found to be ESBL producers. A significant inverse correlation existed between the subtype I-E CRISPR-Cas system’s presence and ESBL production in K. pneumoniae isolates. Additionally, the frequency of the ESBL genes blaCTX−M1 (3%), blaCTX−M9 (12.1%), blaSHV (51.5%), and blaTEM (33.3%), as well as some AME genes such as aac(3)-Iva (21.2%) and ant(2’’)-Ia (3%) was significantly lower in the isolates with the subtype I-E CRISPR-Cas system in comparison to CRISPR-negative isolates. There was a significant inverse correlation between the presence of ESBL and some AME genes with subtype I-E CRISPR-Cas system.

Conclusion
The presence of the subtype I-E CRISPR-Cas system was correlated with the antibiotic-resistant gene (ARGs). The isolates with subtype I-E CRISPR-Cas system had a lower frequency of ESBL genes and some AME genes than CRISPR-negative isolates.
The effect of cumulative energy in repeated subliminal transscleral cyclophotocoagulation: a retrospective study
Authors: Szabó Áron , Árpádffy-Lovas Tamás , Hagyó Krisztina , Cseke István , Vámosi Péter , Tóth-Molnár Edit 
Published: June 2024

Abstract
Background
The long-term safety and efficacy of repeated applications of subliminal transscleral cyclophotocoagulation (SL-TSCPC) with a focus on cumulative energy was evaluated in glaucoma patients.

Methods
In this retrospective, multicentric study the data of a total of 82 eyes with various causes of glaucoma that were treated with a single or multiple applications of SL-TSCPC were collected. Treatments were performed under general or local anesthesia with an 810 nm diode laser. Power was 2000 mW; duty cycle, 31.3%; total treatment duration, 80–320 s; equaling a total energy of 50–200 J per treatment session. Fifty-five eyes (55 patients) presented for all follow-ups, and these eyes were selected for further statistical analysis. The mean age was 60.0 ± 17.1 years, and 22 (40%) of the patients were female. Intraocular pressure (IOP) and dependence on further glaucoma medication were evaluated at 12 months following the initial treatment.

Results
Eyes underwent 1 or 2 consecutive SL-TSCPC treatments. Median (min–max) baseline IOP of 34 (13–69) decreased to 21.5 (7–61), 22 (8–68), 20 (9–68), and 19.5 (3–60) mmHg at the 1, 3, 6, and 12-month postoperative timepoints respectively. The mean (± SD) IOP decrease at 12 months was 26 ± 27%, 39 ± 32%, and 49 ± 33% in the low (below 120 J, n = 18), medium (120–200 J, n = 24), and high (above 200 J, n = 13) cumulative energy groups respectively. At the 12-month timepoint, oral carbonic anhydrase use was discontinued in ¾ of the cases.

Conclusions
It was found that the repeated application of SL-TSCPC safely and efficiently decreases IOP in a Caucasian population with heterogenous causes of glaucoma, eyes with silicone oil responded to a greater extent. Inclusion of cumulative energy scales may contribute to better addressing repeated procedures in a standardized fashion.
Interventions to increase vaccination in vulnerable groups: rapid overview of reviews
Authors: Norman Gill , Kletter Maartje , Dumville Jo 
Published: June 2024

Abstract
Objective
Groups which are marginalised, disadvantaged or otherwise vulnerable have lower uptake of vaccinations. This differential has been amplified in COVID-19 vaccination compared to (e.g.) influenza vaccination. This overview assessed the effectiveness of interventions to increase vaccination in underserved, minority or vulnerable groups.

Methods
In November 2022 we searched four databases for systematic reviews that included RCTs evaluating any intervention to increase vaccination in underserved, minority or vulnerable groups; our primary outcome was vaccination. We used rapid review methods to screen, extract data and assess risk of bias in identified reviews. We undertook narrative synthesis using an approach modified from SWiM guidance. We categorised interventions as being high, medium or low intensity, and as targeting vaccine demand, access, or providers.

Results
We included 23 systematic reviews, including studies in high and low or middle income countries, focused on children, adolescents and adults. Groups were vulnerable based on socioeconomic status, minority ethnicity, migrant/refugee status, age, location or LGBTQ identity. Pregnancy/maternity sometimes intersected with vulnerabilities. Evidence supported interventions including: home visits to communicate/educate and to vaccinate, and facilitator visits to practices (high intensity); telephone calls to communicate/educate, remind/book appointments (medium intensity); letters, postcards or text messages to communicate/educate, remind/book appointments and reminder/recall interventions for practices (low intensity). Many studies used multiple interventions or components.

Conclusion
There was considerable evidence supporting the effectiveness of communication in person, by phone or in writing to increase vaccination. Both high and low intensity interventions targeting providers showed effectiveness. Limited evidence assessed additional clinics or targeted services for increasing access; only home visits had higher confidence evidence showing effectiveness. There was no evidence for interventions for some communities, such as religious minorities which may intersect with gaps in evidence for additional services. None of the evidence related to COVID-19 vaccination where inequalities of outcome are exacerbated.

Prospero registration
CRD42021293355