bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nationwide Management of Trauma in Child Abuse
Authors: Joseph Bellal , Sakran Joseph V. , Obaid Omar , Hosseinpour Hamidreza , Ditillo Michael , Anand Tanya , Zakrison Tanya L. 
Published: June 2022

Objective:
Child abuse is a major cause of childhood injury, morbidity, and death. There is a paucity of data on the practice of abuse interventions among this vulnerable population. The aim of our study was to identify the factors associated with interventions for child abuse on a national scale.

Methods:
Retrospective analysis of 2017 to 2018 American College of Surgeons (ACS) Pediatric Trauma Quality Improvement Program (TQIP). All children presenting with suspected/confirmed child abuse and an abuse report filed were included. Patients with missing information regarding abuse interventions were excluded. Outcomes were abuse investigations initiated among those with abuse reports, and change of caregiver at discharge among survivors with an investigation initiated. Multivariable regression analyses were performed.

Results:
A total of 7774 child abuse victims with an abuse report were identified. The mean age was 5±5 years, 4221 (54%) patients were White, 2297 (30%) Black, 1543 (20%) Hispanic, and 5298 (68%) had government insurance. The most common mechanism was blunt (63%), followed by burns (10%) and penetrating (10%). The median Injury Severity Score was 5 (1–12). The most common form of abuse was physical (92%), followed by neglect (6%), sexual (3%), and psychological (0.1%). The most common perpetrator of abuse was a care provider/teacher (49.5%), followed by a member of the immediate family (30.5%), or a member of the extended/step/foster family (20.0%). Overall, 6377 (82%) abuse investigations were initiated for those with abuse reports. Of these, 1967 (33%) resulted in a change of caregiver. Black children were more likely to have abuse investigated, and Black and Hispanic children were more likely to experience change of caregiver after investigations, while privately insured children were less likely to experience both.

Conclusions:
Significant racial, ethnic, and socioeconomic disparities exist in the nationwide management of child abuse. Further studies are strongly warranted to understand contributing factors and possible strategies to address them.

Level of Evidence:
Level III—therapeutic/care management.
PhiPipe: a multi-modal MRI data processing pipeline with test-retest reliability and predicative validity assessments
Authors: Hu Yang , Li Qingfeng , Qiao Kaini , Zhang Xiaochen , Chen Bing , Yang Zhi 
Published: June 2022

AbstractMagnetic Resonance Imaging (MRI) has been one of the primary instruments to measure the properties of the human brain non-invasively in vivo. MRI data generally needs to go through a series of processing steps (i.e., a pipeline) before statistical analysis. Currently, the processing pipelines for multi-modal MRI data are still rare, in contrast to single-modal pipelines. Furthermore, the reliability and validity of the output of the pipelines are critical for the MRI studies. However, the reliability and validity measures are not available or adequate for almost all pipelines.Here, we present PhiPipe, a multi-modal MRI processing pipeline. PhiPipe could process T1-weighted, resting-state BOLD, and diffusion-weighted MRI data and generate commonly used brain features in neuroimaging. We evaluated the test-retest reliability of PhiPipe’s brain features by computing intra-class correlations (ICC) in four public datasets with repeated scans. We further evaluated the predictive validity by computing the correlation of brain features with chronological age in three public adult lifespan datasets. The multi-variate reliability and predictive validity of the PhiPipe results were also evaluated. The results of PhiPipe were consistent with previous studies, showing comparable or better reliability and validity when compared with two popular single-modality pipelines, namely DPARSF and PANDA.The publicly available PhiPipe provides a simple-to-use solution to multi-modal MRI data processing. The accompanied reliability and validity assessments could help researchers make informed choices in experimental design and statistical analysis. Furthermore, this study provides a framework for evaluating the reliability and validity of image processing pipelines.
Mechanical Loading due to Muscle Movement Regulates Establishment of the Collagen Network in the Developing Murine Skeleton
Authors: Ahmed S. , Rogers A.V. , Nowlan N. C. 
Published: June 2022

AbstractMechanical loading is critical for collagen network maintenance and remodelling in adult skeletal tissues, but the role of loading in collagen network formation during development is poorly understood. We test the hypothesis that mechanical loading is necessary for the onset and maturation of spatial localisation and structure of collagens in prenatal cartilage and bone, using in vivo and in vitro mouse models of altered loading. The majority of collagens studied were aberrant in structure or localisation, or both, when skeletal muscle was absent in vivo. Using in vitro bioreactor culture system, we demonstrate that mechanical loading directly modulates the spatial localisation and structure of collagens II and X. Furthermore, we show that mechanical loading in vitro rescues aspects of collagens II and X development from the effects of fetal immobility. In conclusion, our findings show that mechanical loading is a critical determinant of collagen network establishment during prenatal skeletal development.Teaser (One line)Mechanical loading is required for normal establishment and maturation of key collagens during prenatal skeletal development.
Modeling the USA Winter 2021 Update and Spring 2022 CoVID-19 Resurgence
Authors: Eng Genghmun 
Published: June 2022

AbstractEvery USA wave, including this latest Spring 2022 Resurgence has been successfully modeled using:

with N (t) being the total number of new CoVID-19 cases above a prior baseline, and tR setting the pandemic wave doubling time tdbl = tR (In 2). The parameters {αS ; δo} measure mitigation efforts among the uninfected population. Here, {αS> 0} is associated with Social Distancing and vaccinations ; while {δo> 0} is associated with mask-wearing, which results in faster post-peak drop-offs. The predicted pandemic wave end is when the calculated N (t) stops increasing.The USA Winter 2021 Resurgence resulted in fewer Omicron CoVID-19 cases than calculated in our prior medrxiv.org preprint*, due to an increased δo component, which gives ∼3/11/22 as the predicted wave end. A relatively quiet CoVID-19 period ensued until ∼4/16/22, when a new Omicron variant caused the present Spring 2022 CoVID-19 resurgence.The recent CoVID-19 waves have decreasing tR values, with the Spring 2022 tR≈ 3.55 days (tdbl ≈ 2.46 days) value being the shortest since the initial 2020 pandemic, indicating increasingly infectious variants. The Winter 2021 and the present Spring 2022 CoVID-19 resurgences have identical αS ≈ 0.043 / day values, but the δo> 0 mask-wearing parameter decreased from δo ≈ 3. 14 × 10−3/ day to δo ≈ 1. 145 × 10−3/ day, giving the Spring 2022 wave a longer tail, and an expected end date of 8/25/22, with these wave totals:
When all the USA CoVID-19 waves are combined, it gives:

assuming no future CoVID-19 Resurgences (with 5 Figures).*(10.1101_2022.02.04.22270491)
Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks
Authors: Nesterenko Luca , Boussau Bastien , Jacob Laurent 
Published: June 2022

AbstractAn important problem in molecular evolution is that of phylogenetic reconstruction, that is, given a set of sequences descending from a common ancestor, the reconstruction of the binary tree describing their evolution from the latter. State-of-the-art methods for the task, namely Maximum likelihood and Bayesian inference, have a high computational cost, which limits their usability on large datasets. Recently researchers have begun investigating deep learning approaches to the problem but so far these attempts have been limited to the reconstruction of quartet tree topologies, addressing phylogenetic reconstruction as a classification problem. We present here a radically different approach with a transformer-based network architecture that, given a multiple sequence alignment, predicts all the pairwise evolutionary distances between the sequences, which in turn allow us to accurately reconstruct the tree topology with standard distance-based algorithms. The architecture and its high degree of parameter sharing allow us to apply the same network to alignments of arbitrary size, both in the number of sequences and in their length. We evaluate our network Phyloformer on two types of simulations and find that its accuracy matches that of a Maximum Likelihood method on datasets that resemble training data, while being significantly faster.
Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams
Authors: Putnam Hollie M. , Trigg Shelly A. , White Samuel J. , Spencer Laura H. , Vadopalas Brent , Natarajan Aparna , Hetzel Jonathan , Jaeger Erich , Soohoo Jonathan , Gallardo-Escárate Cristian , Goetz Frederick W. , Roberts Steven B. 
Published: June 2022

ABSTRACTGiven the rapidly changing global climate, there is a growing need to understand the acclimatory basis of animal response to environmental change. To investigate the role of DNA methylation in environmental acclimatization, we generated a reference genome and surveyed the physiology and DNA methylomes of juvenile geoduck clams, Panopea generosa, under differing seawater pH regimes. Juveniles were initially exposed to one of three seawater pH conditions, followed by ambient common-garden conditions, then a second reciprocal exposure to ambient pH or pH 7.4. Within 10 days of the initial low pH exposure, juvenile clams showed decreased shell size relative to ambient pH with corresponding differential DNA methylation. Following four months of ambient common-garden conditions, juveniles initially exposed to low pH compensatorily grew larger, with DNA methylation indicative of these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. Functional enrichment analysis of differentially methylated genes revealed regulation of signal transduction through widespread changes in the Wnt signaling pathways that influence cell growth, proliferation, tissue and skeletal formation, and cytoskeletal change. After 10 days of secondary exposure to pH 7.4, naive juvenile clams were more sensitive to low pH compared to those initially exposed, showing reduced growth and having nearly a 2-fold greater change in DNA methylation. Collectively, this new genomic resource and coordinated phenotypic and methylomic response support that epigenetic mechanisms underlie acclimatization to provide beneficial phenotypes.
Arabidopsis mutants representing each of the four Mediator modules reveal unique functions in the transcriptional response to salt stress
Authors: Karamat Fazelaat , Vergara Alexander , Blomberg Jeanette , Crawford Tim , Lehotai Nóra , Rentoft Matilda , Strand Åsa , Björklund Stefan 
Published: June 2022

AbstractChanges in growth environment trigger stress responses in most organisms. The mechanisms mediating these responses are only partly understood and involve signaling pathways and transcription factors. Mediator is a conserved co-regulator complex required for transcriptional regulation of all eukaryotic protein-encoding genes. However, its function in abiotic stress responses is elusive. We here describe global gene expression changes triggered by salt stress in Arabidopsis. To explore the involvement of Mediator in salt stress response we characterized med9, med16, med18, and cdk8 mutants representing each of the four modules of Mediator. Our transcriptome data revealed enrichment of shared and specific cis-elements corresponding to unique transcription factors in promoters of mis-regulated genes for each mutant. We show that individual Mediator subunits interact with specific transcription factors to generate a transcriptional stress response and that the mutant phenotypes support the transcriptome data. med16 and med18, and to some extent cdk8, display defects in abscisic acid and anthocyanin metabolism and we identify signal molecules, transcription factors and target genes involved in these pathways as dysregulated in the Mediator mutants. Our results reveal how signals from different stress response pathways are dependent on and integrated by Mediator subunits to coordinate a functional response to salt stress.
SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery
Authors: Chaung Kaitlin , Baharav Tavor Z. , Henderson George , Zheludev Ivan N. , Wang Peter L. , Salzman Julia 
Published: June 2022

SummaryToday’s genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a new unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), an approach that directly analyzes raw sequencing data to detect a signature of regulation: sample-specific sequence variation. The approach, which includes a new statistical test, is computationally efficient and can be run at scale. SPLASH unifies detection of myriad forms of sequence variation. We demonstrate that SPLASH identifies complex mutation patterns in SARS-CoV-2 strains, discovers regulated RNA isoforms at the single cell level, documents the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a new unifying approach to genomic analysis that enables an expansive scope of discovery without metadata or references.One-sentence summarySPLASH is a unifying, statistically driven approach to biological discovery from raw sequencing data, bypassing alignment.
Predicting Confrontation Naming in the Logopenic Variant of Primary Progressive Aphasia
Authors: Jebahi Fatima , Nickels Katlyn Victoria , Kielar Aneta 
Published: June 2022

AbstractNaming difficulties are prominent and pervasive in the logopenic variant of primary progressive aphasia (lvPPA) and are related to its underlying deficits in phonological processing. Importantly, some words appear to be more vulnerable to deterioration than others. We hypothesize that these differences can be explained, in part, by words’ unique psycholinguistic properties. Our study investigated the role of psycholinguistic properties of words, along with their underlying psycholinguistic factors, on confrontation naming performance in individuals with lvPPA. Naming accuracy data were collected from 10 individuals with lvPPA using the Boston Naming Test (BNT). For each test item, values were extracted for frequency, contextual diversity, age of acquisition (AoA), word length, phonological neighborhood density (PND), concreteness, semantic neighborhood density (SND), familiarity, arousal, and valence. We examined the effects of these psycholinguistic properties on naming accuracy using logistic regression analyses at the individual level and multiple linear regression analysis at the group level. Age of acquisition emerged as the strongest psycholinguistic predictor of naming accuracy in lvPPA at both the individual and group levels. Given that AoA and frequency are highly correlated, mediation analyses were performed to identify the relationships between AoA, frequency, and naming accuracy. The influence of AoA on naming accuracy was only partially mediated by frequency. Principal component analysis was performed to extract fundamental factors of the psycholinguistic properties. Four principal psycholinguistic factors were extracted. These were interpreted as “lexical-semantic usage”, “phonological simplicity”, “semantic disembodiment”, and “semantic pleasantness”. These factor scores were entered into multiple linear and logistic regression analyses to investigate their relative contribution to naming accuracy in lvPPA. Results indicated that “lexical-semantic usage”, “semantic disembodiment”, and “semantic pleasantness” predicted naming performance at the group level. Additionally, “lexical-semantic usage” and “semantic disembodiment” emerged as significant predictors at the individual level. The effects of the psycholinguistic properties and their factors and their theoretical implications are discussed in the context of phonological deficits in lvPPA and models of word naming.Highlights:–Age of acquisition (AoA) predicts naming in lvPPA–The effect of AoA on naming corresponds with lvPPA’s phonological impairment–The effect of AoA on naming is mostly direct and partially mediated by frequency–PCA-extracted psycholinguistic factors independently predict naming in lvPPA–Factors related to lexical semantics, semantics, and emotionality affect naming
A Subtractive Proteomics Approach for the Identification of Immunodominant Acinetobacter baumannii Vaccine Candidate Proteins
Authors: Acar Mustafa Burak , Ayaz-Güner Şerife , Güner Hüseyin , Dinç Gökçen , Kılıç Ayşegül Ulu , Doğanay Mehmet , Özcan Servet 
Published: June 2022

AbstractAcinetobacter baumannii is one of the most dangerous multidrug-resistant pathogens worldwide. Currently, 50-70% of clinical isolates of A. baumannii are extensively drug-resistant (XDR) and available antibiotic options against A. baumannii infections are limited. There are still needs to discover specific de facto bacterial antigenic proteins that could be effective vaccine candidates in human infection. With the growth of research in recent years, several candidate molecules have been identified for vaccine development. So far, there is no public health authorities approved vaccine against A. baumannii. The purpose of this study was to identify immunodominant vaccine candidate proteins that can be immunoprecipitated specifically with patients’ IgGs. Relaying on hypothesis that IgGs of infected person have capacity to capture immunodominant bacterial proteins. Herein, outer membrane and secreted proteins of sensitive and drug resistant A. baumannii were captured by using IgGs obtained from patient and healthy control sera and were identified by LC-MS/MS analysis. By using subtractive proteomic approach, we determined 34 unique proteins which were captured only in drug-resistant A. baumannii strain via patient sera. After extensive evaluation of predicted epitope regions, solubility, membrane transverse characteristics, and structural properties, we selected several notable vaccine candidates. We identified vaccine candidate proteins that triggered de facto response of human immune system against the antibiotic-resistant A. baumannii.
Identifying recent cholera infections using a multiplex bead serological assay
Authors: Jones Forrest K. , Bhuiyan Taufiqur R. , Mills Rachel , Khan Ashraful I , Slater Damien , Vater Kian Robert Hutt , Chowdhury Fahima , Kelly Meagan , Xu Peng , Kováč Pavol , Biswas Rajib , Kamruzzaman Mohammad , Ryan Edward T. , Calderwood Stephen B. , LaRocque Regina C. , Lessler Justin , Charles Richelle C. , Leung Daniel T. , Qadri Firdausi , Harris Jason B. , Azman Andrew S. 
Published: June 2022

AbstractBackgroundEstimates of incidence based on medically attended cholera can be severely biased. Vibrio cholerae O1 leaves a lasting antibody signal and recent advances show that these can be used to estimate infection incidence rates from cross-sectional serologic data. Current laboratory methods are resource intensive and challenging to standardize across laboratories. A multiplex bead assay (MBA) could efficiently expand the breadth of measured antibody responses and improve seroincidence accuracy.MethodsWe tested 305 serum samples from confirmed cholera cases (4-1083d post-infection) and uninfected contacts in Bangladesh using an MBA (IgG/IgA/IgM for 7 Vibrio cholerae O1-specific antigens) as well as traditional vibriocidal and enzyme-linked immunosorbent assays (2 antigens, IgG and IgA).ResultsWhile post-infection vibriocidal responses were larger than other markers, several MBA-measured antibodies demonstrated robust responses with similar half-lives. Random forest models combining all MBA antibody measures allowed for accurate identification of recent cholera infections (e.g. past 200 days) including a cross-validated AUC (cvAUC200) of 92% with simpler 3 IgG antibody models having similar accuracy. Across infection windows between 45- and 300-days, accuracy of models trained on MBA measurements were non-inferior to models based on traditional assays.ConclusionsOur results illustrate a scalable cholera serosurveillance tool that can be incorporated into multi-pathogen serosurveillance platforms.
Transition to Endemic: Acceptance of Additional COVID-19 Vaccine Doses Among Canadian Adults in A National Cross-Sectional Survey
Authors: Reifferscheid Laura , Wun Lee Janet Sau , MacDonald Noni E , Sadarangani Manish , Assi Ali , Lemaire-Paquette Samuel , MacDonald Shannon E. 
Published: June 2022

AbstractBackgroundAdditional doses of COVID-19 vaccine have been proposed as solutions to waning immunity and decreased effectiveness of primary doses against infection with new SARS-CoV-2 variants. However, the effectiveness of additional vaccine doses relies on widespread population acceptance. We aimed to assess the acceptance of additional COVID-19 vaccine doses (third and annual doses) among Canadian adults and determine associated factors.MethodsWe conducted a national, cross-sectional online survey among Canadian adults from October 14 to November 12, 2021. Weighted multinomial logistic regression analyses were used to identify sociodemographic and health-related factors associated with third and annual dose acceptance and indecision, compared to refusal. We also assessed influences on vaccine decision-making, and preferences for future vaccine delivery.ResultsOf 6010 respondents, 70% reported they would accept a third dose, while 15.2% were undecided. For annual doses, 64% reported acceptance, while 17.5% were undecided. Factors associated with third dose acceptance and indecision were similar to those associated with annual dose acceptance and indecision. Previous COVID-19 vaccine receipt, no history of COVID-19 disease, intention to receive an influenza vaccine, and increasing age were strongly associated with both acceptance and indecision. Chronic illness was associated with higher odds of acceptance, while self-reported disability was associated with higher odds of being undecided. Higher education attainment and higher income were associated with higher odds of accepting additional doses. Minority first language was associated with being undecided about additional doses, while visible minority identity was associated with being undecided about a third dose and refusing an annual dose. All respondents reported government recommendations were an important influence on their decision-making and identified pharmacy-based delivery and drop-in appointments as desirable. Co-administration of COVID-19 and influenza vaccines was viewed positively by 75.5% of the dose 3 acceptance group, 12.3% of the undecided group, and 8.4% of the refusal group.ConclusionsTo increase acceptance, targeted interventions among visible minority and minority language populations, and those with a disability, are required. Offering vaccination at pharmacies and through drop-in appointments are important to facilitate uptake, while offering COVID-19/influenza vaccine co-administration may have little benefit among those undecided about additional doses.