bluuebunny/crossref_metadata_2025_split huggingface dataset:
Same-day Ileostomy Closure Discharge Reduces Costs Without Compromising Outcomes
Authors: Ferrari Davide , Violante Tommaso , Moriarty James P. , Borah Bijan J. , Merchea Amit , Stocchi Luca , Larson David W. 
Published: March 2024

Objective:
This study aims to assess the costs of a same-day discharge (SDD) enhanced recovery pathway for diverting loop ileostomy (DLI) closure compared with a standard institutional enhanced recovery protocol.

Background:
Every year, 50,155 patients in the United States undergo temporary stoma reversal. While ambulatory stoma closure has shown promise, widespread adoption remains slow. This study builds on previous research, focusing on the costs of a novel SDD protocol introduced in 2020.

Methods:
A retrospective case-control study was conducted at Mayo Clinic, Rochester, Minnesota, and Mayo Clinic, Jacksonville, Florida, comparing patients undergoing SDD DLI closure from August 2020 to February 2023 to those in a matched cohort receiving standard inpatient enhanced recovery protocol. Patients were matched based on age, sex, american society of anesthesiologists score, surgery period, and hospital. Primary outcomes included direct hospitalization and additional costs in the 30 days postdischarge.

Results:
The SDD group (n = 118) demonstrated a significant reduction in median index episode hospitalization and 30-day postoperative costs compared with the inpatient group (n = 236), with savings of $4827 per patient. Complication rates were similar, and so were readmission and reoperation rates.

Conclusions:
Implementation of the SDD for DLI closure is associated with substantial cost savings without compromising patient outcomes. The study advocates for a shift towards SDD protocols, offering economic benefits and potential improvements in health care resource utilization.
Association of National Accreditation Program for Rectal Cancer Accreditation with Outcomes after Rectal Cancer Surgery
Authors: Harbaugh Calista M , Kunnath Nicholas J , Suwanabol Pasithorn A , Dimick Justin B , Hendren Samantha K , Ibrahim Andrew M 
Published: March 2024

BACKGROUND:
The National Accreditation Program for Rectal Cancer (NAPRC) defined a set of standards in 2017 centered on multidisciplinary program structure, evidence-based care processes, and internal audit to address widely variable rectal cancer practices and outcomes across US hospitals. There have been no studies to-date testing the association between NAPRC accreditation and rectal cancer outcomes.

STUDY DESIGN:
This was a retrospective, observational study of Medicare beneficiaries aged 65 to 99 years with rectal cancer who underwent proctectomy from 2017 to 2020. The primary exposure was NAPRC accreditation and the primary outcomes included mortality (in-hospital, 30 day, and 1 year) and 30-day complications, readmissions, and reoperations. Associations between NAPRC accreditation and each outcome were tested using multivariable logistic regression with risk-adjustment for patient and hospital characteristics.

RESULTS:
Among 1,985 hospitals, 65 were NAPRC-accredited (3.3%). Accredited hospitals were more likely to be nonprofit and teaching with 250 or more beds. Among 20,202 patients, 2,078 patients (10%) underwent proctectomy at an accredited hospital. Patients at accredited hospitals were more likely to have an elective procedure with a minimally invasive approach and sphincter preservation. Risk-adjusted in-hospital mortality (1.1% vs 1.3%; p = 0.002), 30-day mortality (2.1% vs 2.9%; p < 0.001), 30-day complication (18.3% vs 19.4%; p = 0.01), and 1-year mortality rates (11% vs 12.1%; p < 0.001) were significantly lower at accredited compared with nonaccredited hospitals.

CONCLUSIONS:
NAPRC-accredited hospitals have lower risk-adjusted morbidity and mortality for major rectal cancer surgery. Although NAPRC standards address variability in practice, without directly addressing surgical safety, our findings suggest that NAPRC-accredited hospitals may provide higher quality surgical care.
Molecular characterization of HBV infected Nigerians reveal diverse mutational profiles within the BCP/PC regions
Authors: Faneye Adedayo Omotayo , Motayo Babatunde Olanrewaju , Mustafa Aisha , Odiabo Georgina 
Published: March 2024

Background; Hepatis B virus (HBV) is the most implicated cause of severe liver disease and hepatocellular carcinoma worldwide. Studies have shown that the basal core protein (BCP) and pre-core protein (PC) of HBV play a significant role in HBV related carcinogenesis. There is paucity of data on type and effect of BCP and PC mutations in Nigeria. This study aims to genotype HBV and investigate any mutations within the BCP and PC among HBV patients in Ibadan, Nigeria.
Methods; Forty HBV DNA positive were recruited into this study, viral load assay and genotyping by nested multiplex PCR was done. The partial X gene region was amplified and Sanger sequenced. The BPC and PC genomic regions were then analyzed using bioinformatics.
Results; Twenty-three participants recorded HBV DNA viral load of >20,000 International Units (IU), while 17 had <20,000 IU, while 28 samples were genotyped. Five genotypes A, B, C, D and E and 4 mixed genotypes AC, AD ACD and ABCD were detected. Genotype AC was the most frequently encountered while genotypes E and B were the least encountered. Mutation was highest in ages 34 to 45 years. Double mutation A1762T and G1764A within the BCP region was the most encountered mutation.
Conclusions; We report a diverse HBV genetic landscape, with mixed infections between genotypes with BCP double mutation A1762T/G1764A, signaling the likelihood of poor HBV related liver disease prognosis. Our findings contribute to our understanding of the molecular characteristics of HBV and its potential implications for disease progression and management among HBV infected Nigerians.
Deciphering changes in the incidence of hemorrhagic stroke and cerebral venous sinus thrombosis during the coronavirus disease 2019 pandemic: a nationwide time-series correlation study
Authors: Cho Soohyeon , Kim Dong Kyu , Song Min Cheol , Lee Euiho , Park Seoncheol , Chung Darda , Ha Jongmok 
Published: March 2024

ABSTRACTIntroductionHemorrhagic stroke and cerebral venous sinus thrombosis (CVST) are associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination. We aimed to investigate changes in the incidence of hemorrhagic stroke and CVST in South Korea before and during the coronavirus disease 2019 pandemic and the factors associated with these changes.Materials and MethodsWe conducted a nationwide time-series study using population-based databases between 2007 and 2022. The real-world and forecasted incidences of acute non-traumatic subarachnoid hemorrhage (SAH), intracerebral hemorrhage (ICH), and CVST during the pandemic period (2020–2022) were estimated and compared with the pre-pandemic period (2007–2019). The prevalence of conventional risk factors was measured using time-series data. Finally, a time-series correlation analysis was performed to examine the temporal association between conventional risk factors, SARS-CoV-2 infection, and SARS-CoV-2 vaccination.ResultsThe incidence of hemorrhagic stroke (SAH and ICH) was lower during the pandemic than during the pre-pandemic period. This observed decrease was associated with a reduction in the prevalence of conventional risk factors but not with SARS-CoV-2 infection or vaccination. The incidence of CVST was higher during the pandemic than during the pre-pandemic period, which may be temporally related to SARS-CoV-2 vaccination (Pearson correlation coefficient [r] = 0.349,P= 0.031).ConclusionWe report reassuring evidence of hemorrhagic stroke associated with SARS-CoV-2 infection and vaccination. However, awareness of CVST may be required for future vaccine rollouts and SARS-CoV-2 outbreaks.
Differences in polygenic associations with educational attainment between West and East Germany before and after reunification
Authors: Fraemke D. , Willems Y.E. , Okbay A. , Wagner G. , Tucker-Drob E.M. , Harden K.P. , Hertwig R. , Koellinger P. , Raffington L. 
Published: March 2024

AbstractHere we examine geographical and historical differences in polygenic associations with educational attainment in East and West Germany around reunification. We test this in n = 1902 25-85-year-olds from the German SOEP-G[ene] cohort. We leverage a DNA-based measure of genetic influence, a polygenic index calculated based on a previous genome-wide association study of educational attainment in individuals living in democratic countries. We find that polygenic associations with educational attainment were significantly stronger among East, but not West, Germans after but not before reunification. Negative control analyses of a polygenic index of height with educational attainment and height indicate that this gene-by-environemt interaction is specific to the educational domain. These findings suggest that the shift from an East German state-socialist to a free-market West German system increased the importance of genetic variants previously identified as important for education.One Sentence SummaryWe find that polygenic associations with educational attainment were significantly stronger among East, but not West, Germans after but not before reunification.
How do Large Language Models understand Genes and Cells
Authors: Fang Chen , Wang Yidong , Song Yunze , Long Qingqing , Lu Wang , Chen Linghui , Wang Pengfei , Feng Guihai , Zhou Yuanchun , Li Xin 
Published: March 2024

Researching genes and their interactions is crucial for deciphering the fundamental laws of biological activity, advancing disease treatment, drug discovery and so on. Large language Models (LLMs), with their profound text comprehension and generation capabilities, have made significant strides across various natural science fields. However, their application in cell biology remains notably scarce. To alleviate this issue, in this paper, we selects seven mainstream LLMs and evaluates their performance across a range of problem scenarios. Our findings indicate that LLMs possess a certain level of understanding of genes and cells, and hold potential for solving real-world problems. Moreover, we have improved the current method of textual representation of cells, enhancing the LLMs’ ability to tackle cell annotation tasks. We encourage cell biology researchers to leverage LLMs for problem-solving while also being mindful of some challenges associated with their use. We release our code and data athttps://github.com/epang-ucas/Evaluate_LLMs_to_Genes.CCS ConceptsApplied computing → Recognition of genes and regulatory elements; Bioinformatics; Computational genomics; Computational transcriptomics.ACM Reference FormatChen Fang, Yidong Wang, Yunze Song, Qingqing Long, Wang Lu, Linghui Chen, Pengfei Wang, Guihai Feng, Yuanchun Zhou, and Xin Li. 2024. How do Large Language Models understand Genes and Cells. 1, 1 (March 2024), 14 pages.https://doi.org/10.1145/nnnnnnn.nnnnnnn
Causality in the natural selection of the population ecological life histories of birds
Authors: Witting Lars 
Published: March 2024

AbstractContingent life history theory explains evolution backwards by analysing the fitness consequences of tradeoffs and constraints in the evolved species of today, bypassing the essential challenge of predicting evolution forwardly by the cause and effect of natural selection. I do the latter to decompose the population ecological life histories of 11,187 species of birds. This shows how the selection of mass accounts for inter-specific variation, with 76% of the within order variance, and 72% of the between order differences, in the body mass, demography, and population ecological traits being reconciled by the response of population dynamic feedback selection to variation in net energy, mortality, and intra-specific interactive competition.
Algorithms for a Commons Cell Atlas
Authors: Booeshaghi A. Sina , Galvez-Merchán Ángel , Pachter Lior 
Published: March 2024

AbstractCell atlas projects curate representative datasets, cell types, and marker genes for tissues across an organism. Despite their ubiquity, atlas projects rely on duplicated and manual effort to curate marker genes and annotate cell types. The size of atlases coupled with a lack of data-compatible tools make reprocessing and analysis of their data near-impossible. To overcome these challenges, we present a collection of data, algorithms, and tools to automate cataloging and analyzing cell types across tissues in an organism, and demonstrate its utility in building a human atlas.
Intercellular Signaling Pathways as Therapeutic Targets for Vascular Dementia Repair
Authors: Tian Min , Kawaguchi Riki , Shen Yang , Machnicki Michal , Villegas Nikole G. , Cooper Delaney R. , Montgomery Natalia , Haring Jacqueline , Lan Ruirui , Yuan Angelina H. , Williams Christopher K. , Magaki Shino , Vinters Harry V. , Zhang Ye , De Biase Lindsay M. , Silva Alcino J. , Carmichael S. Thomas 
Published: March 2024

AbstractVascular dementia (VaD) is a white matter ischemic disease and the second-leading cause of dementia, with no direct therapy. Within the lesion site, cell-cell interactions dictate the trajectory towards disease progression or repair. To elucidate the underlying intercellular signaling pathways, a VaD mouse model was developed for transcriptomic and functional studies. The mouse VaD transcriptome was integrated with a human VaD snRNA-Seq dataset. A custom-made database encompassing 4053 human and 2032 mouse ligand-receptor (L-R) interactions identified significantly altered pathways shared between human and mouse VaD. Two intercellular L-R systems, Serpine2-Lrp1 and CD39-A3AR, were selected for mechanistic study as both the ligand and receptor were dysregulated in VaD. Decreased Seprine2 expression enhances OPC differentiation in VaD repair. A clinically relevant drug that reverses the loss of CD39-A3AR function promotes tissue and behavioral recovery in the VaD model. This study presents novel intercellular signaling targets and may open new avenues for VaD therapies.
Topographical polarity reveals continuous EEG microstate transitions and electric field direction in healthy aging
Authors: Kashihara Shiho , Asai Tomohisa , Imamizu Hiroshi 
Published: March 2024

AbstractEEG microstate sequences, representing whole-brain spatial potential distribution patterns of the EEG, offer valuable insights for capturing spatiotemporally continuous and fluctuating neural dynamics with high temporal resolution through appropriate discretization. Recent studies suggest that EEG microstate transitions are gradual and continuous phenomena, contrary to the classical view of binary transitions. This study aimed to update conventional microstate analysis to reflect continuous EEG dynamics and examine differences in age-related electrophysiological state transitions. We considered the relative positions of EEG microstates on the neural manifold and their topographical polarity. Transition probability results showed fewer transitions on the microstate D-C-E axis in older adults. In contrast, transitions among microstates A, D, and B increased in the older group and were mainly observed within polarity. Furthermore, the 100 microstate transitions, which are variations of the shortest transitions between 10 microstates, could be reduced to 8 principal components based on the co-occurrence of each transition, including hubs C and E, planar transitions through msA/B and D, and unidirectional transition components. Several transition components were potentially significant predictors of age group. These features were nearly replicated in independent data, indicating their robustness in characterizing age-related electrophysiological spatiotemporal dynamics.
Evolutionary Co-Option of an Ancestral Cloacal Regulatory Landscape During the Emergence of Digits and Genitals
Authors: Hintermann Aurélie , Bolt Christopher Chase , Brent Hawkins M. , Valentin Guillaume , Lopez-Delisle Lucille , Gitto Sandra , Gómez Paula Barrera , Mascrez Bénédicte , Mansour Thomas A. , Nakamura Tetsuya , Harris Matthew P. , Shubin Neil H. , Duboule Denis 
Published: March 2024

SUMMARYThe transition from fins to limbs has been a rich source of discussion for more than a century. One open and important issue is understanding how the mechanisms that pattern digits arose during vertebrate evolution. In this context, the analysis ofHoxgene expression and functions to infer evolutionary scenarios has been a productive approach to explain the changes in organ formation, particularly in limbs. In tetrapods, the transcription ofHoxdgenes in developing digits depends on a well-characterized set of enhancers forming a large regulatory landscape1,2. This control system has a syntenic counterpart in zebrafish, even though they lackbona fidedigits, suggestive of deep homology3between distal fin and limb developmental mechanisms. We tested the global function of this landscape to assess ancestry and source of limb and fin variation. In contrast to results in mice, we show here that the deletion of the homologous control region in zebrafish has a limited effect on the transcriptionof hoxdgenes during fin development. However, it fully abrogateshoxdexpression within the developing cloaca, an ancestral structure related to the mammalian urogenital sinus. We show that similar to the limb,Hoxdgene function in the urogenital sinus of the mouse also depends on enhancers located in this same genomic domain. Thus, we conclude that the current regulation underlyingHoxdgene expression in distal limbs was co-opted in tetrapods from a preexisting cloacal program. The orthologous chromatin domain in fishes may illustrate a rudimentary or partial step in this evolutionary co-option.
Aging-associated weakening of the action potential in fast-spiking interneurons in the human neocortex
Authors: Szegedi Viktor , Tiszlavicz Ádám , Furdan Szabina , Douida Abdennour , Bakos Emoke , Barzo Pal , Tamas Gabor , Szucs Attila , Lamsa Karri 
Published: March 2024

ABSTRACTAging is associated with the slowdown of neuronal processing and cognitive performance in the brain; however, the exact cellular mechanisms behind this deterioration in humans are poorly elucidated. Recordings in human acute brain slices prepared from tissue resected during brain surgery enable the investigation of neuronal changes with age. Although neocortical fast-spiking cells are widely implicated in neuronal network activities underlying cognitive processes, they are vulnerable to neurodegeneration. Herein, we analyzed the electrical properties of 147 fast-spiking interneurons in neocortex samples resected in brain surgery from 106 patients aged 11–84 years. By studying the electrophysiological features of action potentials and passive membrane properties, we report that action potential overshoot significantly decreases and spike half-width increases with age. Moreover, the action potential maximum-rise speed (but not the repolarization speed or the afterhyperpolarization amplitude) significantly changed with age, suggesting a particular weakening of the sodium channel current generated in the soma. Cell passive membrane properties measured as the input resistance, membrane time constant, and cell capacitance remained unaffected by senescence. Thus, we conclude that the action potential in fast-spiking interneurons shows a significant weakening in the human neocortex with age. This may contribute to the deterioration of cortical functions by aging.
Approach to standardized material characterization of the human lumbopelvic system – Testing and evaluation
Authors: Gebhardt Marc , Kurz Sascha , Grundmann Fanny , Klink Thomas , Slowik Volker , Heyde Christoph-Eckhard , Steinke Hanno 
Published: March 2024

AbstractThe osseo-ligamentous lumbopelvic complex is a crucial component of the human musculoskeletal system and has been increasingly the focus of medical research and treatment planning. Numerical simulations can play a key role in better understanding the load-carrying behavior of this system, but material data in this arena remain rare. In addition, the literature lacks standardized and reproducible methods for determining biomechanical material parameters.To address these shortcomings, we obtained bone and soft tissue samples from three female and two male cadavers (average age: 77.3 years) for testing and evaluation. The elastic modulus of cortical bone averaged at 1750 MPa with a mean ultimate strength of 28.2 MPa. Whereas for trabecular bone the evaluation yields to 32.7 MPa and 1.26 MPa. Furthermore, the soft tissue specimens exhibited a mean elastic modulus of 148 MPa and an ultimate strength of 14.3 MPa for fascial tissue, in contrast to ligamentous tissue with 103 MPa and 10.7 MPa.Knowledge of these material parameters of the human pelvis, which differ from those of long bones, could, in combination with the revealed dependence on harvesting location and density, lead to more precise mechanical simulations. Such simulations might in turn promote the development of better suited implants.Together with a previous publication dealing with sample preparation, this work is intended to contribute to the standardization of mechanical testing of human tissue. Easy-to-conduct bending tests as well as direct tension and compression tests are recommended, and the proposed mechanical boundary conditions are explained and documented. These technical recommendations allow for better comparability and reproducibility in future biomechanical studies. This protocol, developed for the human pelvis, could easily be transferred to other anatomical regions.
A hybrid simulation-based workshop improves knowledge and confidence in the management of hemorrhagic conversion of stroke among interventional neurology trainees
Authors: Pergakis Melissa B. , Misra Asit , Al-Mufti Fawaz , Motola Ivette , Morris Nicholas A. 
Published: March 2024

AbstractObjectivesTo assess the feasibility of a hybrid simulation-based workshop at a national meeting for interventional neurology trainees focused on the management of acute ischemic stroke and tissue-plasminogen activator (tPA)-related hemorrhage.MethodsIn this prospective, observational, hybrid simulation-based study at a fellows’ workshop at a national conference, participants were asked to manage a patient with acute ischemic stroke in the neurointerventional suite followed by thrombolytic-related hemorrhage leading to cerebral herniation during mechanical thrombectomy. We evaluated the participants’ ability to complete critical actions that were developed based on best practices and relevant American Heart Association guidelines and the Neurocritical Care Society’s Emergency Neurological Life Support protocols. The primary outcome was the improvement in knowledge from a pre-course to post-course test. Secondary outcomes included participant reactions.ResultsSixty trainees completed the simulation session in 8 groups. The mean sum of critical actions completed by trainees was 9.75/14 (70%). There was a moderate effect of the intervention on trainees’ knowledge from pre-test (mean 3.8, standard deviation (SD) = 0.3) to post-test (mean 4.3, SD=0.3). The simulation scenario was described as moderately realistic, very engaging, and extremely satisfactory. Following the workshop, all fellows endorsed an increase in proficiency and confidence in neurological emergency management.ConclusionsSimulation-based workshops at national conferences are feasible and a potentially useful tool for safely educating a large audience of trainees who may not have access to high-fidelity simulation platforms at their institutions.