bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Care Organizational Support for Nurse Practitioner Practice and Emotional Health Care Delivery
Authors: Turi Eleanor , Schlak Amelia , Trexler Jamie , Courtwright Suzanne , Flandrick Kathleen , Liu Jianfang , Poghosyan Lusine 
Published: May 2024

Objectives
Nurse practitioners (NPs) are key to delivery of primary care services. However, poor organizational support for independent NP practice, such as lack of access to clinic resources, may lead to prioritizing patient physical health over emotional health. We investigated the relationship between organizational support for independent NP practice and emotional health care delivery.

Methods
This was a secondary analysis of cross-sectional survey data collected from 397 NPs in 2017. We measured organizational support for independent NP practice using the independent practice and support subscale of the NP Primary Care Organizational Climate Questionnaire. Emotional health care delivery was measured by asking NPs how frequently they addressed emotional concerns of patients. We utilized multilevel mixed effects linear regression models, adjusting for NP and practice covariates.

Results
Controlling for NP age, gender, marital status, race, and ethnicity, along with practice setting and size, as the independent practice and support score increased, NPs reported addressing emotional concerns of patients more frequently (beta = 0.34, 95% confidence interval = 0.02–0.66, P = 0.04). This indicates that as organizations provided more support for independent NP practice, NPs were able to more frequently address emotional concerns of patients.

Conclusions
Organizational support for independent NP practice is associated with addressing emotional concerns of patients. To support NP practice, primary care organizations should ensure that NPs manage patients independently and have access to ancillary staff and support for care management.
Do Anthropometric Measurements of The Orbital Region Differ Between Healthy Children and Children With Attention Deficit Hyperactivity Disorder?
Authors: Karadağ Mehmet , Arslanoğlu Sami , Hangül Zehra , Bahşi İlhan 
Published: May 2024

Objective:
The aim of this study is to investigate whether there may be differences in the measurements of the orbital region between healthy children and children with attention deficit hyperactivity disorder (ADHD).

Methods:
In this study, the orbital region measurements of 310 children, including 130 ADHD children and 180 healthy children aged 7 to 11 years, were analyzed. For this analysis, anterior view photographs of these individuals were used. For both sides, endocanthion (en), exocanthion (ex), and pupil (p) were determined in these photographs. A total of 5 distances (ex-ex, en-en, ex-en for the right side, ex-en for the left side and p-p) were analyzed using these points.

Results:
In both sexes, no statistically significant difference was observed between the 2 groups in all 6 parameters analyzed.

Conclusion:
Although it was concluded that there was no difference in orbital measurements between healthy children and children with ADHD in this study, it was thought that a definite conclusion could not be reached because the cases examined belonged to a single center. Therefore, it is thought that multicenter studies in which more individuals are evaluated are needed.
Differential Effects of Ascites and Hepatic Encephalopathy on Waitlist Mortality in Liver Transplantation by MELD 3.0
Authors: Lee Brian T. , Chen Nathan T. , Fong Tse-Ling , Dodge Jennifer L. 
Published: May 2024

Background.
MELD 3.0 introduces changes to address waitlist disparities for liver transplant (LT) candidates. Ascites and hepatic encephalopathy (HE) are important milestones in the natural history of cirrhosis regardless of the Model for End-Stage Liver Disease (MELD) score. We aim to assess the impact of ascites and HE and its interaction with MELD 3.0 on waitlist mortality.

Methods.
This is a retrospective study of patients listed for LT in the Organ Procurement and Transplantation Network database from 2016 to 2021. The primary outcome was waitlist mortality (death/delisting for too sick to LT). Ascites/HE were classified as moderate ascites without moderate HE (mAscites), moderate HE without moderate ascites (mHE), both moderate ascites/HE (mBoth), and neither. MELD 3.0 scores were categorized as <20, 20–29, 30–39, and ≥40.

Results.
Of 39 025 candidates, 29% had mAscites, 3% mHE, and 8% mBoth. One-year waitlist mortality was 30%, 38%, and 47%, respectively, compared with 17% (all P < 0.001) for those with neither. In multivariable Cox regression, the adjusted risk of waitlist mortality associated with mAscites (versus neither) was a hazard ratio (HR) of 1.76 (95% confidence interval [CI], 1.55-2.00) when the MELD 3.0 score was <20, significantly higher than when the MELD 3.0 score was 20–29 (HR 1.40; 95% CI, 1.27-1.54), 30–39 (HR 1.19; 95% CI, 1.04-1.35), and ≥40 (HR 1.14; 95% CI, 0.91-1.43, interaction P < 0.05 for all). A similar pattern was observed by MELD 3.0 for both moderate ascites/HE.

Conclusions.
The presence of moderate ascites alone, or combined with moderate HE, not only increases the risk of waitlist mortality but also has a differential effect by MELD 3.0, especially at lower MELD scores. Earlier strategies addressing this group and improving treatment plans or access to LT regardless of MELD remain needed.
Recruitment of a Diverse Community-based Older Adult Cohort for a Longitudinal Aging Study
Authors: Jacobsen Erin , Lucas Heather , Moran Catherine , Dixon Reverend Gloria , Ganguli Mary 
Published: May 2024

Introduction:
Enrolling individuals from underrepresented ethnoracial groups in aging research is often a challenge.

Methods:
We sought a diverse sample of older adults from a small-town area for a longitudinal aging study. We employed an intensive community engagement approach encompassing a range of recruitment strategies.

Results:
Over 4 years a steady trickle of individuals, 66% self-identifying as Black, signed up for study information; the proportion of those who eventually enroll in the study has been rising each year, from 68% to 94%. Community events, word-of-mouth referrals, and mailed postcards brought in the most contacts. The highest percentage of contacts who ultimately enrolled were from postcards, flyers, and word-of-mouth. Significantly more word-of-mouth referrals were endorsed by Black individuals than White and by Black men than other race/sex groups.

Conclusions:
We have had some success in building relationships and trust with the local community, enrolling Black study participants in a proportion equal to their representation in the target community using a variety of recruitment methods. Patience, immersion in the community, and partnerships with key community members alongside traditional advertisements, and the utilization of study participants as recruiters are critical to designing optimal, targeted, recruitment strategies.
Lack of Concordance Between Abbreviated Injury Scale and American Association for the Surgery of Trauma Organ Injury Scale in Patients with High-Grade Solid Organ Injury
Authors: Santos Jeffrey , Kunz Shelby , Grigorian Areg , Park Stephen , Tabarsi Emiliano , Matsushima Kazuhide , Penaloza-Villalobos Liz , Luo-Owen Xian , Mukherjee Kaushik , Alvarez Claudia , Nahmias Jeffry 
Published: May 2024

BACKGROUND:
The Abbreviated Injury Scale (AIS) is widely used for body region-specific injury severity. The American Association for the Surgery of Trauma Organ Injury Scale (AAST-OIS) provides organ-specific injury severity but is not included in trauma databases. Previous researchers have used AIS as a surrogate for OIS. This study aims to assess AIS-abdomen concordance with AAST-OIS grade for liver and spleen injuries, hypothesizing concordance in terms of severity (grade of OIS and AIS) and patient outcomes.

STUDY DESIGN:
This retrospective study (July 2020 to June 2022) was performed at 3 trauma centers. Adult trauma patients with AAST-OIS grade III to V liver and spleen injury were included. AAST-OIS grade for each organ was compared with AIS-abdomen by evaluating the percentage of AAST-OIS grade correlating with each AIS score as well as rates of operative intervention for these injuries. Analysis was performed with chi-square tests and univariate analysis.

RESULTS:
Of 472 patients, 274 had liver injuries and 205 had spleen injuries grades III to V. AAST-OIS grade III to V liver injuries had concordances rates of 85.5%, 71%, and 90.9% with corresponding AIS 3 to 5 scores. AAST-OIS grade III to V spleen injuries had concordances rates of 89.7%, 87.8%, and 87.3%, respectively. There was a statistical lack of concordance for both liver and spleen injuries (both p < 0.001). Additionally, there were higher rates of operative intervention for AAST-OIS grade IV and V liver injuries and grade III and V spleen injuries vs corresponding AIS scores (p < 0.05).

CONCLUSIONS:
AIS should not be used interchangeably with OIS due to lack of concordance. AAST-OIS should be included in trauma databases to facilitate improved organ injury research and quality improvement projects.
How to Use Gravity to Accelerate Bone Adaptation: A Computational/Experimental Investigation of Exercises for Bone
Authors: Wilzman Andrew R. , Wong Devin Tomoko , Troy Karen L. 
Published: May 2024

AbstractImpact exercises are known to increase bone mineral density (BMD) and in turn, bone strength and resistance to fracture. The biochemical pathways driving changes in BMD take months to complete, complicating our ability to understand how specific exercises influence the remodeling stimulus received by the bone. The purpose of this study was to compare several measures that have been theoretically linked to bone remodeling stimulus, including accelerations measured by Inertial Measurement Units (IMUs) at the middle of the tibia, ground reaction forces measured by force plate, joint contact forces estimated by musculoskeletal modeling, and tibia strains estimated by finite element modeling informed by high-resolution CT imaging. Twenty healthy adults (10 male: 22.1 +/- 2.2 years; 10 female: 21.3 +/- 1.3 years) participated in a biomechanical investigation of how drop height and landing style (bilateral vs. unilateral) affect the various bone remodeling stimuli. The results showed that while drop height consistently had significant direct relationships with stimulus magnitude, there was little benefit to drop heights greater than 0.4 m. In contrast, switching from a bilateral to a unilateral landing had a large positive effect. The stimuli calculated based on IMU data showed opposite trends compared to force plate and musculoskeletal modeling-based calculations, highlighting the need for caution in how IMUs are placed, and the resulting data interpreted, in the context of bone loading. A post-hoc analysis showed that a linear regression with predictor variables of kinematics, jump height, landing type (unilateral vs. bilateral) and the Ground Reaction Force FFT Integral could explain 79% of the variance in the bone remodeling stimulus that was predicted using much more sophisticated (and labor intensive) modeling. We conclude that higher level biomechanical modeling may not be necessary to understand the magnitude of a bone remodeling stimulus of an exercise.
Reconstructing parent genomes using siblings and other relatives
Authors: Qiao Ying , Jewett Ethan M. , McManus Kimberly F. , Freyman William A. , Curran Joanne E. , Williams-Blangero Sarah , Blangero John ,   The 23andMe Research Team, Williams Amy L. 
Published: May 2024

AbstractReconstructing the DNA of ancestors from their descendants has the potential to empower phenotypic analyses (including association and genetic nurture studies), improve pedigree reconstruction, and shed light on the ancestral population and phenotypes of ancestors. We developed HAPI-RECAP, a method that reconstructs the DNA of parents from full siblings and their relatives. This tool leverages HAPI2’s output, a new phasing approach that applies to siblings (and optionally one or both parents) and reliably infers parent haplotypes but does not link the ungenotyped parents’ DNA across chromosomes or between segments flanking ambiguities. By combining IBD between the reconstructed parents and the relatives, HAPI-RECAP resolves the source parent of these segments. Moreover, the method exploits crossovers the children inherited and sex-specific genetic maps to infer the reconstructed parents’ sexes. We validated these methods on research participants from both 23andMe, Inc. and the San Antonio Mexican American Family Studies. Given data for one parent, HAPI2 reconstructs large fractions of the missing parent’s DNA, between 77.6% and 99.97% among all families, and 90.3% on average in three- and four-child families. When reconstructing both parents, HAPI-RECAP inferred between 33.2% and 96.6% of the parents’ genotypes, averaging 70.6% in four-child families. Reconstructed genotypes have average error rates < 10−3, or comparable to those from direct genotyping. HAPI-RECAP inferred the parent sexes 100% correctly given IBD-linked segments and can also reconstruct parents without any IBD. As datasets grow in size, more families will be implicitly collected; HAPI-RECAP holds promise to enable high quality parent genotype reconstruction.
Convolutional architectures are cortex-aligned de novo
Authors: Kazemian Atlas , Elmoznino Eric , Bonner Michael F. 
Published: May 2024

ABSTRACTWhat underlies the emergence of cortex-aligned representations in deep neural network models of vision? The success of widely varied architectures has motivated the prevailing hypothesis that large-scale pre-training is the primary factor underlying the similarities between brains and neural networks. Here, we challenge this view by revealing the role of architectural inductive biases in models with minimal training. We examined networks with varied architectures but no pre-training and quantified their ability to predict image representations in the visual cortices of both monkeys and humans. We found that cortex-aligned representations emerge in convolutional architectures that combine two key manipulations of dimensionality: compression in the spatial domain and expansion in the feature domain. We further show that the inductive biases of convolutional architectures are critical for obtaining performance gains from feature expansion—dimensionality manipulations were relatively ineffective in other architectures and in convolutional models with targeted lesions. Our findings suggest that the architectural constraints of convolutional networks are sufficiently close to the constraints of biological vision to allow many aspects of cortical visual representation to emerge even before synaptic connections have been tuned through experience.
Efficacy of BianShi Moxibustion for bowel preparation: study protocol for a randomized controlled trial
Authors: Zhang Qiang , Zhang Xiao-Ping , Wang Li-Jie 
Published: May 2024

AbstractBackgroundAdequate bowel preparation is one of the most important prerequisite during the colonoscopy. It is conductive to detect the polypus, adenoma and early colorectal carcinoma and decrease the rate of overuse of medical resource. BianShi Moxibustion(BSM) is one of the most important Traditional Chinese Medicine(TCM) treatment options, which is called TCM proper technology. BSM is applied to prevent and cure digestive system disorder widely, including functional constipation(FC), irritable bowel syndrome(IBS), functional dyspepsia(FD) etc. we speculate that BSM can improve the bowel preparation quality through ameliorating the function of digestive tract, especially in high risk of inadequate bowel preparation patients, including elderly individual, diabetes mellitus, neurodegenerative changes etc. Hence, the objective of this research is to evaluate the efficacy of BSM on the quality of bowel preparation before colonoscopy.MethodThis is a randomized triple-blinded, single-center, prospective study. We will recruit 72 inpatients who are scheduled to undergo colonoscopy for screening and diagnostic or therapeutical purposes for the first time will be randomized to assign into treatment group or control group at a ratio of 1:1. The intervention plan in the treatment group consists of 3L polyethylene glycol(PEG) solution plus BSM(Treatment period is 3 days, Qd). In the control group, the plan is 3L PEG plus sham BSM. Boston Bowel Preparation Scale(BBPS) will be used to evaluate the efficacy of the bowel preparation and regarded as the primary outcome measure. The secondary outcomes including caecal intubation rate, the willingness to repeat colonoscopy, the tolerance of bowel preparation regimens, the rate of adverse events.DiscussionThe aim of this clinical trial is to confirm the influence of BSM on the quality of bowel preparation. The hypothesis of this study is that the BSM has a positive role on the quality of bowel preparation. The routine bowel preparation regime combines with TCM proper technology will enhance bowel preparation quality and ameliorate the subjective feeling of participants. In addition, it will provide the reliable evidence of bowel preparation prior to colonoscopy from the point of view of integrative medicine.Trial registrationThis protocol and trial was registered in the Chinese Clinical Trial Registry(ChiCTR2300077168).
COCOA: A Framework for Fine-scale Mapping Cell-type-specific Chromatin Compartmentalization Using Epigenomic Information
Authors: Li Kai , Zhang Ping , Xu Jinsheng , Wen Zi , Zhang Junying , Zi Zhike , Li Li 
Published: May 2024

AbstractChromatin compartmentalization and epigenomic modification are crucial factors in cell differentiation and diseases development. However, mapping precise chromatin compartmental patterns across multiple cell types requires Hi-C or Micro-C data at high sequencing depth. Exploring the systematic relationship between epigenomic modifications and compartmental patterns remains a challenge. To address these issues, we present COCOA, a deep neural network framework that uses convolution and attention mechanisms to infer reliable fine-scale chromatin compartment patterns from six representative histone modification signals. COCOA achieves this by extracting 1-D track features through bi-directional feature reconstruction after resolution-specific binning epigenomic signals. These track features are then cross-fused with contact features using an attention mechanism. Subsequently, the contact features are transformed into chromatin compartment patterns through residual feature reduction. COCOA demonstrates accurate inference of chromatin compartmentalization at a fine-scale resolution and exhibits stable performance on test sets. In addition, we explored the impact of histone modifications on the chromatin compartmentalization throughin silicoepigenomic perturbation experiments. When using 1kb resolution high-depth experimental data, obscure compartments are observed, whereas COCOA can generate clear and detailed compartmental patterns. Finally, we demonstrated that COCOA enables cell-type-specific prediction of unrevealed chromatin compartment patterns in various biological processes. Thus, COCOA is an effective tool for gaining chromatin compartmentalization insights from epigenomics in a wide range of biological scenarios.
IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data
Authors: Wang Wenjia , Li Yuzhen , Ko Sungjin , Feng Ning , Zhang Manling , Liu Jia-Jun , Zheng Songyang , Ren Baoguo , Yu Yan P. , Luo Jian-Hua , Tseng George C. , Liu Silvia 
Published: May 2024

AbstractAdvancements in long-read transcriptome sequencing (long-RNA-seq) technology have revolutionized the study of isoform diversity. These full-length transcripts enhance the detection of various transcriptome structural variations, including novel isoforms, alternative splicing events, and fusion transcripts. By shifting the open reading frame or altering gene expressions, studies have proved that these transcript alterations can serve as crucial biomarkers for disease diagnosis and therapeutic targets. In this project, we proposed IFDlong, a bioinformatics and biostatistics tool to detect isoform and fusion transcripts using bulk or single-cell long-RNA-seq data. Specifically, the software performed gene and isoform annotation for each long-read, defined novel isoforms, quantified isoform expression by a novel expectation-maximization algorithm, and profiled the fusion transcripts. For evaluation, IFDlong pipeline achieved overall the best performance when compared with several existing tools in large-scale simulation studies. In both isoform and fusion transcript quantification, IFDlong is able to reach more than 0.8 Spearman’s correlation with the truth, and more than 0.9 cosine similarity when distinguishing multiple alternative splicing events. In novel isoform simulation, IFDlong can successfully balance the sensitivity (higher than 90%) and specificity (higher than 90%). Furthermore, IFDlong has proved its accuracy and robustness in diverse in-house and public datasets on healthy tissues, cell lines and multiple types of diseases. Besides bulk long-RNA-seq, IFDlong pipeline has proved its compatibility to single-cell long-RNA-seq data. This new software may hold promise for significant impact on long-read transcriptome analysis. The IFDlong software is available athttps://github.com/wenjiaking/IFDlong.
Metabolic adaptations of micrometastases alter EV production to generate invasive microenvironments
Authors: Gounis Michalis , Campos America V. , Shokry Engy , Mitchell Louise , Dornier Emmanuel , Rooney Nicholas , Dhayade Sandeep , Pardo Luis , Moore Madeleine , Novo David , Mowat Jenna , Jamieson Craig , Kay Emily , Zanivan Sara , Nixon Colin , Macpherson Iain , Tardito Saverio , Sumpton David , Blyth Karen , Norman Jim C. , Clarke Cassie J. 
Published: May 2024

AbstractAltered cellular metabolism has been associated with acquisition of invasive phenotypes during metastasis. To study this, we combined a genetically engineered mouse model of mammary carcinoma with syngeneic transplantation and primary tumour resection to generate isogenic cells from primary tumours and their corresponding lung micrometastases. Metabolic analyses indicated that micrometastatic cells increase proline production at the expense of glutathione synthesis leading to a reduction in total glutathione levels. Micrometastatic cells also have altered sphingomyelin metabolism leading to increased intracellular levels of specific ceramides. The combination of these two metabolic adaptations alters small extracellular vesicle (sEV) production to drive generation of an invasive microenvironment. Indeed, micrometastatic cells shut-down Rab27-dependent production of sEVs and, instead, switch-on neutral sphingomyelinase-2 (nSM2)-dependent sEV release. sEVs released in a nSM2-dependent manner from micrometastatic cells, in turn, influence the ability of fibroblasts to deposit extracellular matrix which promotes cancer cell invasiveness. These data provide evidence that metabolic rewiring drives invasive processes in metastasis by influencing sEV release.SummaryBreast cancer cells isolated from lung micrometastases have altered metabolism which influences extracellular vesicle production to generate invasive microenvironments.