bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of Research Quality and Transparency in Neurosurgery Through the Utilization of Open Science Practices
Authors: Alam Zahin , Desai Kush , Maddali Anirudh , Sivan Vijay , Prem Kumar Rohit , O’Malley Geoffrey R. , Patel Nitesh 
Published: August 2024

ABSTRACTBackground and ObjectiveNeurosurgical research is a rapidly evolving field, with numerous studies continuously published. As the body of research grows, upholding high-quality standards becomes increasingly essential. Open science practices offer tools to ensure quality and transparency. However, the prevalence of these practices remains unclear. This study investigated the extent to which neurosurgical publications have implemented open science practices.MethodsFive open science practices (preprint, equator guidelines, published peer review comments, preregistration, and open accessibility to data and methods) were measured from five top-ranked neurosurgical journals (Neurosurgery, Journal of Neurosurgery, World Neurosurgery, Neurosurgical Review, andActa Neurochirurgica), according to Google Scholar. One hundred fifty articles were randomly sampled from January 1, 2022, to December 31, 2023. Two reviewers analyzed these articles for their utilization of open science practices. A third reviewer settled disagreements.ResultsOne journal required (20%) and three journals (60%) recommended utilizing EQUATOR guidelines. Three journals (60%) allowed preprints, and all five journals (100%) recommended or required preregistration of clinical trials, but only two (40%) recommended preregistration for systematic reviews (Figure 1). All five journals (100%) recommended or required methods to be publicly available, but none (0%) published peer-review comments.Neurosurgical Reviewutilized the most open science practices, with a mean utilization of 1.4 open science practices per publication versus 0.9 across the other four journals (p < 0.001). Moreover,Neurosurgical Reviewsignificantly utilized more open science practices versusJournal of Neurosurgery(p < .05) andWorld Neurosurgery(p < .05). Both randomized controlled trials (p < .001) and systematic reviews (p < .001) significantly utilized more open science practices compared to observational studies.ConclusionsDespite advocacy from neurosurgical journals, the adoption of open science practices still needs improvement. Implementing incentives and clearer requirements may prove beneficial. Promoting these practices is crucial to enhancing transparency and research quality in neurosurgery.
A modular self-assembling and self-adjuvanting multiepitope peptide nanoparticle vaccine platform to improve the efficacy and immunogenicity of BCG
Authors: Zhao Guangzu , Sathkumara Harindra D. , Miranda-Hernandez Socorro , Seifert Julia , Valencia-Hernandez Ana Maria , Puri Munish , Huang Wenbin , Toth Istvan , Daly Norelle , Skwarczynski Mariusz , Kupz Andreas 
Published: August 2024

AbstractAfter more than a century since its initial development, Bacille Calmette-Guérin (BCG) remains the only licensed vaccine against tuberculosis (TB). Subunit boosters are considered a viable strategy to enhance BCG efficacy, which often wanes in adolescence. While many studies on booster subunit vaccines have concentrated on recombinant proteins, here we developed a novel modular peptide-based subunit vaccine platform that is flexible, cold-chain independent and customizable to diverse circumstances and populations. Each individual peptide building block consists of a linear arrangement comprising a 15-leucine self-assembly inducer moiety, aMycobacterium tuberculosis(Mtb) target epitope and an HLA-E binding moiety, with each moiety separated by a triple lysine spacer. The building blocks, in any combination, were able to form a multiepitope nanoparticle. Six Mtb epitopes were selected to produce the self-assembling and self-adjuvanting peptide-based TB nano-vaccine candidate PNx6.In vivovaccination-challenge experiments demonstrated that subcutaneous boost of parenteral BCG immunization with PNx6 significantly enhanced its immunogenicity and improved its protective efficacy in a murine model of TB by more than 5-fold. Our study present evidence that purely amphiphilic peptides self-assemble into self-adjuvanting nanoparticles with appropriate size and morphology for TB vaccination with great potential for a multitude of other diseases.
Increased vowel contrast and intelligibility in connected speech induced by sensorimotor adaptation
Authors: Beach Sara D. , Johnson Sophie A. , Parrell Benjamin , Niziolek Caroline A. 
Published: August 2024

AbstractAlterations to sensory feedback can drive robust adaptive changes to the production of consonants and vowels, but these changes often have no behavioral relevance or benefit to communication (e.g., making “head” more like “had”). This work aims to align the outcomes of adaptation with changes known to increase speech intelligibility – specifically, adaptations that increase the acoustic contrast between vowels in running speech. To this end, we implemented a vowel centralization feedback perturbation paradigm that pushes all vowels towards the center of vowel space, making them sound less distinct from one another. Speakers across the adult lifespan adapted to the centralization perturbation during sentence production, increasing the global acoustic contrast among vowels and the articulatory excursions for individual vowels. These changes persisted after the perturbation was removed, including after a silent delay, and showed robust transfer to words that were not present in the sentences. Control analyses demonstrated that these effects were unlikely to be due to explicit pronunciation strategies and occurred in the face of increasingly more rapid and less distinct production of familiar sentences. Finally, sentence transcription by crowd-sourced listeners showed that speakers’ vowel contrast predicted their baseline intelligibility and that experimentally-induced increases in contrast predicted intelligibility gains. These findings establish the validity of a sensorimotor adaptation paradigm to implicitly increase vowel contrast and intelligibility in connected speech, an outcome that has the potential to enhance rehabilitation in individuals who present with a reduced vowel space due to motor speech disorders, such as the hypokinetic dysarthria associated with Parkinson’s disease.Significance statementDuring speech production, humans learn from perceived errors by adjusting their speech to compensate, a process known as sensorimotor adaptation. Here we leveraged sensorimotor adaptation to cause an increase in the distinctiveness of speech sounds. Specifically, speakers rapidly and implicitly learned vowel-specific articulation changes during sentence production, with positive effects on their intelligibility. This study is important for models of sensorimotor integration across all motor domains, as it demonstrates the simultaneous learning of multiple opposing transformations in the course of continuous movement. Our findings show that sensorimotor adaptation can be successfully applied to drive changes relevant to a vital ecological behavior: intelligible communication.
Somatic development of Wilms tumour via normal kidneys in predisposed children
Authors: Treger Taryn D. , Wegert Jenny , Wenger Anna , Coorens Tim H. H. , Al-Saadi Reem , Kemps Paul , Kennedy Jonathan , Parks Conor , Anderson Nathaniel D. , Hodder Angus , Letunovska Aleksandra , Jung Hyunchul , Ogbonnah Toochi , Trinh Mi K. , Lee-Six Henry , Morcrette Guillaume , van den Heuvel-Eibrink J. Marry M , Drost Jarno , van Boxtel Ruben , Bertrums Eline J.M. , Goemans Bianca F. , Antoniou Evangelia , Reinhardt Dirk , Streitenberger Heike , Ziegler Barbara , Bartram Jack , Hutchinson J. Ciaran , Vujanic Gordan , Vokuhl Christian , Chowdhury Tanzina , Furtwängler Rhoikos , Graf Norbert , Pritchard-Jones Kathy , Gessler Manfred , Behjati Sam 
Published: August 2024

ABSTRACTTen percent of children with cancer harbour a predisposition mutation. In children with the kidney cancer, Wilms tumour, the prevalence is as high as 30%. Certain predispositions are associated with defined histological and clinical features, suggesting differences in tumour genetic development. To investigate this, we assembled a cohort of 137 children with Wilms tumour, of whom 71 had a pathogenic germline or mosaic predisposition. We examined 237 neoplasms (including two secondary leukaemias), utilising whole genome sequencing, RNA sequencing and genome wide methylation, validating our findings in an independent cohort. Tumour development differed between predisposed and sporadic cases, and amongst predisposed children according to specific mutations and their developmental timing. Differences pervaded the repertoire of driver events, including high risk mutations, the clonal architecture of normal kidneys, and the relatedness of neoplasms from the same individual. Predisposition constrains the development of Wilms tumour, suggesting that a variant specific approach to the management of these children merits consideration.STATEMENT OF SIGNIFICANCETumours that arise in children with a cancer predisposition may, or may not, develop through the same mutational pathways as sporadic tumours. We examined this question in the childhood kidney cancer, Wilms tumour. We found that some predispositions strongly constrain the genetic development of tumours, which may have clinical implications.
White matter microstructural changes in post-traumatic headache: A diffusion tensor imaging (DTI) study
Authors: Yang Ho-Ching , Nguyen Tyler , Naugle Kelly M. , White Fletcher A. , Wu Yu-Chien 
Published: August 2024

ABSTRACTIntroductionPost-traumatic headache (PTH) is a common consequence of mild traumatic brain injury (mTBI) that can severely impact an individual’s quality of life and rehabilitation. However, the underlying neuropathogenesis mechanisms contributing to PTH are still poorly understood. This study utilized diffusion tensor imaging (DTI) to detect microstructural alterations in the brains of mTBI participants with or at risk of developing PTH.MethodThis study investigated associations between DTI metrics 1-month postinjury and pain sensitivity, as well as psychological assessments 6-months postinjury to identify differences between mTBI (n = 12) and healthy controls (HC; n = 10). MRI scans, including T1-weighted anatomical imaging and DTI were acquired at 1-month postinjury. Pain sensitivity assays included quantitative sensory testing and psychological assessment questionnaires at 1-month and 6-months postinjury.ResultsSignificant aberrations of mean axial diffusivity in the forceps major were observed in mTBI relative to HCs at 1-month postinjury (p =0.02). Within the mTBI group, DTI metrics at 1-month postinjury were significantly associated (p’s < 0.05) with pain-related measures and psychological outcomes at 6-month postinjury in several white matter tracts (right sagittal stratum, left anterior thalamic radiation, left corticospinal tract, left insula, left superior longitudinal fasciculus). Notably, the associations between DTI metrics at 1-month postinjury and pain-related measures at 6-month postinjury showed significant group differences in the right sagittal stratum (p’s < 0.01), white matter tract in left insula (p < 0.04), and left superior longitudinal fasciculus (p’s < 0.05).ConclusionThis study suggests that “Post-Traumatic Stress Disorder for DSM-5” and “Center for Epidemiological Studies-Depression Scale” are the most sensitive psychological measures to early microstructural changes after mTBI, and that the DTI metrics are predictive of pain and psychological measures in mTBI. Together, these results suggest that white matter microstructure plays an important role in the PTH following mTBI.
A SIMULATION MODEL TO QUANTIFY THE EFFICACY OF DRY CLEANING INTERVENTIONS ON A CONTAMINATED MILK POWDER LINE
Authors: Daeschel Devin , Chen Long , Zoellner Claire , Snyder Abigail B. 
Published: August 2024

ABSTRACTOutbreaks ofSalmonellaand other pathogens associated with low moisture foods have been caused by cross-contamination from the processing environment into product. We used Monte Carlo simulations to model the impact of hypothetical cross-contamination scenarios ofSalmonellafrom production equipment into milk powder. Model outputs include the quantity and extent of contaminated product from a production line, which can be useful for comparing the efficacy of different cleaning interventions. We also modeled the cross-contamination of potential dry cleaning surrogates to see how they responded to cleaning interventions in comparison toSalmonella. Input parameters for the model included log reductions from wiping an inoculated surface with a dry towel and transfer coefficients from an inoculated surface into milk powder that were measured experimentally and fitted to probability distributions. After a 2 log CFU contamination breach, the number of consumer size milk powder units (300 g) contaminated withSalmonellawas 72 [24, 96] (median [p5, p95] across 1000 simulation iterations). The average concentration ofSalmonellawithin contaminated units was -2.33 log CFU/g [-2.46, -1.86]. Wiping with a dry towel reduced the number of contaminated units to 26 [12, 64]. After product flushing with 150 kg of milk powder, the number of contaminated units dropped to 0 [0, 41].E. faeciumwas the most appropriate surrogate forSalmonellatransfer from surface to milk powder, whileL. innocuawas a more appropriate surrogate for the dry towel wiping intervention. These results suggest that product flushing, and to a lesser degree dry wiping, may be effective interventions in reducing contaminated milk powder product after a contamination breach. Further, simulation modeling is a useful tool for evaluatingSalmonelladry transfer surrogates for their use in dry cleaning validation and modeling applications.IMPORTANCEThis work demonstrates the utility ofin silicomodeling as a decision support tool that can 1) estimate the cross-contamination ofSalmonellainto milk powder under different processing scenarios, 2) compare the efficacy of different cleaning interventions and 3) help inform surrogate selection for the dry transfer ofSalmonellain modeling and cleaning validation applications. The model presented here contributes to the risk-benefit analysis of tradeoffs associated with dry cleaning in low moisture food environments. For example, the model can be applied to estimate the efficacy of cleaning interventions like product flushing at a lower resource cost than experimental trials in a processing line. The model presented here also provides a more interpretable metric for choosing appropriateSalmonellasurrogates for dry cleaning validation.
Associations between work characteristics and large joint osteoarthritis: a cross-sectional study of 285,947 UK Biobank participants
Authors: Hashmi A , Scott S , Jung M , Meng Q-J , Tobias JH , Beynon RA , Faber BG 
Published: August 2024

AbstractObjectivesShift work-induced circadian rhythm disruption has been identified as a risk factor for specific diseases. Additionally, physically demanding work has been linked to osteoarthritis. This study investigated the independent associations of shift work and physical work with risk of large joint osteoarthritis.DesignUK Biobank participants completed questionnaires detailing their employment status, including shift work, night shifts, heavy manual work and prolonged non-sedentary work. Responses were categorised into binary and categorical variables. Knee and hip osteoarthritis diagnoses were extracted from hospital records and osteoarthritis (any site) was self-reported. Logistic regression models, adjusted for age, sex, BMI, Townsend Deprivation Index and other work factors, were used to investigate the relationships between work characteristics and osteoarthritis outcomes.ResultsThis study included 285,947 participants (mean age 52.7 years; males 48.0%). Shift work and night shifts were associated with knee osteoarthritis (fully adjusted OR: 1.12 [95% CI:1.07-1.17] and 1.12 [1.04-1.20], respectively), and self-reported osteoarthritis but there was little evidence of an association with hip osteoarthritis (1.01 [0.95-1.08] and 1.03 [0.93-1.14]). Heavy manual work and prolonged non-sedentary work were associated with increased risk of all osteoarthritis outcomes.ConclusionsShift work showed independent associations with knee osteoarthritis and self-reported osteoarthritis but not hip osteoarthritis, suggesting circadian rhythm dysfunction may play a role in knee osteoarthritis pathogenesis. Heavy manual work and prolonged non-sedentary work were associated with all outcomes, with stronger associations in knee osteoarthritis, possibly reflecting the knee’s higher susceptibility to biomechanical stress. Further research is needed to explore workplace interventions for reducing these risks.
Secular trends in the incidence, prevalence, and survival of primary liver cancer in the United Kingdom from 2000-2021: a population-based cohort study
Authors: Cuyàs Berta , Alvarado-Tapias Edilmar , Tan Eng Hooi , Golozar Asieh , Duarte-Salles Talita , Delmestri Antonella , Ballbé Josep Maria Argemí , Man Wai Yi , Burn Edward , Guarner-Argente Carlos , Prieto Alhambra Daniel , Newby Danielle 
Published: August 2024

ABSTRACTBackgroundPrimary liver cancer (PLC) remains a global health challenge. Understanding trends in the disease burden and survival is crucial to inform decisions regarding screening, prevention and treatment.MethodsPopulation-based cohort study using UK primary care data from the Clinical Practice Research Datalink (CPRD) GOLD (2000 to 2021), replicated in CPRD Aurum. PLC incidence rates (IR), period prevalence (PP) and survival at one, five and ten years over the study period were calculated, and stratified by age, sex and diagnosis year.ResultsThe crude IR of PLC was 4.56 (95%CI 4.42-4.70) per 100,000 person-years between 2000 and 2021, with an increase over time across age and sex strata. Sex-specific IR for males was higher than females, 6.60 (95%CI 6.36-6.85) vs. 2.58 (95%CI 2.44-2.74) per 100,000 person-years. Crude PP showed a 7-fold increase over the study period, with PP 0.02% (95%CI 0.019%-0.022%) in 2021, and a 2.8-fold higher PP in males. Survival at one, five and ten years after diagnosis was 41.7%, 13.2% and 7.1%, respectively, for both sexes. One-year survival increased only in men, from 33.2% in 2005-2009 to 49.3% in 2015-2019.ConclusionOver the past two decades, there has been a significant increase in the number of patients diagnosed with PLC. Despite a slight improvement in median and one-year survival in men, prognosis remains poor. To improve the survival of PLC patients, it is necessary to understand the epidemiological changes and address the preventable risk factors associated with liver disease and promote early detection and access to care.LAY SUMMARYThis population-based cohort study shows that the incidence and prevalence of primary liver cancer in the UK has increased in the last 20 years across both sexes and age groups, with a 7-fold increase in crude period prevalence over the study period. One-year survival has improved only in males over the study period and, regrettably, no increases in long-term survival were observed. Our findings are a call for awareness to stimulate further research and public health actions on liver cancer.
Triaging clients at risk of disengagement from HIV care: Application of a predictive model to clinical trial data in South Africa
Authors: Maskew Mhairi , Smith Shantelle , De Voux Lucien , Sharpey-Schafer Kieran , Crompton Thomas , Govender Ashley , Pisa Pedro , Rosen Sydney 
Published: August 2024

ABSTRACTBackgroundTo reach South Africa’s targets for HIV treatment and viral suppression, retention on antiretroviral therapy (ART) must increase. Much effort and resources have been invested in tracing those already disengaged and returning them to care programs with mixed success. Here we aim to successfully identify ART clients at risk of loss from care prior to disengagement.Methods and FindingsWe applied a previously developed machine learning and predictive modelling algorithm (PREDICT) to routinely collected ART client data from the SLATE I and SLATE II trials, which evaluated same-day ART initiation in 2017-18. Using a primary outcome of an interruption in treatment (IIT), defined as missing the next scheduled clinic visit by >28 days, we investigated the reproducibility of PREDICT in SLATE datasets. We also tested two risk triaging approaches: 1) threshold approach classifying individuals into low, moderate, or high risk of IIT; and 2) archetype approach identifying subgroups with characteristics associated with risk of ITT. We report associations between risk category groups and subsequent IIT at the next scheduled visit using crude risk differences and relative risks with 95% confidence intervals. SLATE datasets included 7,199 client visits for 1,193 clients over ≤14 months of follow-up. The algorithm achieved 63% accuracy, 89% negative predictive value, and an area under the curve of 0.61 for attendance at next scheduled visit, similar to previous results using only medical record data. The threshold approach consistently and accurately assigned levels of IIT risk for multiple stages of the care cascade. The archetype approach identified several subgroups at increased risk of IIT, including those late to previous appointments, those returning after a period of disengagement, those living alone or without a treatment supporter. Behavioural elements of the archetypes tended to drive risk of treatment interruption more consistently than demographics; e.g. adolescent boys/young men who attended visits on time experienced lowest rates of treatment interruption (10%, PREDICT datasets and 7% SLATE datasets), while adolescent boys/young men returning after previously disengaging from care had highest rates of subsequent treatment interruption (31%, PREDICT datasets and 40% SLATE datasets).ConclusionRoutinely collected medical record data can be combined with basic demographic and socioeconomic data to assess individual risk of future treatment disengagement using machine learning and predictive modelling. This approach offers an opportunity to intervene prior to and potentially prevent disengagement from HIV care, rather than responding only after it has occurred.