bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epihiper—A high performance computational modeling framework to support epidemic science
Authors: Chen Jiangzhuo , Hoops Stefan , Mortveit Henning S , Lewis Bryan L , Machi Dustin , Bhattacharya Parantapa , Venkatramanan Srinivasan , Wilson Mandy L , Barrett Chris L , Marathe Madhav V 
Published: December 2024

Abstract
This paper describes Epihiper, a state-of-the-art, high performance computational modeling framework for epidemic science. The Epihiper modeling framework supports custom disease models, and can simulate epidemics over dynamic, large-scale networks while supporting modulation of the epidemic evolution through a set of user-programmable interventions. The nodes and edges of the social-contact network have customizable sets of static and dynamic attributes which allow the user to specify intervention target sets at a very fine-grained level; these also permit the network to be updated in response to nonpharmaceutical interventions, such as school closures. The execution of interventions is governed by trigger conditions, which are Boolean expressions formed using any of Epihiper’s primitives (e.g. the current time, transmissibility) and user-defined sets (e.g. people with work activities). Rich expressiveness, extensibility, and high-performance computing responsiveness were central design goals to ensure that the framework could effectively target realistic scenarios at the scale and detail required to support the large computational designs needed by state and federal public health policymakers in their efforts to plan and respond in the event of epidemics. The modeling framework has been used to support the CDC Scenario Modeling Hub for COVID-19 response, and was a part of a hybrid high-performance cloud system that was nominated as a finalist for the 2021 ACM Gordon Bell Special Prize for high performance computing-based COVID-19 Research.
In silico prediction of pathogen's pandemic potential using the viral trait assessment for pandemics (ViTAP) model
Authors: Jones Charles H , Beitelshees Marie , Williams B Adam , Hill Andrew B , Welch Verna L , True Jane M 
Published: December 2024

Abstract
Our world is ever evolving and interconnected, creating constant opportunities for disease outbreaks and pandemics to occur, making pandemic preparedness and pathogen management crucial for global health security. Early pathogen identification and intervention play a key role in mitigating the impacts of disease outbreaks. In this perspective, we present the Viral Trait Assessment for Pandemics (ViTAP) model to aid in the early identification of high-risk viruses that have pandemic potential, which incorporates lessons from past pandemics, including which key viral characteristics are important such as genetic makeup, transmission modes, mutation rates, and symptom severity. This model serves as the foundation for the development of powerful, quantitative tools for the early prediction of pandemic pathogens. The use of such a tool, in conjunction with other pandemic preparedness measures, can allow for early intervention and containment of the virus. This proactive approach could enable timely interventions, guiding public health responses, and resource allocation to prevent widespread outbreaks and mitigate the impact of emerging pathogens.
Assessing the utility of a virtual reality arson crime scene investigation simulation
Authors: Halford Eric , Keningale Paige , Taleb Hussain AlShaima , Condon Camie 
Published: December 2024

Abstract
This study examines the utility of a virtual reality (VR) arson crime scene investigation simulation developed by the Abu Dhabi Police service. Utilizing qualitative interviews with participants from the Saif Bin Zayed Academy for Security and Policing Sciences, the study captures views of the VR training experience with an emphasis on learning effectiveness, engagement, skill acquisition, cost and time efficiency, and inclusivity and accessibility. The findings are discussed in the context of a theoretical framework provided by the technology acceptance model (TAM) and indicate high levels of engagement and immersion among the participants. Many expressed a preference for VR training over classroom training. Thus, the ‘perceived usefulness’ of the technology was high. The interviewees also reported significant perceived benefits in terms of acquiring procedural knowledge and skills. The immersive nature of the VR was identified as a key factor in its utility. The cost and time efficiencies driven by the capability to train multiple officers simultaneously without the need for physical resources and with fewer of the risks commonly associated with live training are also outlined. The study also identified limitations regarding the inclusivity and accessibility of the technology, including among individuals with disabilities. Nevertheless, the overall reception of the simulation was positive. The findings indicate that VR is widely accepted within the police service and has great potential for wider use to enhance training in other areas if it serves to deliver content focused on policies and practice.
Resolving velocity distribution function parameters from observations with significant Poisson statistical uncertainty
Authors: Nicolaou G , Livadiotis G , Sarlis N , Ioannou C 
Published: December 2024

ABSTRACT
Several analyses of particle observations aim to determine the distribution functions of physical parameters that characterize observed systems. Some standard analysis methods determine these distributions by fitting mathematical models to the data. The accuracy of the fitting techniques depends on the treatment of the observations and their uncertainties. Here, we evaluate the performance of three fitting techniques by applying them to simulated electron observations, which are governed by the Poisson distribution. We specifically examine and quantify the accuracy of two standard chi-squared minimization techniques and a maximum-likelihood method. The chi-squared minimization techniques simplify the analysis by treating the measurement uncertainties as Gaussian errors. Although such a simplification reduces the complexity of the calculations in some occasions, it may lead to systematic errors in the determined parameters. On the other hand, the maximum-likelihood method considers the exact Poisson probability for each data-point and returns accurate parameters for all the examples we examine here. We highlight the importance of using the appropriate method when the observations are accompanied by significant statistical uncertainty. Nevertheless, the methods we examine here, converge to the same answer as the statistical uncertainty of the observations reduces.
Bark water vapor conductance varies among temperate forest tree species and is affected by flooding and stem bending
Authors: Zhou Yinuo , Rosseau Grace , Dao Viet , Wolfe Brett T 
Published: December 2024

Abstract
Bark water vapor conductance (gbark) modulates forest transpiration during droughts, when leaf transpiration is highly reduced. If disturbances such as windstorms and floods impact gbark, they could affect tree performance during subsequent droughts. Bark traits, particularly lenticel traits, likely drive variation in gbark and may influence the effects of disturbances on gbark. We assessed variation in gbark and bark traits in tree branches of 15 tree species in a temperate forest in Louisiana, USA, and performed experiments to test whether gbark in tree branches was affected by bending (simulating wind) and whether gbark of tree saplings was affected by soil flooding. Among tree species, mean branch gbark ranged from 2.22 to 12.02 mmol m−2 s−1. Stem bending increased gbark by 23% compared with unbent controls. Although gbark was unaffected by 38 days of flooding, after 69 days post-flood it was reduced by 41% compared with unflooded controls. The relationships between gbark and bark traits, including bark thickness, lenticel density and lenticel size, were inconsistent across the survey and experiments. Together, these results show that gbark is variable among species and mutable. Uncovering the drivers of gbark variation within and among trees, including exposure to extreme weather events, will inform projections of forest dynamics under climate change.
Contrasting the soil–plant hydraulics of beech and spruce by linking root water uptake to transpiration dynamics
Authors: Martinetti Stefano , Molnar Peter , Carminati Andrea , Floriancic Marius G 
Published: December 2024

Abstract
Tree water status is mainly determined by the amount of water taken up from roots and lost through leaves by transpiration. Variations in transpiration and stomatal conductance are often related to atmospheric conditions and leaf water potential. Yet, few experimental datasets exist that enable to relate leaf water potential, transpiration dynamics and temporal variation of root water uptake from different depths during soil drying. Here we explored the soil–plant hydraulic system using field measurements of water potentials and fluxes in soils, roots, stems and leaves of beech (Fagus sylvatica) and spruce (Picea abies) trees. Spruce maintained less negative water potentials than beech during soil drying, reflecting a more stringent stomatal control. While root water uptake depths were similar between species, water potentials in plant tissues of spruce were rather constant and less correlated across roots and the stem, possibly because of large water storage and hydraulic capacitance in these tissues. Root water uptake from deep soil layers increased during dry periods, particularly for beech. Our data suggest that species-specific root hydraulic conductance, capacitance and water uptake strategy are linked and affect transpiration dynamics. Thus, it is important to include such species-specific hydraulics when predicting transpiration rates based on plant water status.
Symbiotic nitrogen fixation in trees: patterns, controls and ecosystem consequences
Authors: Taylor Benton N 
Published: December 2024

Abstract
Symbiotic nitrogen fixation (SNF) represents the largest natural input of bioavailable nitrogen into the biosphere, impacting key processes spanning from local community dynamics to global patterns of nutrient limitation and primary productivity. While research on SNF historically focused largely on herbaceous and agricultural species, the past two decades have seen major advances in our understanding of SNF by tree species in forest and savanna communities. This has included important developments in the mathematical theory of SNF in forest ecosystems, experimental work on the regulators of tree SNF, broad observational analyses of tree N-fixer abundance patterns and increasingly process-based incorporation of tree SNF into ecosystem models. This review synthesizes recent work on the local and global patterns, environmental drivers and community and ecosystem effects of nitrogen-fixing trees in natural ecosystems. By better understanding the drivers and consequences of SNF in forests, this review aims to shed light on the future of this critical process and its role in forest functioning under changing climate, nutrient cycling and land use.
Impact of Masking Academic Metrics on Enrolling a Broadly Diverse and Mission-Aligned Student Body
Authors: Harrison Leila E. , Nandagopal Radha , Garcia David , Tomkowiak John 
Published: December 2024

Abstract

Problem
The June 2023 U.S. Supreme Court decision overturning affirmative action required medical schools to discontinue considering race/ethnicity in admissions decisions. Medical schools must now identify different strategies if they aim to recruit and admit applicants from groups underrepresented in medicine (URiM; race/ethnicity), as enrolling broadly diverse students remains critical for serving the U.S. population.

Approach
Washington State University Elson S. Floyd College of Medicine (established in 2015) has an admissions process that assesses academic metrics using national threshold combinations of undergraduate grade point averages (UGPAs) and Medical College Admission Test (MCAT) scores (published on school’s website), and legal residency in or ties to Washington state, as prescreening criteria for secondary applications. UGPAs and MCAT scores are then masked from further consideration, allowing for decisions to be made with a focus on mission-aligned criteria, such as certain personal attributes and lived experiences and coming from specific environments (i.e., educationally or socioeconomically disadvantaged backgrounds, rural communities, military service, or a member of a federally recognized Tribe).

Outcomes
In the last 5 admissions cycles (enrollment years 2018–2022), cohort data demonstrate that as the admissions funnel narrows and each subsequent pool is smaller than the preceding one, the representation of mission-aligned applicants increases, despite the masking of academic metrics. The most recently enrolled class (enrollment year 2022) of 80 had 14 (17.5%) URiM students, closely mirroring the state’s general population. The overall yield (acceptance/matriculation) has steadily improved with the last 2 cycles to 1.68:1 and 1.65:1, indicating slightly more than 1.5 times the number of offers needed to fill the class are being made.

Next Steps
Next steps include further refining the process by considering more granular data on applicants’ childhood community characteristics and rural background and examining how admissions data may correlate with residency and practice location and communities served.
Intraoperative Hyperspectral Imaging Predicts Early Allograft Dysfunction and Overall Survival in Liver Transplantation
Authors: Lederer Andri , Alina Geisler Antonia , Sucher Robert , Seehofer Daniel , Hau Hans-Michael , Scheuermann Uwe , Rademacher Sebastian 
Published: December 2024

Objective:
This study explored the novel application of hyperspectral imaging (HSI) for in vivo allograft perfusion assessment during liver transplantation (LT) and its potential value for predicting early allograft dysfunction (EAD), graft, and overall survival (OS).

Background:
LT is a well-established therapy for acute and chronic liver diseases, with excellent outcomes. However, a significant proportion of recipients experience EAD, which affects graft and OS. EAD is associated with ischemia-reperfusion injury. HSI is a noninvasive imaging modality that provides information on tissue characteristics, such as tissue hemoglobin, water index, oxygenation, and perfusion.

Methods:
We included all patients who underwent orthotopic LT with full-size allografts between 2019 and 2021. HSI was performed 15 minutes after reperfusion of the donor liver and subsequently analyzed. Furthermore, we collected data on postoperative graft function and clinical outcomes.

Results:
A total of 73 LT recipients were included in this study. Around 56.9% had expanded criteria donors (N = 41). The mean model for end-stage liver disease score was 22 (±10). Eighteen patients (25%) had EAD. The statistical analysis demonstrated that recipients with EAD had significantly lower near-infrared (NIR) perfusion values after reperfusion. Recipients with low NIR had more pronounced reperfusion injury in postoperative laboratory studies. OS was significantly lower in recipients with low NIR than in those with high NIR (P = 0.049).

Conclusions:
HSI is a promising, noninvasive tool, offering real-time, detailed graft perfusion assessment during LT. The fusion of spatial and spectral information is unique to HSI, making it an essential imaging technology for the further development of AI applications in surgery.
Through the Pupils’ Lens: Multilingual Effort in First and Second Language Listening
Authors: Bsharat-Maalouf Dana , Schmidtke Jens , Degani Tamar , Karawani Hanin 
Published: December 2024

Objectives:
The present study aimed to examine the involvement of listening effort among multilinguals in their first (L1) and second (L2) languages in quiet and noisy listening conditions and investigate how the presence of a constraining context within sentences influences listening effort.

Design:
A group of 46 young adult Arabic (L1)–Hebrew (L2) multilinguals participated in a listening task. This task aimed to assess participants’ perceptual performance and the effort they exert (as measured through pupillometry) while listening to single words and sentences presented in their L1 and L2, in quiet and noisy environments (signal to noise ratio = 0 dB).

Results:
Listening in quiet was easier than in noise, supported by both perceptual and pupillometry results. Perceptually, multilinguals performed similarly and reached ceiling levels in both languages in quiet. However, under noisy conditions, perceptual accuracy was significantly lower in L2, especially when processing sentences. Critically, pupil dilation was larger and more prolonged when listening to L2 than L1 stimuli. This difference was observed even in the quiet condition. Contextual support resulted in better perceptual performance of high-predictability sentences compared with low-predictability sentences, but only in L1 under noisy conditions. In L2, pupillometry showed increased effort when listening to high-predictability sentences compared with low-predictability sentences, but this increased effort did not lead to better understanding. In fact, in noise, speech perception was lower in high-predictability L2 sentences compared with low-predictability ones.

Conclusions:
The findings underscore the importance of examining listening effort in multilingual speech processing and suggest that increased effort may be present in multilingual’s L2 within clinical and educational settings.
Prognostic Factors Associated With Intracranial Hemorrhage and Ischemic Stroke During Venovenous Extracorporeal Membrane Oxygenation: A Systematic Review
Authors: Thiara Sonny , Willms Alexander J. , Tran Alexandre , Mitra Anish R. , Sekhon Mypinder , Hoiland Ryan , Griesdale Donald 
Published: December 2024

OBJECTIVES:
Venovenous extracorporeal membrane oxygenation (ECMO) is a life-preserving intervention for patients with respiratory failure refractory to conventional mechanical ventilation. Intracranial hemorrhage (ICH) and ischemic stroke are life-threatening complications associated with venovenous ECMO. Despite this, little is known regarding the prognostic factors associated with these adverse neurologic events. We conducted a systematic review that characterizes these predictors of ICH and ischemic stroke during venovenous ECMO.

DATA SOURCES:
We conducted a comprehensive search of MEDLINE and Embase via the Ovid interface.

STUDY SELECTION:
We developed and performed a literature search to identify articles that evaluated ICH and ischemic stroke in adult patients undergoing venovenous ECMO. We excluded studies based on design, target population, and outcomes.

DATA EXTRACTION:
Data were extracted manually by one reviewer. Risk of bias assessment was completed using the Quality in Prognostic Studies approach for each included study. Prognostic factors associated with ICH and ischemic stroke that were identified in two or more included studies were evaluated through the Grading of Recommendations, Assessment, Development, and Evaluation approach.

DATA SYNTHESIS:
Three hundred thirty-three studies met criteria for screening. Seventeen studies met final inclusion criteria. Seventeen studies addressed predictors of ICH. Five studies demonstrated an increased risk of ICH with lower pH before venovenous ECMO (moderate certainty). Five studies demonstrated an increased risk of ICH with greater decreases in Paco
2 pre- to post-venovenous ECMO cannulation (moderate certainty). Four studies addressed predictors of ischemic stroke; however, there were no predictors of ischemic stroke identified in two or more of the included studies.

CONCLUSIONS:
This systematic review demonstrates that abnormalities and changes in blood gas parameters from pre- to post-venovenous ECMO cannulation are probably associated with increased risk of ICH. Additional high-quality studies dedicated to probable predictors of these adverse neurologic events are crucial to understanding the pathophysiology of ICH and ischemic stroke in this population and informing clinical practice to mitigate the risk of these life-threatening events.
Malignant Phyllodes Tumor of the Breast With Multiple Cutaneous Metastasis Resembling Pleomorphic Rhabdomyosarcoma
Authors: Zieba Denise , Pories Susan , Thota Hima Bindu , Suster David I. 
Published: December 2024

Abstract:
Malignant phyllodes tumor (PT) of the breast is a rare fibroepithelial neoplasm that shows variegated histomorphology and an aggressive clinical course. Cutaneous metastases are rare. A 68 year old woman presented with a palpable left breast mass identified on a routine breast exam. Mammogram showed an oval circumscribed heterogeneous mass measuring 3.7 × 3.7 × 2.7 cm. Patient underwent core needle biopsy with subsequent excision and received a diagnosis of malignant phyllodes tumor with rhabdomyosarcomatous elements with negative margins. The patient suffered a local recurrence 5 months later and was scheduled for re- excision; however prior to that procedure the patient represented to clinic with several cutaneous and subcutaneous nodules located on the left flank, left arm, and bilateral buttocks; described as itchy but not painful. Biopsies of the left flank and the left arm were performed and pathologic examination of both biopsies demonstrated a high- grade rhabdomyoblastic neoplasm that closely resembled so-called pleomorphic rhabdomyosarcoma. The tumor cells in both biopsies marked for immunohistochemical markers of rhabdomyoblastic differentiation and re-review of the original resection specimen showed identical areas confirming the skin and subcutaneous nodules as metastatic malignant phyllodes tumor. We report an unusual case of malignant PT with cutaneous metastases that demonstrated a pure rhabdomyosarcoma phenotype with pleomorphic morphology. Awareness that malignant PT may rarely involve cutaneous sites and present with a pure rhabdomyosarcomatous morphology is important for proper recognition and diagnosis of these tumors, as out of context they may be confused with sarcomas.
Differential Expression of p53 in Mycosis Fungoides, Sezary Syndromes, and Their Transformed Forms
Authors: Courtois Anna , Allaume Pierre , Raby Maxime , Pastoret Cédric , Droitcourt Catherine , Le Naourès Cécile , Adamski Henri , Dupuy Alain , Le Gall François , Kammerer-Jacquet Solène-Florence 
Published: December 2024

Abstract:
Mycosis fungoides (MF) and Sezary syndrome (SS) are common entities among primary cutaneous lymphomas. Large cell transformation is challenging for diagnosis and therapy. Molecular mechanisms by which these lymphomas undergo this transformation are poorly defined. We studied the immunohistochemical status of p53 in these entities and assessed whether p53 expression could be a useful tool for diagnosis and assessment of transformation. We extracted patients with transformed and untransformed SS or MF from the French Study Group on Cutaneous Lymphoma database between 2014 and 2021, followed in the Rennes University Hospital. An immunohistochemical study of p53 expression was performed on the biopsies sampled as part of routine care. We compared p53 overexpression in the different groups. We included 25 patients with MF, 7 patients with transformed MF (T-MF), 11 patients with SS, and 5 patients with transformed SS (T-SS). Using a cut-off set at 30% expression of neoplastic cells, we noted an overexpression of p53 in T-MF and T-SS compared with nontransformed forms (47% vs. 12%, respectively, P < 0.01) and in MF compared with SS (23% vs. 7%, respectively, P < 0.01). Overexpression of p53 with a cut-off at 30% therefore seems to be a discriminating tool in the differential diagnosis of MF/SS versus their transformed forms as well as the differential diagnosis between MF and SS.