bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of the Nurse Work Environment on Older Hispanic Surgical Patient Readmissions
Authors: Daus Marguerite , McHugh Matthew D. , Kutney-Lee Ann , Brooks Carthon Margo J. 
Published: September 2023

Background
Readmissions following hospitalization for common surgical procedures are prevalent among older adults and are disproportionally experienced by Hispanic patients. One potential explanation for these disparities is that Hispanic patients may receive care in hospitals with lower-quality nursing care.

Objectives
The objective of this study was to evaluate the relationship between the hospital-level work environment of nurses and hospital readmissions among older Hispanic patients.

Methods
Using linked data sources from 2014 to 2016, we conducted a cross-sectional analysis of 522 hospitals and 732,035 general, orthopedic, and vascular surgical patients (80,978 Hispanic patients and 651,057 non-Hispanic White patients) in four states. Multivariable logistic regression models were employed to determine the relationship between the work environment and older Hispanic patient readmissions at multiple time periods (7, 30, and 90 days).

Results
In final adjusted models that included an interaction between work environment and ethnicity, an increase in the quality of the work environment resulted in a decrease in the odds of readmission that was greater for older Hispanic surgical patients at all time periods. Specifically, an increase in three of the five work environment subscales (Nurse Participation in Hospital Affairs, Nursing Foundations for Quality of Care, and Staffing and Resource Adequacy) was associated with a reduction in the odds of readmission that was greater for Hispanic patients than their non-Hispanic White counterparts.

Discussion
System-level investments in the work environment may reduce Hispanic patient readmission disparities. This study’s findings may be used to inform the development of targeted interventions to prevent hospital readmissions for Hispanic patients.
Management and outcomes of chemotherapy-associated pneumoperitoneum in cancer patients: a scoping review protocol
Authors: Maina Renee M. , Rader Caroline A. , Kypa Jeevan , Jasmin Hilary M. , Asahngwa Constantine , Muenyi Clarisse S. , Foretia Denis A. 
Published: September 2023

Introduction:
Pneumoperitoneum – free air within the peritoneal cavity – is often the result of bowel perforation, though other causes include residual postprocedural or postoperative air and barotrauma. In non-cancer patients, operative intervention is often required. Cancer patients, on the other hand, present a unique set of challenges as they usually have elevated risk of pneumoperitoneum from local radiation therapy, frequent endoscopic procedures, and tumor invasion. Factors such as malnutrition, neutropenia, chemotherapy, and steroid use make emergent surgery tenuous in cancer patients. There is a paucity of published literature on the management of pneumoperitoneum in patients actively undergoing chemotherapy. The main objective of this scoping review is to assess the presentation, management, and subsequent outcomes of this unique patient population.

Materials and Methods:
The authors will utilize the framework for performing scoping reviews as outlined by Arksey and O’Malley. They will perform the search for articles in three electronic databases (i.e. SCOPUS, PubMed, Embase) and relevant gray literature. Only articles available in English and published between 1999 and 2022 will be included. Inclusion criteria will be a known diagnosis of cancer, chemotherapy within 6 months of presentation, and imaging confirmation of pneumoperitoneum. Exclusion criteria will be cancer diagnosis at the time of presentation, perforation secondary to cancer itself, and chemotherapy greater than 6 months prior to presentation. A tailored extraction frame to extract relevant information from published articles that meet our inclusion criteria. The data using both descriptive statistics and thematic analysis of the main study questions.

Ethics and Dissemination:
Since the authors will not be collecting primary data, formal ethical approval is not required. They study findings will be disseminated through abstracts, conference presentations, and peer-reviewed publications.
Development of LIBRA-seq for the Guinea Pig Model System as a Tool for the Evaluation of Antibody Responses to Multivalent HIV-1 Vaccines
Authors: Vukovich Matthew J. , Raju Nagarajan , Kgagudi Prudence , Manamela Nelia P. , Abu-Shmais Alexandra A. , Gripenstraw Kathryn R. , Wasdin Perry T. , Shen Shaunna , Dwyer Bridget , Akoad Jumana , Lynch Rebecca M. , Montefiori David C. , Richardson Simone I. , Moore Penny L. , Georgiev Ivelin S. 
Published: September 2023

ABSTRACTConsistent elicitation of serum antibody responses that neutralize diverse clades of HIV-1 remains a primary goal of HIV-1 vaccine research. Prior work has defined key features of soluble HIV-1 Envelope (Env) immunogen cocktails that influence the neutralization breadth and potency of multivalent vaccine-elicited antibody responses including the number of Env strains in the regimen. We designed immunization groups that consisted of different numbers of Env strains to be used in a cocktail immunization strategy: the smallest cocktail (group 2) consisted of a set of two Env strains, which were a subset of the three Env strains that made up group 3, which in turn were a subset of the six Env strains that made up group 4. Serum neutralizing titers were broadest in guinea pigs that were immunized with a cocktail of three Envs compared to cocktails of two and six, suggesting that multivalent Env immunization provides a benefit but may be detrimental when the cocktail size is too large. We then adapted the LIBRA-seq platform for antibody discovery to be compatible with guinea pigs, and isolated several tier 2 neutralizing monoclonal antibodies. Three antibodies isolated from two separate guinea pigs were similar in their gene usage and CDR3s, establishing evidence for a guinea pig public clonotype elicited through vaccination. Taken together, this work investigated multivalent HIV-1 Env immunization strategies and provides a novel methodology for screening guinea pig B cell receptor antigen specificity at a high throughput level using LIBRA-seq.IMPORTANCEMultivalent vaccination with soluble Env immunogens is at the forefront of HIV-1 vaccination strategies, but little is known about the influence of the number of Env strains included in vaccine cocktails. Our results suggest that adding more strains is sometimes beneficial but may be detrimental when the number of strains is too high. Additionally, we adapted the LIBRA-seq platform to be compatible with guinea pig samples and isolated several tier 2 neutralizing monoclonal antibodies, some of which share V and J gene usage and >80% CDR3 identity, thus establishing the existence of public clonotypes in guinea pigs elicited through vaccination.
Poly ADP-ribosylation regulatesArcexpression and promotes adaptive stress-coping
Authors: Dahan Eliyahu , Taub Tze’ela , Pergamenchik Leah , Vovk Arthur , Manier Jade , Avneri Raphael , Lax Elad 
Published: September 2023

AbstractRapid adaptation to stressful events is essential for survival and requires acute stress response and stress-coping strategy. Yet, the molecular mechanisms that govern this coping strategy have to be fully discovered. Poly ADP-ribosylation (PARylation) is a post-translational protein modification that plays a vital role in histone modification following neuronal activity and is required for long-term memory formation. Previous studies showed that inhibiting Parp1, the primary enzyme that catalyzes poly ADP-ribose polymers (PAR), impairs long-term memory formation. However, the target genes of Parp1-induced PARylation following acute stress are unknown. Here, we showed that the forced swim test, a well-established acute stress paradigm, induced elevated cortical PARylation and increased the expression of activity-dependent genes in mice. Systemic pharmacological Parp1 inhibition with ABT888 (Veliparib), impaired stress-coping in a second forced swim test done 24 hours later as measured by diminished immobility response. This effect was associated with reduced PARylation of Arc promoter and reduced Arc expression, 1 hour after Parp1 inhibition, suggesting Arc PARylation regulates its expression and hence successful stress-coping behavior.
Afferents to Action: Cortical proprioceptive processing assessed with corticokinematic coherence specifically predicts gross motor skills
Authors: Scott Mongold , Christian Georgiev , Thomas Legrand , Mathieu Bourguignon 
Published: September 2023

AbstractVoluntary motor control is thought to be predicated on the ability to efficiently integrate and process somatosensory afferent information. However, current approaches in the field of motor control have not factored in objective markers of how the brain actually tracks incoming somatosensory information. Here, we asked whether motor performance relates with such markers obtained with an analysis of the coupling between peripheral kinematics and cortical oscillations during continuous movements, best known as corticokinematic coherence (CKC). Motor performance was evaluated by measuring both gross and fine motor skills using the Box and Blocks Test (BBT) and the Purdue Pegboard Test (PPT), respectively, and with a biomechanics measure of coordination. Sixty-one participants completed the BBT, while equipped with electroencephalography and electromyography, and the PPT. We evaluated CKC, from the signals collected during the BBT, as the coherence between movement rhythmicity and brain activity, and coordination as the cross-correlation between muscle activity. CKC at movements’ first harmonic was positively associated with BBT scores, and showed a relationship with PPT scores, but only in synergy with BBT scores, where participants with lower PPT score had higher CKC than expected based on their BBT score. Coordination was not associated with motor performance and at most, weakly related to CKC. These findings demonstrate that cortical somatosensory processing in the form of strengthened brain-peripheral coupling is specifically associated with better gross motor skills. CKC might be considered as a valuable addition to classical tests of proprioceptive acuity, with important perspectives for future clinical studies and practice.Significance StatementWhether standing upright, jogging, or in Olympic competition, our nervous system not only sends out motor commands prompting muscles to contract, but also receives incoming information to fine-tune motor actions. Though the machinery involved in sensing mechanical changes is well-described, the neural processing of this information is not, making its relevance to motor function unresolved. We found that the coupling strength between peripheral kinematics and cortical activity was related to motor function and at most, only weakly related to conventional muscle-only assessments. We present novel behavioral relevance of this coupling and its specific relationship to gross motor skill. Our study paves the way for including novel brain-centered approaches to complement classical assessment sensorimotor functions in health and disease.
Colonic spermidine promotes proliferation and migration of intestinal epithelial cells
Authors: Flory Madison , Gao Angela , Morrow Morgan , Alam Ashfaqul 
Published: September 2023

AbstractThe gut microbiome, comprising trillions of diverse microorganisms, profoundly influences the efficient development and maintenance of the intestinal barrier. While shifts in microbial composition are observed in Inflammatory Bowel Disease (IBD) and Colorectal Cancer (CRC), the causal relationship between these changes and resolution of inflammation remains elusive. Notably, IBD is not only marked by shifts in microbial composition but also by changes in microbial metabolites. Polyamines, produced by both gut bacteria and human cells, have emerged as potential regulators of gut pathology, cancer and mucosal repair. Investigating how elevated polyamine levels influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. To dissect the complex interplay between the gut microbiome, polyamines, and IEC, we focused on the overrepresented bacteriumB. uniformisand its primary metabolite, spermidine. Here, we show thatB. uniformis, a dominant member of gut microbiota, expands during the repair & resolution phase of the chemically induced chronic murine colitis. Furthermore, we found that the abundance of colonic polyamines was also altered, with spermidine being the abundant polyamine. Our RNA sequencing and transcriptomic analysis of cultured colonic epithelial cells demonstrate that spermidine regulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. We also found that spermidine stimulates the proliferation of cultured colonic epithelial cells in vitro. Additionally, our findings indicate that spermidine enhances the migrations of enterocytes. Our study emphasizes the crucial functions of the gut microbiome and polyamines in governing the functions of intestinal epithelial cells. Thus, these microorganisms and their metabolic byproducts hold promise as prospective therapeutic agents.
Cell Typing and Sub-typing Based on Detecting Characteristic Subspaces of Morphological Features Derived from Neuron Images
Authors: Zhao Sujun , Qian Penghao , Liu Lijuan 
Published: September 2023

AbstractMotivationRecent advances in reconstructing 3D neuron morphologies at the whole brain level offer exciting opportunities to study single cell genotyping and phenotyping. However, it remains challenging to define cell types and sub-types properly.ResultsAs morphological feature spaces are often too complicated to classify neurons, we introduce a method to detect the optimal subspace of features so that neurons can be well clustered. We have applied this method to one of the largest curated databases of morphological reconstructions that contains more than 9,400 mouse neurons of 19 cell types. Our method is able to detect the distinctive feature subspaces for each cell type. Our approach also outperforms prevailing cell typing approaches in terms of its ability to identify key morphological indicators for each neuron type and separate superclasses of these neuron types. the subclasses of neuronal types could supply information for brain connectivity and modeling, also promote other analysis including feature spaces.AvailabilityAll datasets used in this study are publicly available. All analyses were conducted with python package Scikitlearn 0.23.1 version. Source code used for data processing, analysis and figure generation is available as an open-source Python package, onhttps://github.com/SEU-ALLEN-codebase/ManifoldAnalysisContactljliu@braintell.org
DeepGO-SE: Protein function prediction as Approximate Semantic Entailment
Authors: Kulmanov Maxat , Guzmán-Vega Francisco J. , Roggli Paula Duek , Lane Lydie , Arold Stefan T. , Hoehndorf Robert 
Published: September 2023

AbstractThe Gene Ontology (GO) is one of the most successful ontologies in the biological domain. GO is a formal theory with over 100,000 axioms that describe the molecular functions, biological processes, and cellular locations of proteins in three sub-ontologies. Many methods have been developed to automatically predict protein functions. However, only few of them use the background knowledge provided in the axioms of GO for knowledge-enhanced machine learning, or adjust and evaluate the model for the differences between the sub-ontologies.We have developed DeepGO-SE, a novel method which predicts GO functions from protein sequences using a pretrained large language model combined with a neuro-symbolic model that exploits GO axioms and performs protein function prediction as a form of approximate semantic entailment. We specifically evaluate DeepGO-SE on proteins that have no significant similarity with training proteins and demonstrate that DeepGO-SE can improve function prediction for those proteins.
Clusterin can mediate apoptosis-induced molecular mechanisms in immune thrombocytopenia
Authors: Stein T. , Bitsina C. , Schmugge M. , Franzoso F. 
Published: September 2023

AbstractAbnormalities in the apoptosis pathway are possible risk factors for various autoimmune diseases including immune thrombocytopenia (ITP). ITP is an autoimmune bleeding disorder characterized by a low platelet count and mostly mild but in rare occasions life threatening bleeding symptoms. Platelets and megakaryocytes (MKs) may be seen as the major targets of the pathogenic immune responses in ITP. A mechanistic understanding of the ITP pathogenesis is still lacking. Our data indicate that mechanisms associated with impaired clusterin-mediated apoptosis might play a role in ITP platelet pathophysiology and platelet production by MKs.We could demonstrate by apoptosis proteomic profiling significantly increased expression levels of some apoptotic genes such as clusterin (CLU), pro-caspase 3, catalase, TRAILR1/DR4, Bax, Bad and Bcl-2 compared to healthy controls in platelet-rich plasma (PRP) from 10 ITP patients. We could validate by both RT-qPCR and Western blotting that CLU, a stress-activated chaperone, is significantly increased in both newly diagnosed and chronic ITP. We used the human megakaryoblastic cell line MEG-01, treated for 4h with plasma from acute and chronic ITP patients and healthy controls. We performed chemical treatments in plasma treated MEG-01 by using pan-caspase inhibitors (Z-VAD-FMK), apoptosis inducer ABT-737, Rotenone and Rapamycin. We determined the expression at mRNA levels of apoptosis pathway regulatory genes Bax, caspase-3, -8, -9 as well as CLU, GRP78 and GRP94 by qRT-PCR. We could demonstrate significantly downregulation of mRNA expression levels of these apoptotic markers in ITP plasma treated and CLU siRNA transfected MEG-01 cells. Our results indicate a possible impairment of apoptosis pathway via upregulation of CLU and Bax in platelets and in their producers MKs that can lead to platelet destruction in ITP disease.
Bacteria colonies modify their shear and compressive mechanical properties in response to different growth substrates
Authors: Kochanowski Jakub A. , Carroll Bobby , Asp Merrill E. , Kaputa Emma , Patteson Alison E. 
Published: September 2023

AbstractBacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct multicellular structures in response to different environmental conditions remains incompletely understood. Here, we investigated the connection between bacteria colony mechanics and the colony growth substrate by measuring the oscillatory shear and compressive rheology of bacteria colonies grown on agar substrates. We found that bacteria colonies modify their own mechanical properties in response to shear and uniaxial compression with the increasing agar concentration of their growth substrate. These findings highlight that mechanical interactions between bacteria and their microenvironment are an important element in bacteria colony development, which can aid in developing strategies to disrupt or reduce biofilm growth.
Influence of preprocessing, distortion correction and cardiac triggering on the quality of diffusion MR images of spinal cord
Authors: Schilling Kurt G , Combes Anna J.E. , Ramadass Karthik , Rheault Francois , Sweeney Grace , Prock Logan , Sriram Subramaniam , Cohen-Adad Julien , Gore John C , Landman Bennett A , Smith Seth A , O’Grady Kristin P. 
Published: September 2023

AbstractDiffusion MRI of the spinal cord (SC) is susceptible to geometric distortion caused by field inhomogeneities, and prone to misalignment across time series and signal dropout caused by biological motion. Several modifications of image acquisition and image processing techniques have been introduced to overcome these artifacts, but their specific benefits are largely unproven and warrant further investigations. We aim to evaluate two specific aspects of image acquisition and processing that address image quality in diffusion studies of the spinal cord: susceptibility corrections to reduce geometric distortions, and cardiac triggering to minimize motion artifacts. First, we evaluate 4 distortion preprocessing strategies on 7 datasets of the cervical and lumbar SC and find that while distortion correction techniques increase geometric similarity to structural images, they are largely driven by the high-contrast cerebrospinal fluid, and do not consistently improve the geometry within the cord nor improve white-to-gray matter contrast. We recommend at a minimum to perform bulk-motion correction in preprocessing and posit that improvements/adaptations are needed for spinal cord distortion preprocessing algorithms, which are currently optimized and designed for brain imaging. Second, we design experiments to evaluate the impact of removing cardiac triggering. We show that when triggering is foregone, images are qualitatively similar to triggered sequences, do not have increased prevalence of artifacts, and result in similar diffusion tensor indices with similar reproducibility to triggered acquisitions. When triggering is removed, much shorter acquisitions are possible, which are also qualitatively and quantitatively similar to triggered sequences. We suggest that removing cardiac triggering for cervical SC diffusion can be a reasonable option to save time with minimal sacrifice to image quality.
SARS-CoV-2 Omicron BA.2.86: less neutralization evasion compared to XBB sub-variants
Authors: An Yaling , Zhou Xuemei , Tao Lifeng , Xie Haitang , Li Dedong , Wang Ruyue , Hu Hua , Xu Zepeng , Dai Lianpan , Xu Kun , Gao George F. 
Published: September 2023

AbstractThe continual emergence and circulation of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused a great challenge for the coronavirus disease 2019 (COVID-19) pandemic control. Recently, Omicron BA.2.86 was identified with more than 30 amino acid changes on the spike (S) protein, compared to Omicron BA.2 or XBB.1.5. The immune evasion potential of BA.2.86 is of great concern. In this study, we evaluated the neutralizing activities of sera collected from participants and mice. Participants were divided into five groups according to their vaccination (inactivated vaccine, protein subunit vaccine ZF2001 or ZF2202-A) and infection (Omicron BF.7/BA.5.2) status. ZF2202-A is ZF2001 vaccine’s next-generation COVID-19 vaccine with updated bivalent Delta-BA.5 RBD-heterodimer immunogen. BALB/c mice were immunized with XBB.1.5 RBD-homodimer, BA.5-BA.2, Delta-XBB.1.5 or BQ.1.1-XBB.1.5 RBD-heterodimers protein vaccine candidates for evaluating the neutralizing responses. We found that Omicron BA.2.86 shows stronger immune evasion than BA.2 due to >30 additional mutations on S protein. Compared to XBB sub-variants, BA.2.86 does not display more resistance to the neutralizing responses induced by ZF2001-vaccination, BF.7/BA.5.2 breakthrough infection or a booster dose of ZF2202-A-vaccination. In addition, the mouse experiment results showed that BQ.1.1-XBB.1.5 RBD-heterodimer and XBB.1.5 RBD-homodimer induced high neutralizing responses against XBB sub-variants and BA.2.86, indicating that next-generation COVID-19 vaccine should be developed to enhance the protection efficacy against the circulating strains in the future.