bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroimaging correlates of syndromal depression following traumatic brain injury: A systematic review of the literature
Authors: Richey Lisa N. , Bryant Barry R. , Krieg Akshay , Bray Michael J. C. , Esagoff Aaron I. , Pradeep Tejus , Jahed Sahar , Luna Licia P. , Trapp Nicholas T. , Adkins Jaxon , Jones Melissa B. , Bledsoe Andrew , Stevens Daniel A. , Roper Carrie , Goldwaser Eric L. , Morris LiAnn , Berich-Anastasio Emily , Pletnikova Alexandra , Lobner Katie , Lee Daniel J. , Lauterbach Margo , Ducharme Simon , Sair Haris I. , Peters Matthew E. 
Published: October 2022

Objective To complete a systematic review of the literature examining neuroimaging findings unique to co-occurring syndromal depression in the setting of TBI. Methods A PRISMA compliant literature search was conducted in PubMed (MEDLINE), PsychINFO, EMBASE, and Scopus databases for articles published prior to April of 2022. The database query yielded 4447 unique articles. These articles were narrowed based on specific inclusion criteria (e.g., clear TBI definition, clear depression construct commenting on the syndrome of major depressive disorder, conducted empirical analyses comparing neuroimaging correlates in TBI subjects with depression versus TBI subjects without depression, controlled for the time interval between TBI occurrence and acquisition of neuroimaging). Results A final cohort of 10 articles resulted, comprising the findings from 423 civilians with brain injury, 129 of which developed post-TBI depression. Four articles studied mild TBI, three mild/moderate, one moderate/severe, and two all-comers, with nine articles focusing on single TBI and one including both single and recurrent injuries. Spatially convergent structural abnormalities in individuals with TBI and co-occurring syndromal depression were identified primarily in bilateral frontal regions, particularly in those with damage to the left frontal lobe and prefrontal cortices, as well as temporal regions including bilateral temporal lobes, the left superior temporal gyrus, and bilateral hippocampi. Various parietal regions and the nucleus accumbens were also implicated. EEG studies showed supporting evidence of functional changes in frontal regions. Conclusion Additional inquiry with attention to TBI without depression control groups, consistent TBI definitions, previous TBI, clinically diagnosed syndromal depression, imaging timing post-injury, acute prospective design, functional neuroimaging, and well-defined neuroanatomical regions of interest is crucial to extrapolating finer discrepancies between primary and TBI-related depression.
The Effect of Psycho-education on the Affiliate Stigma in Family Caregivers of People with Bipolar Disorder
Authors: Bahrami Raheleh , Khalifi Talieh 
Published: October 2022

Introduction Paying attention to stigma among caregivers to provide proper care for patients is necessary, and promoting awareness (about mental illness and mental health) to taking care of the caregivers’ health, is crucial. Objective This study aimed to investigate the effect of psycho-education on the affiliate stigma in family caregivers of people with bipolar disorder. Method This study is a quasi-experimental research with an experimental and control groups. 64 family caregivers of people with bipolar disorder participated in this study (32 in each group). Data was collected using the demographic questionnaire and Affiliate Stigma Scale before and after intervention (with 4 weeks gap). The experimental group received a psycho-education program for four weeks. The control group carried on their normal routine lifestyle. Results The mean scores of the affiliate stigma of both control and experimental groups before the intervention did not show a statistically significant difference ( P = .36), however after the intervention the results were statistically significant and increased in the experimental group ( P < .001). Conclusion According to the findings of this study psycho-education is an effective intervention that can reduce the affiliate stigma among family caregivers of people with bipolar disorder and it can be considered as one of the de-stigmatization strategies for them.
Human-centered design methods to achieve preparation phase goals in the multiphase optimization strategy framework
Authors: O’Hara Karey L. , Knowles Lindsey M. , Guastaferro Kate , Lyon Aaron R. 
Published: October 2022

Background The public health impact of behavioral and biobehavioral interventions to prevent and treat mental health and substance use problems hinges on developing methods to strategically maximize their effectiveness, affordability, scalability, and efficiency. Methods The multiphase optimization strategy (MOST) is an innovative, principled framework that guides the development of multicomponent interventions. Each phase of MOST ( Preparation, Optimization, Evaluation) has explicit goals and a range of appropriate research methods to achieve them. Methods for attaining Optimization and Evaluation phase goals are well-developed. However, methods used in the Preparation phase are often highly researcher-specific, and concrete ways to achieve Preparation phase goals are a priority area for further development. Results We propose that the discover, design, build, and test (DDBT) framework provides a theory-driven and methods-rich roadmap for achieving the goals of the Preparation phase of MOST, including specifying the conceptual model, identifying and testing candidate intervention components, and defining the optimization objective. The DDBT framework capitalizes on strategies from the field of human-centered design and implementation science to drive its data collection methods. Conclusions MOST and DDBT share many conceptual features, including an explicit focus on implementation determinants, being iterative and flexible, and designing interventions for the greatest public health impact. The proposed synthesized DDBT/MOST approach integrates DDBT into the Preparation phase of MOST thereby providing a framework for rigorous and efficient intervention development research to bolster the success of intervention optimization. Plain Language Summary 1.  What is already known about the topic? Optimizing behavioral interventions to balance effectiveness with affordability, scalability, and efficiency requires a significant investment in intervention development. 2.  What does this paper add? This paper provides a structured approach to integrating human-centered design principles into the Preparation phase of the multiphase optimization strategy (MOST). 3.  What are the implications for practice, research, or policy? The proposed synthesized model provides a framework for rigorous and efficient intervention development research in the Preparation phase of MOST that will ensure the success of intervention optimization and contribute to improving public health impact of mental health and substance use interventions.
The evolution of educational wage differentials for women and men in Germany, from 1996 to 2019
Authors: Ordemann Jessica , Pfeiffer Friedhelm 
Published: October 2022

AbstractThis paper studies the evolution of three higher education wage differentials from 1996 to 2019 in Germany. We distinguish between degrees from academic universities, degrees from universities of applied sciences, and the master craftsman\craftswoman certificate. The educational reference category is a standard degree within the German vocational education and training system. Based on samples of male and female workers from the Socio-Economic Panel Study (SOEP), regression methods show that all three educational wage differentials in 2019 exceeded the ones in 1996. However, workers graduating from universities experienced an inverse u-shape pattern with a maximum of about 0.5 log points around 2012. Since then, their wage differential decreased by nearly ten percent (about 0.045 log points). Although the decrease is not statistically significant at conventional levels, we think that nearly ten percent can be regarded as economically meaningful. We argue that this pattern is related to university expansion and changes in graduates’ subject-choice composition during that expansion. The paper concludes with a discussion of possible alternative explanations.
Inbreeding and pedigree analysis of the European red dairy cattle
Authors: Nyman Sofia , Johansson Anna M. , Palucci Valentina , Schönherz Anna A. , Guldbrandtsen Bernt , Hinrichs Dirk , de Koning Dirk-Jan 
Published: October 2022

AbstractBackgroundRed dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals with the highest genetic contributions were identified. Pedigree data included 9,073,403 animals that were born between 1900 and 2019 from Denmark, Finland, Germany, Latvia, Lithuania, the Netherlands, Norway, Poland, and Sweden, and covered 32 breeds. The numerically largest breeds were Red Dairy Cattle and Meuse-Rhine-Yssel.ResultsThe deepest average complete generation equivalent (9.39) was found for Red Dairy Cattle in 2017. Mean pedigree completeness ranged from 0.6 for Finncattle to 7.51 for Red Dairy Cattle. An effective population size of 166 animals was estimated for the total pedigree and ranged from 35 (Rotes Höhenvieh) to 226 (Red Dairy Cattle). Average generation intervals were between 5 and 7 years. The mean inbreeding coefficient for animals born between 1960 and 2018 was 1.5%, with the highest inbreeding coefficients observed for Traditional Angler (4.2%) and Rotes Höhenvieh (4.1%). The most influential animal was a Dutch Meuse-Rhine-Yssel bull born in 1960. The mean inbreeding level for animals born between 2016 and 2018 was 2% and highest for the Meuse-Rhine-Yssel (4.64%) and Rotes Hohenvieh breeds (3.80%).ConclusionsWe provide the first detailed analysis of the genetic diversity and inbreeding levels of the European red dairy cattle breeds. Rotes Höhenvieh and Traditional Angler have high inbreeding levels and are either close to or below the minimal recommended effective population size, thus it is necessary to implement tools to monitor the selection process in order to control inbreeding in these breeds. Red Dairy Cattle, Vorderwälder, Swedish Polled and Hinterwälder hold more genetic diversity. Regarding the Meuse-Rhine-Yssel breed, given its decreased population size, increased inbreeding and low effective population size, we recommend implementation of a breeding program to prevent further loss in its genetic diversity.
CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants
Authors: Chattopadhyay Amrita , Shih Ching-Yu , Hsu Yu-Chen , Juang Jyh-Ming Jimmy , Chuang Eric Y. , Lu Tzu-Pin 
Published: October 2022

AbstractBackgroundAvailability of next generation sequencing data, allows low-frequency and rare variants to be studied through strategies other than the commonly used genome-wide association studies (GWAS). Rare variants are important keys towards explaining the heritability for complex diseases that remains to be explained by common variants due to their low effect sizes. However, analysis strategies struggle to keep up with the huge amount of data at disposal therefore creating a bottleneck. This study describes CLIN_SKAT, an R package, that provides users with an easily implemented analysis pipeline with the goal of (i) extracting clinically relevant variants (both rare and common), followed by (ii) gene-based association analysis by grouping the selected variants.ResultsCLIN_SKAT offers four simple functions that can be used to obtain clinically relevant variants, map them to genes or gene sets, calculate weights from global healthy populations and conduct weighted case–control analysis. CLIN_SKAT introduces improvements by adding certain pre-analysis steps and customizable features to make the SKAT results clinically more meaningful. Moreover, it offers several plot functions that can be availed towards obtaining visualizations for interpretation of the analyses results. CLIN_SKAT is available on Windows/Linux/MacOS and is operative for R version 4.0.4 or later. It can be freely downloaded fromhttps://github.com/ShihChingYu/CLIN_SKAT, installed through devtools::install_github("ShihChingYu/CLIN_SKAT", force=T) and executed by loading the package into R using library(CLIN_SKAT). All outputs (tabular and graphical) can be downloaded in simple, publishable formats.ConclusionsStatistical association analysis is often underpowered due to low sample sizes and high numbers of variants to be tested, limiting detection of causal ones. Therefore, retaining a subset of variants that are biologically meaningful seems to be a more effective strategy for identifying explainable associations while reducing the degrees of freedom. CLIN_SKAT offers users a one-stop R package that identifies disease risk variants with improved power via a series of tailor-made procedures that allows dimension reduction, by retaining functionally relevant variants, and incorporating ethnicity based priors. Furthermore, it also eliminates the requirement for high computational resources and bioinformatics expertise.
PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data
Authors: Voorrips Roeland E. , Tumino Giorgio 
Published: October 2022

AbstractBackgroundFor genetic analyses, multi-allelic markers have an advantage over bi-allelic markers like SNPs (single nucleotide polymorphisms) in that they carry more information about the genetic constitution of individuals. This is especially the case in polyploids, where individuals carry more than two alleles at each locus. Haploblocks are multi-allelic markers that can be derived by phasing sets of closely-linked SNP markers. Phased haploblocks, similarly to other multi-allelic markers, will therefore be advantageous in genetic tasks like linkage mapping, QTL mapping and genome-wide association studies.ResultsWe present a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays, which is applicable to polyploids. This method is implemented in the software package PolyHaplotyper. In contrast to existing packages for polyploids it makes use of full-sib families among the samples to guide the haplotyping process. We show that in this situation it is much more accurate than other available software, using experimental hexaploid data and simulated tetraploid data.ConclusionsOur method and the software package PolyHaplotyper in which it is implemented extend the available tools for haplotyping in polyploids. They perform especially well in situations where one or more full-sib families are present.
EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms
Authors: Mittal Varnika , Reid Robert W. , Machado Denis Jacob , Mashanov Vladimir , Janies Daniel A. 
Published: October 2022

Abstract
Background
Here we release a new version of EchinoDB, EchinoDB v2.0 (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity.

Results
The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling.

Conclusion
EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
Study design of an interdisciplinary and participatory nature-based palliative rehabilitation intervention in a Danish nursing home for people with severe dementia
Authors: Schmidt Tanja , Gramkow Marie Christoffersen , Poulsen Dorthe Varning , Miller Louise Holm , Wermuth Lene , Stigsdotter Ulrika K. 
Published: October 2022

Abstract
Background
A limited amount of research has examined how nature-based palliative rehabilitation can be implemented in nursing homes for people with dementia, even though evidence suggests that these gardens are underused. This paper will present the study protocol of an intervention study co-designed in an interdisciplinary collaboration with a nursing home for people with dementia, to develop a tailored nature-based palliative rehabilitation program to increase qualified use of garden with the purpose of promoting a range of health outcomes.

Methods
The study is a single-cased quasi-experimental mixed methods study. The intervention will be developed, designed, and implemented in collaboration with the nursing home, using different co-design tools and methods. The effect of the intervention will be evaluated using the The Neuropsychiatric Inventory Nursing Home version in combination with medication use, a survey on staff burnout, and cameras in the garden to register garden use. A process evaluation with single- and focus group interviews consisting of various stakeholders in the study will be used to gain knowledge on the intervention processes and implementation.

Discussion
The paper presents new approaches in the field of palliative rehabilitation for people with dementia using nursing home gardens, through interdisciplinary collaboration, participatory co-design approach and mixed methods design. Using both effect and process evaluation, the study will provide unique insights in the role and importance of participatory process, interdisciplinary collaboration, and tailoring palliative rehabilitation activities in gardens at nursing homes to local needs and wishes. These results can be used to guide other nursing homes and renewal projects in the future.

Trial registration
ISRCTN, ISRCTN14095773. Registered 15 July 2022—Retrospectively registered.
Iranian Multi-center Osteoporosis Study (IMOS), 2021–2022: the study protocol
Authors: Khalagi Kazem , Fahimfar Noushin , Hajivalizadeh Fatemeh , Sanjari Mahnaz , Mansourzadeh Mohammad Javad , Gharibzadeh Safoora , Shafiee Gita , Kamali Koorosh , Alaeddini Farshid , Farzadfar Farshad , Mohseni Samaneh , Namazi Nazli , Razi Farideh , Gorgani Kobra , Kateb Saber Katayoun , Panahi Nekoo , Heshmat Ramin , Raeisi Alireza , Larijani Bagher , Ostovar Afshin 
Published: October 2022

Abstract
Background
This paper presents the protocol of the 4th round of Iranian Multi-center Osteoporosis Study (IMOS), a national survey with the primary objective of estimating the prevalence of osteoporosis and sarcopenia and their risk factors in a representative sample of urban and rural populations.

Methods
The target population of the survey is all individuals ≥ 50 years in Iran. A multi-stage random sampling method has been used in the study. We stratified the 31 provinces of the country into 5 strata based on the distribution of their potential risk factors for osteoporosis and randomly selected one or two provinces from each stratum. Then, we invited 2530 people aged ≥ 50 years recruited in the 8th National Survey of None Communicable Diseases (NCD) Risk Factors (STEPs-2021) in the selected provinces to participate in IMOS. Body composition measurements including bone mineral density, muscle mass, and fat mass are measured through Dual-energy X-ray Absorptiometry (DXA) method using HOLOGIC (Discovery and Horizon) devices; and Trabecular Bone Score (TBS) is measured on the DXA scans using iNsight software. Anthropometric measurement and physical examinations are made by a trained nurses and other required information are collected through face-to-face interviews made by trained nurses. Laboratory measurements are made in a central lab. The prevalence of osteoporosis and sarcopenia will be estimated after applying sampling design, non-response, and post-stratification weights to the data.

Discussion
IMOS will provide valuable information on the prevalence and determinants of osteoporosis and sarcopenia at the national level, and the results can be used in evaluating health system interventions and policymaking in the field of musculoskeletal diseases.
Multidisciplinary management of disseminated Exophiala dermatitidis mycosis in an infant with mixed phenotype acute leukemia: a case report
Authors: Nakatani Ryo , Ashiarai Miho , Yoshihara Hiroki , Yada Keigo , Nozaki Taiki , Ushigusa Takeshi , Mori Nobuyoshi , Hasegawa Daisuke 
Published: October 2022

Abstract
Background
Exophiala dermatitidis is a dematiaceous fungus isolated from various environmental sources. Systemic E. dermatitidis infections can lead to fatal outcomes, and treatment has not yet been standardized. Although E. dermatitidis is also known to cause cutaneous infection, it has not been previously reported to appear as ecthyma gangrenosum (EG), an uncommon cutaneous lesion in neutropenic patients that is mainly caused by Pseudomonas aeruginosa.

Case presentation
A 2-month-old male infant with mixed-phenotype acute leukemia presented with prolonged fever unresponsive to antibacterial and antifungal agents during myelosuppression due to remission induction therapy. He also presented with skin lesions on the left wrist and left lower quadrant of the abdomen. The abdominal lesion gradually turned black and necrotic, which was consistent with the findings of the EG. E. dermatitidis was isolated from the blood, stool, wrist skin, and endotracheal aspirate. During hematopoietic recovery, consolidation in both lungs was evident. Multiagent antifungal treatment failed to eliminate E. dermatitidis from blood. In order to salvage the central venous catheter, ethanol lock therapy (ELT) was adopted, following which the blood culture became negative. The abdominal lesion that evolved as a necrotic mass connecting the small intestine and subcutaneous tissue adjacent to the skin was surgically resected. After these interventions, the general condition improved.

Conclusion
Disseminated E. dermatitidis mycosis in the neutropenic infant was successfully managed with a multidisciplinary treatment consisting of multiagent antifungal treatment, ELT, and surgery.