bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome reveals the dysfunction of pancreatic islets after wound healing in severely burned mice
Authors: Liu Xinzhu , Xie Xiaoye , Li Dawei , Liu Zhaoxing , Niu Yuezeng , Shen Bowen , Zhang Bohan , Song Yaoyao , Ma Jinglong , Zhang Ming , Shi Zhiyuan , Shen Chuan’an 
Published: October 2022

BACKGROUND
Severely burned patients have a higher risk of diabetes mellitus after healing, but its mechanism remains unclear. Therefore, the purpose of the study was to explore the influence of burns on pancreatic islets of mice after wound healing.

METHODS
Forty-two male C57BL/6 mice were randomized into a sham group and a burn group and subjected to sham treatment or a third-degree burn model of 30% total body surface area. Fasting blood glucose was detected weekly for 8 weeks after severe burns. Glucose-stimulated insulin secretion was measured 8 weeks post severe burns. Islets of the two groups were isolated and mRNA libraries were sequenced by the Illumina sequencing platform. The expressions of differentially expressed genes (DEGs) related to the cell cycle and the amounts of mitochondrial DNA were detected by quantitative real-time polymerase chain reaction after gene ontology, gene set enrichment analysis, and protein-protein network analysis. Hematoxylin-eosin staining of pancreatic tail tissue and adenosine triphosphate (ATP) assay of islets were performed.

RESULTS
The levels of fasting blood glucose were significantly higher within 8 weeks post severe burns. Glucose-stimulated insulin secretion was impaired at the eighth week post severe burns. Totally 128 DEGs were selected. Gene ontology and gene set enrichment analysis indicated that the pathways related to the cell cycle, protein processing, and oxidative phosphorylation were downregulated. The expressions of DEGs related to the cell cycle showed a consistent trend with mRNA sequencing data, and most of them were downregulated post severe burns. The cell mass of the burn group was less than that of the sham group. Also, the concentration of ATP and the amount of mitochondrial DNA were lower in the burn group.

CONCLUSION
In the model of severe-burned mice, disorders in glucose metabolism persist for 8 weeks after burns, which may be related to low islet cell proliferation, downregulation of protein processing, and less ATP production.
Promoting oral and dental healthcare among the elderly in a residential care home in Isfahan: a best practice implementation project
Authors: Vedaei Amirhossein , Iranmanesh Pedram , Tahani Bahareh , Mostafaei Ali , Talebpour Amin 
Published: October 2022

Introduction:
Oral health is an important aspect of general health, which affects the wellbeing and quality of life of older adults. Residents in aged care facilities often suffer from overall dental neglect and insufficient oral healthcare, leading to moderate-to-high levels of oral diseases. Furthermore, physical or mental health concerns may result in difficulties in maintaining good oral health.

Objectives:
This implementation project aims to audit and improve the oral healthcare status of the elderly living in a residential care home in Isfahan, Iran using the JBI evidence summary.

Methods:
The methods are preimplementation and postimplementation design using audit and feedback with a situational analysis to guide implementation planning. Seven evidence-based quality indicators were used to measure preintervention compliance with the best practice. Situational analysis was used to identify and target barriers through locally developed practice change strategies following which a repeat audit was conducted at 4 months. Four nursing staff, 11 caregivers, and 38 residents were interviewed for both the baseline and the follow-up audit.

Results:
Compliance rates improved for all seven criteria except the use of a soft-bristled toothbrush (criterion 6). All eight categories of criterion 2 measuring assessment of oral health improved by at least 10%, with the largest improvements in saliva assessment and gingiva assessment. Criterion 1 (oral health training for caregivers) reached the greatest compliance rate (100%).

Conclusion:
The implemented strategies included improving knowledge and changing the attitudes of the caregivers through organizing educational sessions. These strategies were developed to address process and structural barriers to best practice and were helpful for staff uptake of evidence.
Evolutionary shaping of human brain dynamics
Authors: Pang James C. , Rilling James K. , Roberts James A. , van den Heuvel Martijn P. , Cocchi Luca 
Published: October 2022

ABSTRACTThe human brain is distinct from those of other species in terms of size, organization, and connectivity. How do these structural evolutionary differences drive patterns of neural activity enabling brain function? Here, we combine brain imaging and biophysical modeling to show that the anatomical wiring of the human brain distinctly shapes neural dynamics. This shaping is characterized by a narrower distribution of dynamic ranges across brain regions compared with that of chimpanzees, our closest living primate relatives. We find that such a sharp dynamic range distribution supports faster integration between regions, particularly in transmodal systems. Conversely, a broad dynamic range distribution as seen in chimpanzees facilitates brain processes relying more on neural interactions within specialized local brain systems. These findings suggest that human brain dynamics have evolved to foster rapid associative processes in service of complex cognitive functions and behavior.
A novel intronic GAA repeat expansion inFGF14causes autosomal dominant adult-onset ataxia (SCA50, ATX-FGF14)
Authors: Rafehi Haloom , Read Justin , Szmulewicz David J , Davies Kayli C. , Snell Penny , Fearnley Liam G , Scott Liam , Thomsen Mirja , Gillies Greta , Pope Kate , Bennett Mark F , Munro Jacob E , Ngo Kathie J. , Chen Luke , Wallis Mathew J , Butler Ernest G , Kumar Kishore R , Wu Kathy HC , Tomlinson Susan E , Tisch Stephen , Malhotra Abhishek , Lee-Archer Matthew , Dolzhenko Egor , Eberle Michael A. , Roberts Leslie J , Fogel Brent L , Brüggemann Norbert , Lohmann Katja , Delatycki Martin B. , Bahlo Melanie , Lockhart Paul J 
Published: October 2022

ABSTRACTAdult-onset cerebellar ataxias are a group of neurodegenerative conditions that challenge both genetic discovery and molecular diagnosis. In this study, we identified a novel intronic GAA repeat expansion in the gene encoding Fibroblast Growth Factor 14 (FGF14). Genetic analysis identified 4/95 previously unresolved Australian affected individuals (4.2%) with (GAA)>335and a further nine individuals with (GAA)>250. Notably, PCR and long-read sequence analysis revealed these were pure GAA repeats. In comparison, no controls had (GAA)>300and only 2/311 control individuals (0.6%) encoded a pure (GAA)>250. In a German validation cohort 9/104 (8.7%) of affected individuals had (GAA)>335and a further six had (GAA)>250. In comparison no controls had (GAA)>335and 10/190 (5.3%) encoded (GAA)>250. The combined data suggests (GAA)>335are disease-causing and fully penetrant [P-value 6.0×10−8, OR 72 (95% CI=4.3-1227)], while (GAA)>250is likely pathogenic, albeit with reduced penetrance. Affected individuals had an adult-onset, slowly progressive cerebellar ataxia with a clinical phenotype that may include vestibular impairment, hyper-reflexia and autonomic dysfunction. A negative correlation between age at onset and repeat length was observed (R2=0.44 p=0.00045, slope = -0.12). This study demonstrates the power of genome sequencing and advanced bioinformatic tools to identify novel repeat expansion loci via model free, genome-wide analysis and identifies SCA50/ATX-FGF14 is a frequent cause of adult-onset ataxia.
Development of criteria for cognitive dysfunction in post-COVID syndrome: the IC-CoDi-COVID approach
Authors: Matias-Guiu Jordi A , Herrera Elena , González-Nosti María , Krishnan Kamini , Delgado-Álvarez Cristina , Díez-Cirarda María , Yus Miguel , Martínez-Petit Álvaro , Pagán Josué , Matías-Guiu Jorge , Luis Ayala José , Busch Robyn , Hermann Bruce P 
Published: October 2022

ABSTRACTBackgroundWe aimed to develop objective criteria for cognitive dysfunction associated with the post-COVID syndrome.MethodsFour hundred and four patients with post-COVID syndrome from two centers were evaluated with comprehensive neuropsychological batteries. The International Classification for Cognitive Disorders in Epilepsy (IC-CoDE) framework was adapted and implemented. A complementary data-driven approach based on unsupervised machine-learning clustering algorithms was also used to evaluate the optimal classification and cutoff points.ResultsAccording to the developed criteria, 41.2% and 17.3% of the sample were classified as having at least one cognitive domain impaired using -1 and -1.5 standard deviations as cutoff points. Attention/processing speed was the most frequently impaired domain. There were no differences in base rates of cognitive impairment between the two centers. Clustering analysis revealed two clusters according to the severity of cognitive impairment, but there was no difference in cognitive profiles. Cognitive impairment was associated with younger age and lower education levels, but not hospitalization.ConclusionsWe propose a harmonization of the criteria to define and classify cognitive impairment in the post-COVID syndrome. These criteria may be extrapolated to other neuropsychological batteries and settings, contributing to the diagnosis of cognitive deficits after COVID-19 and facilitating multicenter studies to guide biomarker investigation and therapies.
NC-COVID: A Time-Varying Compartmental Model for Estimating SARS-CoV-2 Infection Dynamics in North Carolina, US
Authors: Delamater Paul L. , Woodul Rachel L. 
Published: October 2022

ABSTRACTEfforts to track and model SARS-CoV-2 infection dynamics in the population have been complicated by certain aspects of the transmission characteristics, which include a pre-symptomatic infectious phase as well as asymptomatic infectious individuals. Another problem is that many models focus on case count, as there has been (and is) limited data regarding infection status of members of the population, which is the most important aspect for constructing transmission models. This paper describes and explains the parameterization, calibration, and revision of the NC-COVID model, a compartmental model to estimate SARS-CoV-2 infection dynamics for the state of North Carolina, US. The model was developed early in the pandemic to provide rapid, up-to-date state-level estimates of the number of people who were currently infected, were immune from a prior infection, and remained susceptible to infection. As a post modeling exercise, we assessed the veracity of the model by comparing its output to SARS-CoV-2 viral particle concentrations detected in wastewater data and to estimates of people infected using COVID-19 deaths. The NC-COVID model was highly correlated with these independently derived estimates, suggesting that it produced accurate estimates of SARS-CoV-2 infection dynamics in North Carolina.
Comparison of COVID-19 Home-Testers vs Laboratory-Testers in New York State (Excluding New York City), November 2021 to April 2022
Authors: Dorabawila Vajeera , Barnes Virgile , Ramesh Nirmala , Hoen Rebecca , Sommer Jamie , Robbins Amy , Backenson Byron , Lutterloh Emily , Hoefer Dina , Rosenberg Eli 
Published: October 2022

AbstractBackgroundThough the use of home testing is increasing, it is not represented in the reported coronavirus disease 2019 (COVID-19) metrics. As the epidemic and its tracking evolve, it is critical to understand who the excluded home-tested persons are relative to those in reported metrics.MethodsFive New York State databases were linked to understand the trends in home-tested COVID-19 cases compared to laboratory-confirmed cases from November 2021 to April 2022. Frequency distributions, logistic regression adjusted odds ratios (aOR), and 95% confidence intervals (CI) were used to compare the characteristics of home-tested and laboratory-tested persons.ResultsOf 592,227 confirmed COVID-19 cases, 71,531 (12%) had a home-test-only, 515,001 (87%) had a laboratory-test-only and 5,695 (1%) had both a home-test and laboratory-test during this period. Home-tested cases, as a percentage of confirmed COVID-19 cases, increased from 1% in November 2021 to 22% in April 2022. Children aged 5-11 years with 3.74 aOR (95% CI:3.53, 3.96) and adolescents aged 12-17 years with 3.24 aOR (95% CI:3.07, 3.43) were more likely to have home-test-only than adults aged 65 and above. Boosted (aOR 1.87, 95% CI:1.82, 1.93), in K-12 school settings (aOR 2.33, 95% CI:2.27, 2.40), or possibly infected by a household member (aOR 1.17, 95% CI:1.13, 1.22) were more likely to report home-test-only than laboratory-test-only. Individuals hospitalized (aOR 0.04, 95% CI:0.03, 0.06), with underlying conditions (aOR 0.85, 95% CI:0.83, 0.87), pregnant (aOR 0.76, 95% CI:0.66, 0.86), Hispanic (aOR 0.50:95% CI:0.48, 0.53), Asian (aOR 0.31, 95% CI:0.28, 0.34), or Black (aOR 0.45, 95% CI:0.42, 047) were less likely to utilize the home test only compared to the laboratory test only.ConclusionThe number of individuals using home tests only as a proportion of confirmed COVID-19 cases continues to increase. Home test-only cases are less likely to be hospitalized and have a lower potential for severe disease as measured by age, vaccination status, and underlying conditions. Thus, those with severe disease and the potential for severe disease are represented as official metrics. Racial and ethnic differences exist between persons reporting home and laboratory tests.
Decoding the endometrial niche of Asherman’s Syndrome at single-cell resolution
Authors: Santamaria Xavier , Roson Beatriz , Perez Raul , Venkatesan Nandakumar , Gonzalez-Fernandez Javier , Fernández Estefania , Moreno Inmaculada , Vankelecom Hugo , Vilella Felipe , Simon Carlos 
Published: October 2022

AbstractAsherman’s Syndrome (AS) is characterized by intrauterine adhesions, which cause infertility, menstrual abnormalities, and recurrent pregnancy loss. While AS occurs as a consequence of traumatic or infectious disruption of the endometrial cell niche, its pathophysiology remains largely unknown and treatment strategies have been restricted to recurrent hysteroscopic removal of intrauterine adhesions with limited success.We decoded the disrupted endometrial cell niche associated with AS at single-cell (sc) resolution by analyzing transcriptomic data from over 230,000 cells. We sought to prove the functional relevance of our findings by incorporating scRNA-seq analysis into a phase I/II clinical trial of CD133+ bone marrow-derived stem cells in AS patients (EudraCT Number: 2016-003975-23) and through in vitro analysis of AS patient-derived endometrial organoids.Our integrated analyses supported the construction of an atlas describing the dysfunctional endometrial niche of AS patients, characterized by significant differences in cell population ratios, differential gene expression, and aberrant cell-to-cell communication. Our AS atlas also highlights the existence of two unique cell types – a stressed epithelial population (AS epithelium) expressing the secretory leukocyte protease inhibitor (SLPI) and a population of smooth muscle cells expressing ACTG2 (SMC). These alterations act together to maintain a dysfunctional pro-fibrotic, pro-inflammatory, and anti-angiogenic environment; however, we describe the partial reversion of the cellular, transcriptomic, and aberrant cell-to-cell communication differencesin vivoandin vitro(using endometrial organoids) by patient-specific cell therapy.This first description of a comprehensive functional endometrial cell atlas of AS provides a holistic view of the disrupted AS-associated endometrial niche, thereby providing insight into pathophysiology and aiding the development of advanced therapeutics.
Interpretable, non-mechanistic forecasting using empirical dynamic modeling and interactive visualization
Authors: Mason Lee , de Gonzalez Amy Berrington , Garcia-Closas Montserrat , Chanock Stephen J , Hicks Blànaid , Almeida Jonas S 
Published: October 2022

AbstractForecasting methods are notoriously difficult to interpret, particularly when the relationship between the data and the resulting forecasts is not obvious. Interpretability is an important property of a forecasting method because it allows the user to complement the forecasts with their own knowledge, a process which leads to more applicable results. In general, mechanistic methods are more interpretable than non-mechanistic methods, but they require explicit knowledge of the underlying dynamics. In this paper, we introduce a tool which performs interpretable, non-mechanistic forecasts using interactive visualization and a simple, data-focused forecasting technique. To ensure the work is FAIR and privacy is ensured, we have released the tool as an entirely in-browser web-application.
Brain Substrates of Episodic Memory for Identity, Location, and Action Information: A Lesion-Behavior Mapping Study
Authors: Feldman Shir Ben-Zvi , Soroker Nachum , Levy Daniel A. 
Published: October 2022

AbstractBrain networks supporting visual memory include extrastriate and other cortical regions associated with visual perception, which manifest domain-specific processing of “where,” “how,” and various aspects of “what” information. However, whether and how such specialization affects memory for these types of information is still a matter of debate. Functional neuroimaging studies point to dissociable as well as common network components supporting the perception and memory of different aspects of visual information. In the current neuropsychological study, we assess the impact of stroke lesion topography on recall of identity, location, and action of event participants, as assessed by the WMS-III Family Pictures subtest. We used voxel-based lesion-behavior mapping (VLBM) to identify brain lesions specifically implicated in memory deficits for each dimension. Behavioral analysis disclosed impaired performance by both right- and left-hemisphere damage patients, with lesions on each side yielding distinct effects. VLBM analysis revealed a bi-hemispheric network supporting these various aspects of visual memory. In the right hemisphere, the network includes frontal, parietal, and temporal cortical regions and the basal ganglia. In the left hemisphere, the network is more restricted, including visual association areas and medial temporal lobe regions. We further observed that a subset of these regions - those included in the ventral (“what”) stream, and in the putative core recollection network - is implicated in multiple aspects of visual memory, whereas other areas are specifically implicated in memory for specific aspects of the visual scene.
Optimal microRNA sequencing depth to predict cancer patient survival with random forest and Cox models
Authors: Jardillier Rémy , Koca Dzenis , Chatelain Florent , Guyon Laurent 
Published: October 2022

Abstract(1)Backgroundtumor profiling enables patient survival prediction. The two essential parameters to be calibrated when designing a study based on tumor profiles from a cohort are the sequencing depth of RNA-seq technology and the number of patients. This calibration is carried out under cost constraints, and a compromise has to be found. In the context of survival data, the goal of this work is to benchmark the impact of the number of patients and of the sequencing depth of miRNA-seq and mRNA-seq on the predictive capabilities for both the Cox model with elastic net penalty and random survival forest.(2)Resultswe first show that the Cox model and random survival forest provide comparable prediction capabilities, with significant differences for some cancers. Second, we demonstrate that miRNA and/or mRNA data improve prediction over clinical data alone. mRNA-seq data leads to slightly better prediction than miRNA-seq, with the notable exception of lung adenocarcinoma for which the tumor miRNA profile shows higher predictive power. Third, we demonstrate that the sequencing depth of RNA-seq data can be reduced for most of the investigated cancers without degrading the prediction abilities, allowing the creation of independent validation sets at lower cost. Finally, we show that the number of patients in the training dataset can be reduced for the Cox model and random survival forest, allowing the use of different models on different patient subgroups.(3)AvailabilityR script is available athttps://github.com/remyJardillier/Survival_seq_depth
Preclinical mobility limitation outcomes in rehabilitation interventions for middle-aged and older adults population: a scoping review protocol
Authors: Lai Aiping , Morgan Ashley , Richardson Julie , Griffith Lauren , Kuspinar Ayse , Smith-Turchyn Jenna 
Published: October 2022

AbstractObjectivesThis scoping review aims to understand the extent of evidence regarding preclinical mobility limitation (PCML) intervention studies that have been implemented or planned in middle-aged and older adult populations.IntroductionIndividuals with PCML are at a high risk of future functional loss and progression to disability. An overview of studies undertaken on this emerging topic is now due.Inclusion criteriaRehabilitation intervention studies that measured PCML outcomes or assessed individuals at the PCML stage will be included. Studies will be considered if the participants are middle-aged (45-64yrs) or older adults (≥ 65yrs) in any setting, including community-dwelling, hospital discharges, or institutional settings.MethodsSeven databases (MEDLINE, EMBASE, AMED, PsycINFO, CINAHL, Web of Science and Cochrane CENTRAL) were searched to locate relevant published and unpublished intervention studies (English evidence from inception onwards). The search strategy will be generated using the PCC framework (population, concept, and context) and refined after consulting with a McMaster research librarian. In addition, a manual search from the reference list of retrieved papers and review articles will also be performed. Two reviewers will use predefined inclusion/exclusion criteria to independently review titles, abstracts, and full texts of potential articles. Any disagreements on study selection will be resolved by discussion or consensus involving a third reviewer. Data will be collected and reported using a predefined data extraction chart and described using qualitative content analysis.