bluuebunny/crossref_metadata_2025_split huggingface dataset:
A data-driven sensitivity analysis of maize stalk models reveals the dominant factors influencing stalk strength
Authors: Carter Joseph , Hall Ryan , Cook Douglas D 
Published: February 2025

Abstract
Morphological factors significantly impact maize stalk strength, but no study has fully characterized the impact of maize stalk shape on stalk strength. This study uses a data-driven and machine-learning modeling approach to characterize these relationships through a comprehensive sensitivity analysis of model inputs.
Using 3D parameterized maize stalk models gave a higher level of control than previous studies by adding more parameters, but with the increase of the dimensionality. The large dimensionality of the models was greatly reduced via principal component analysis (PCA). Analysis revealed that model flexural stiffness, failure strength, and biomass was primarily determined by the first principal component. Material sensitivity analysis was also conducted on the models, and its results were consistent with past studies.
The results of this study improve researchers' understanding of the parameters that influence 3D parameterized maize stalk models. Statistical analysis indicates a strong relationship between the first principal component and section modulus, which further validates the 3D parameterized maize stalk model. Results also show that maize stalk morphology is primarily controlled by only one factor: the first principal component. This may limit researchers’ ability to increase stalk strength without increasing mass.
Fc gamma receptors activate different protein kinase C isoforms in human neutrophils
Authors: Alemán Omar Rafael , Blanco-Camarillo Carlos , Naranjo-Pinto Nathalia , Mora Nancy , Rosales Carlos 
Published: February 2025

Abstract
Receptors for the Fc portion of IgG antibodies (FcγR) on human neutrophils constitute an important mechanism for recognition of opsonized microorganisms and for cell activation. Human neutrophils express two FcγR: FcγRIIa and FcγRIIIb. Previously, it has been reported that activation of each FcγR induces different neutrophil responses, by triggering distinct signal transduction pathways. Though, what particular signal transduction pathway is triggered by each FcγR has not been completely elucidated. It has also been reported that PKC is important for FcγR signaling, and that each FcγR may activate different PKC isoforms. Therefore, we explored whether FcγRIIa or FcγRIIIb activates different PKC isoforms in human neutrophils, and whether activation of these PKC isoforms results in different neutrophil responses. Hence, either FcγRIIa or FcγRIIIb was selectively cross-linked by monoclonal antibodies in the presence or absence of pharmacological inhibitors for various PKC isoforms. Inhibition of PKCα or PKCδ blocked FcγRIIa-induced reactive oxygen species (ROS) productions. In contrast, inhibition of PKCα and/or PKCβ blocked FcγRIIIb-induced ROS production. Also, inhibition of all PKC isoforms did not affect FcγRIIa-induced increase in intracellular calcium concentration ([Ca2+]i), while inhibition of PKCα blocked FcγRIIIb-induced increase in [Ca2+]i. Additionally, inhibition of PKCδ blocked FcγRIIa-induced ERK phosphorylation, while inhibition of PKCα prevented FcγRIIIb-induced ERK phosphorylation. These results suggest that both FcγRIIa and FcγRIIIb activate unique PKC isoforms, and that activation of these PKC isoforms can selectively regulate different neutrophil functions. These findings also reinforce the idea that each FcγR in human neutrophils triggers distinct signal transduction pathways.
Time-dependent models of AGN discs with radiation from embedded stellar-mass black holes
Authors: Epstein-Martin Marguerite , Tagawa Hiromichi , Haiman Zoltán , Perna Rosalba 
Published: February 2025

ABSTRACT
The brightest steady sources of radiation in the universe, active galactic nuclei (AGNs), are powered by gas accretion on to a central supermassive black hole (SMBH). The large sizes and accretion rates implicated in AGN accretion discs are expected to lead to gravitational instability and fragmentation, effectively cutting off mass inflow to the SMBH. Radiative feedback from disc-embedded stars has been invoked to yield marginally stable, steady-state solutions in the outer discs. Here, we examine the consequences of this star formation with a semi-analytical model in which stellar-mass black hole (sBH) remnants in the disc provide an additional source of stabilizing radiative feedback. Assuming star formation seeds the embedded sBH population, we model the time-evolving feedback from both stars and the growing population of accreting sBHs. We find that in the outer disc, the luminosity of the sBHs quickly dominates that of their parent stars. However, because sBHs consume less gas than stars to stabilize the disc, the presence of the sBHs enhances the mass flux to the inner disc. As a result, star formation persists over the lifetime of the AGN, damped in the outer disc, but amplified in a narrow ring in the inner disc. Heating from the embedded sBHs significantly modifies the disc’s temperature profile and hardens its spectral energy distribution, and direct emission from the sBHs adds a new hard X-ray component.
The complex relationship between black hole feedback, star formation, and stellar bars in TNG50
Authors: Frosst Matthew , Obreschkow Danail , Ludlow Aaron , Bottrell Connor , Genel Shy 
Published: February 2025

ABSTRACT
We use the cosmological magneto-hydrodynamical simulation TNG50 to study the relationship between black hole feedback, the presence of stellar bars, and star formation quenching in Milky Way-mass disc galaxies. Of our sample of 198 discs, 125 develop stellar bars that last until $z=0$. Tracking their evolution from $z=4$ to 0, we demonstrate that barred galaxies tend to form within dark matter haloes that become centrally disc dominated early on (and are thus unstable to bar formation) and typically host central black holes that grow more rapidly than those of unbarred galaxies. As a result, most barred galaxies eventually experience kinetic wind feedback that operates when the mass of the central supermassive black hole exceeds ${M_{\rm {BH}}} \gtrsim 10^8\, {\rm {\rm M}_{\odot }}$. This feedback ejects gas from the central disc and rapidly quenches barred galaxies of their central star formation, resulting in persistent 3–15 kpc wide holes in the centres of their gas discs; bar formation itself does not significantly affect the central star formation in this model. Interestingly, bars almost always form before gas holes, but if kinetic black hole feedback occurs in a previously unbarred galaxy, bars rarely form thereafter. Consequently, most barred galaxies develop gas holes from ejective black hole feedback, though a gas hole alone does not guarantee the presence of a stellar bar. This subtle relationship between black hole feedback, cold gas disc morphology, and stellar bars may provide constraints on subgrid physics models for supermassive black hole feedback.
Accretion disc reverberation mapping of the quasar 3C 273
Authors: Thorne James P , Landt Hermine , Huang Jiamu , Hernández Santisteban Juan V , Horne Keith , Cackett Edward M , Winkler Hartmut , Sanmartim David 
Published: February 2025

ABSTRACT
We present accretion disc size measurements for the well-known quasar 3C 273 using reverberation mapping performed on high-cadence light curves in seven optical filters collected with the Las Cumbres Observatory (LCO). Lag estimates obtained using Javelin and PyROA are consistent with each other and yield accretion disc sizes a factor of ${\sim} 2{\!-\!}7$ larger than ‘thin disc’ theoretical expectations. This makes 3C 273 one of a growing number of active galactic nuclei (AGN) to display the so-called ‘accretion disc size’ problem usually observed in low-luminosity AGN. Power-law fits of the form $\tau \propto \lambda ^{\beta }$ to the lag spectrum, and $\nu \, f_\nu \propto \nu ^\beta$ to the spectral energy distribution (SED) of the variations, both give results consistent with the ‘thin disc’ theoretical expectation of $\beta = 4/3$. The Starkey et al. ‘flat disc with a steep rim’ model can fit both the lag estimates and the SED variations. Extrapolating the observed optical lags to putative dust-forming regions of the disc gives $r\sim 100-200$  light-days. These radii are consistent with the size of the broad line region (BLR) as determined by near-infrared interferometric studies as well as with the best-fitting location of the outer edge for the ‘flat disc with a steep rim’ model. Therefore, the accretion disc in 3C 273 might be sufficiently extended to be dusty, allowing the BLR to emerge from it in a dusty outflow. A flux variation gradient analysis and the structure function of our LCO light curves confirm that the optical variability in 3C 273 is dominated by the accretion disc rather than its radio jet.
Validation of the Revised American Physical Therapy Association Physical Therapist Clinical Performance Instrument 3.0
Authors: Campbell Derrick F , Alameri Mansoor , Macahilig-Rice Felicity , Witkin Sean E , Hellman Nancy G 
Published: February 2025

Abstract

Importance
Validation of the revised American Physical Therapy Association (APTA) Physical Therapist Clinical Performance Instrument (PT CPI 3.0) is essential to ensure that we are effectively assessing Doctor of Physical Therapy (DPT) students’ clinical performance.

Objective
The purpose was to validate the revised PT CPI 3.0 for use with DPT students as a measure of clinical performance.

Design
A descriptive and exploratory combined cross-sectional retrospective and prospective cohort design was used.

Setting
University DPT students’ clinical education experiences were explored.

Participants
Participants were selected using a convenience sample of 693 DPT students from 1 US multi-campus DPT program(s) during Fall 2023 and Spring 2024 clinical education experiences.

Exposure(s)
DPT students on (1) integrated (ICE) and (2) 2 terminal clinical education experiences (TCE I and TCE II) participated in the study.

Main Outcome(s)
Clinical instructor (CI) PT CPI 3.0 item ratings of DPT students at midterm and final assessments during clinical education experiences were investigated.

Measure(s)
Descriptive and inferential statistics evaluated differences between CI PT CPI 3.0 item ratings of DPT students during clinical education experiences.

Results
The PT CPI 3.0 demonstrated good internal reliability, and factor analysis with a 1-factor solution explained 81.3% of variance. Construct validity was supported by significant differences in PT CPI item scores between DPT students on integrated (ICE) and each of 2 terminal clinical education experiences (TCE I and TCE II). Construct and convergent validity were supported by significant score increases from midterm to final assessments for DPT students on integrated and terminal clinical education experiences and by moderate to large correlations between prior clinical experiences and remaining didactic coursework.

Conclusions
Findings support validity of the revised PT CPI 3.0 as a measure of clinical performance. A limitation is that this study did not assess rater reliability.

Relevance
This study provides preliminary support for validation of the newly revised APTA PT CPI 3.0 as a measure to assess entry-level physical therapist student clinical performance.
Topological Analysis of Vascular Networks: A Proof-of-Concept Study in Cerebral Angiography
Authors: Tozzi Arturo 
Published: February 2025

ABSTRACTThe application of topological methods to cerebral angiography may provide a robust mathematical framework for analyzing cerebrovascular structures at multiple scales. In this proof-of concept study, we explored the use of algebraic and differential topology to characterize structural integrity, connectivity, flow dynamics and hierarchical organization of cerebral vascular networks. Through a hierarchical approach, we examined the topology from general to local, capturing macroscopic vascular organization down to individual vessel bifurcations. By leveraging key theorems, we assessed various aspects of topological analysis, including evaluation of total features, transition from total to local features, evaluation of local features, transition from local to total features, interaction between total and local features. These steps enable the analysis of the global connectivity of the vascular network, the detection of regional clusters and the identification of critical junctions at a local scale. A computational approach was developed to extract mathematical skeletons from angiographic images, constructing graph-based representations to study connectivity and homotopy equivalence. The Fourier decomposition of the vascular structures revealed dominant periodic patterns, indicative of structural stability and redundancy in the blood supply. Moreover, Betti number computations quantified vascular loops and branches, offering insights into collateral circulation potential. Our findings demonstrate that topological invariants can serve as diagnostic biomarkers for cerebrovascular diseases, including aneurysm susceptibility and ischemic risk assessment. This interdisciplinary methodology bridges mathematical topology with medical imaging, offering a novel lens for cerebrovascular analysis. Future work will integrate persistent homology and machine learning techniques for automated vascular topology classification.
Oxalotrophic bacteria in desert and drylands: Enzymatic pathways and Carbon sequestration
Authors: Prasanna Arun N. , Parween Sabiha , Froehlich Katja , Schmidt Tanja , Shekhawat Kirti , Prabhu Durga D. , Saad Maged M. , Hirt Heribert 
Published: February 2025

AbstractOxalotrophy refers to the ability of bacteria to utilize oxalate as a carbon and energy source. This is a critical process with significant implications for the global carbon cycle. Oxalate-degrading bacteria play a key role in carbon sequestration through the oxalate-carbonate pathway (OCP), contributing to stable inorganic carbon pools. In this study, we identified and cataloged 20 enzymes associated with various facets of oxalate metabolism to characterize the oxalotrophic potential of bacteria. Within this group, sets of enzymes were grouped into two functional categories in the context of carbon sequestration: a biomineralization toolkit for converting oxalate to inorganic carbon and an assimilation toolkit for incorporating oxalate into metabolic pathways such as amino acid biosynthesis and energy production. Using bioinformatic approaches, we analyzed a collection of 536 bacterial genomes from desert and dryland strains spanning 81 genera to identify oxalotrophs. To validate our findings, we tested several bacterial strains for growth on media supplemented with exogenous oxalate. Notably, while multiple bacterial strains grew on oxalate media, two Pseudomonas species, namely JZ043 and JZ097, failed to grow despite genomic predictions suggesting otherwise. Further investigation of these strains revealed several non-conservative amino acid substitutions in the glyoxylate carboligase enzyme (EC 4.1.1.47), a key player in oxalate metabolism, suggesting a potential link between these mutations and their inability to metabolize oxalate. Our findings highlight the significance of our approach for identifying oxalotrophic bacteria (OxB) and offer valuable insights into the molecular basis of oxalate metabolism.Graphical Abstract
How does methamphetamine affect the brain? A systematic review of magnetic resonance imaging studies
Authors: Liu GXH , Tayebi M , Bristow B , Wang J , Lin Y , Newburn G , Condron P , McHugh P , Schierding W , Holdsworth S , Scadeng M 
Published: February 2025

AbstractMethamphetamine (METH) is an addictive psychostimulant that is associated with significant physical and psychological harm. Magnetic resonance imaging (MRI) is a non-invasive and powerful imaging modality that can reveal structural and functional brain changes. We conducted a systematic review to identify and appraise the existing literature examining brain MRI changes associated with METH exposure. A comprehensive literature search was conducted on PubMed, Web of Science, and Scopus. Any study that used MRI to evaluate brain changes in people who used or had been exposed to METH using MRI were included. Data were collected on study design, participant demographics, METH use parameters, MRI acquisition details, and key findings. Quality appraisal was conducted using ana prioriquality appraisal tool. One hundred and thirty seven studies with 8313 participants were included in our review. Nearly all were conducted in adults/adolescents (121/137, 88%), and most studies were cross-sectional (107/137, 78%). Task-based functional MRI was the most common modality used (48/137, 35%), followed by structural MRI (38/137, 28%). Quality appraisal scores ranged from 40 – 100% (mean 88%). Overall, METH is associated with numerous adverse changes in brain structure and function, including reduced grey matter volume and thickness in frontal and limbic regions and decreased fractional anisotropy in various white matter structures, with associated socio-emotional dysregulation, impaired decision-making and learning processes, and cognitive deficits. Targeted, higher-order, or multi-modal MRI sequences may be useful in further clarifying the impact of METH on the brain and evaluating the use of potential therapeutic agents.
Statistical Analysis Plan for the manuscript reporting the primary outcome of the MSU-TELEMED study
Authors: Churilov Leonid , Johns Hannah , Yogendrakumar Vignan , Balabanski Anna ,   MSU-TELEMED Trial Investigators
Published: February 2025

AbstractThis manuscript describes the Statistical Analysis Plan (SAP) for the following study: Evaluating the Safety and Efficacy of Telemedicine Physician Assessments on a Mobile Stroke Unit: a Prospective Open-Label Blinded End-Point Randomized Controlled Trial (MSU-TELEMED)This document is a supplement to the MSU-TELEMED study protocol and contains the statistical analysis plan (SAP) for the main paper of the trial in which the primary outcome will be reported. This document complies with the guidelines for the content of statistical analysis plans in clinical trials
Calcium signaling is a universal carbon source signal transducer and effects an ionic memory of past carbon sources
Authors: Simpson-Lavy Kobi , Kupiec Martin 
Published: February 2025

SummaryGlucose is the preferred carbon source for most cells. However, cells may encounter other carbon sources that can be utilized. How cells match their metabolic gene expression to their carbon source, beyond a general glucose repressive system (catabolite repression), remains little understood. By studying the effect of up to seven different carbon sources on Snf1 phosphorylation and on the expression of downstream regulated genes, we searched for the mechanism that identifies carbon sources. We found that the glycolysis metabolites glucose-6-phosphate (G6P) and glucose-1-phosphate (G1P) play a central role in the adaptation of gene expression to different carbon sources. The ratio of G1P and G6P activates an analogue calcium signaling via the proton-exporter Pma1, to regulate downstream genes. The signaling pathway bifurcates with calcineurin reducingADH2(alcohol dehydrogenase) expression and with Cmk1 increasingZWF1(glucose-6-phosphate dehydrogenase) expression. Furthermore, calcium signaling is not only regulated by the present carbon source; it is also regulated by past carbon sources. We were able to manipulate thisionic memorymechanism to obtain high expression ofZWF1in media containing galactose. Our findings provide auniversalmechanism by which cells respond to all carbon sources.
Understanding preferences for self-sampling in a national cervical screening programme: a protocol for a discrete choice experiment
Authors: Thapa Shabnam , Davies Jennifer C. , Crosbie Emma J. , Payne Katherine , Wright Stuart J. 
Published: February 2025

ABSTRACTIntroductionThe NHS cervical screening programme (NHSCSP) currently involves a healthcare professional collecting a cervical sample in a healthcare setting. This method of screening has barriers associated with access to screening appointments, and the poor acceptability of the speculum examination. Primary screening through HPV testing has led to the development of self-sampling screening methods including vaginal and urine self-sampling, with many UK studies comparing these screening methods with the current NHSCSP. It is not known what features of self-sampling influence individual’s preferences and cervical screening uptake. To understand these preferences, we plan to undertake a discrete choice experiment (DCE). This protocol aims to describe the steps taken to design the DCE and the proposed approach to fielding the DCE to identify preferences for different sampling approaches in cervical screening.Methods and analysisAn online survey comprising a DCE was designed to understand preferences of individuals for self-sampling methods within the NHSCSP. Attributes and levels for the DCE were generated through an iterative process including a literature review of qualitative studies about self-sampling cervical screening methods, input from cervical screening clinical experts and a patient and public involvement group (n=6). A D-efficient design was used to create choice sets for the DCE survey. Regression based analysis will be used to estimate the impact of each attribute and level on individual choices.Ethics and disseminationThis study has been approved by The University of Manchester Proportionate Research Ethics Committee (2024-20767-37669). The results of the DCE will be submitted for publication in a relevant peer review journal and the results will be presented at national and international conferences.STRENGTHS AND LIMITATIONS OF THIS STUDYTo our knowledge, this study will be the first to quantify stated preferences for self-sampling methods within a CSP focusing on all individuals who are eligible for screening in the UK.The attributes and levels will be selected based on previous qualitative work as well as from multiple discussions with relevant stakeholders, including clinicians and public contributors.The results will contribute towards understanding what aspects of self-sampling methods within a CSP are important for the target population.Since the survey will only be available online, there is a potential to miss individuals without technological access and literacy.