bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new model for the extragalactic radio sky at low frequency calibrated using the LOFAR Two-metre Survey
Authors: Lin Jinyang , Zhu Zhenghao , Ma Renyi , Bonaldi Anna , Shan Huanyuan 
Published: November 2024

ABSTRACT
Building the radio sky template are crucial for detecting the 21 cm emission line signal from the epoch of reionization, as well as for other cosmological research endeavours. Utilizing data from the LOFAR Two-meter Sky Survey at 150 MHz, we recalibrated the luminosity function for various types of radio sources, including high excitation radio galaxies, low excitation radio galaxies, radio-quiet active galactic nuclei, and star-forming galaxies. We subsequently updated the Tiered Radio Extragalactic Continuum Simulation (T-RECS) code to generate refined mock radio source catalogues. The simulated source counts from this work align more closely with observed data at redshifts greater than $z\gt 4$. Additionally, the differential source counts in total intensity within the flux density range of $0.1-1~\mathrm{mJy}$ closely mirror actual observations. Due to our model incorporating a lower number of faint sources compared to T-RECS, it predicts a reduced power spectrum for point sources, suggesting a potential advantage in studies in low frequency band.
Adjunctive Use of Gabapentinoids Increases Opioid Consumption Following 1- to 3-Level Anterior Lumbar Interbody Fusion with Posterior Fixation
Authors: Tao Xu , Kaghazchi Aydin , Shukla Geet , Karnati Janesh , Wu Andrew , Shankar Sachin , Ashraf Ahmed , Ranganathan Sruthi , Garcia-Vargas Julia , Barve Parikshit , Childress Kelly , Adogwa Owoicho 
Published: November 2024

Study Design.
Retrospective cohort.

Objective.
To evaluate the impact of adjunctive gabapentinoid therapy on postoperative opioid consumption following 1-3 levels anterior lumbar interbody fusion (ALIF) with posterior fixation.

Summary of Background Data.
Gabapentin and pregabalin are analogues of the inhibitory neurotransmitter Gamma-Aminobutyric Acid (GABA) and are frequently employed as adjuncts in multimodal anesthesia strategies for managing acute pain. However, the opioid-sparing effect of gabapentinoids in the context of spine surgery has yet to be consistently demonstrated.

Methods.
The PearlDiver Database was queried from 2010 to 2021 for patients who underwent primary 1-3 levels ALIF with posterior fixation. Patients with opioid or gabapentinoid use within 6 months prior to index surgery were excluded. Patients with both gabapentinoid and opioid treatment were propensity score-matched to patients with opioid-only treatment.

Results.
The propensity score-matching resulted in two equal groups of 2,617 patients with and without adjunctive gabapentinoid treatment for pain management. Adjunctive use of gabapentinoids was associated with a modest 2.9% reduction in average Morphine Milligram Equivalent (MME) per day (Standardized Mean Difference (SMD) −1.33, 95% Confidence Interval (CI) [−2.657, −0.002], P=0.050). However, this was accompanied by a 37.1% increase in the total duration of opioid prescriptions (SMD 94.97, 95% CI [56.976, 132.967], P<0.001) and a 41.7% increase in total MME consumption per patient (SMD 4817.23, 95% CI [1864.410, 7770.044], P=0.001). Additionally, gabapentinoid use was associated with an increased risk of readmission due to pain (Relative Risk (RR) 1.10, 95% CI [1.002, 1.212], P=0.050) and the development of drug abuse (RR 1.37, 95% CI [1.016, 1.833], P=0.046).

Conclusion.
Despite the modest daily opioid-sparing effect observed, adjunctive gabapentinoid treatment appears to increase total opioid consumption due to prolonged opioid use and may compromise pain management in the context of ALIF with posterior fixation.
Remaining Steadfast on Diversity and Inclusion in Plastic Surgery
Authors: Sommer Nicole Z. , Butler Paris D. 
Published: November 2024

Summary:
Organized plastic and reconstructive surgery has recognized the importance of diversity for optimal patient care and advancement of the specialty. Initial goals focused on increasing opportunities for underrepresented members of the society: women and Blacks and Hispanic/Latino members. The diversity lens has expanded to not only include race and sex but also diversity of religion, sexual orientation, gender identity, disability, geography, economic status, membership status, and employment type. In response to diversity antagonists who argue that diversity abandons a system based on “excellence,” we counter that diversity efforts demand excellence but realize that success often requires a more level playing field with the elimination of discriminatory barriers.
Real-world Use of AlloDerm Acellular Dermal Matrix in Head and Neck Procedures in the United States
Authors: Dominguez Annaliza , Liang Yi , Abbed Turkia M. , Mukhatyar Vivek , Shimoga Sandhya 
Published: November 2024

Background:
Real-world literature evaluating the use of AlloDerm SELECT Regenerative Tissue Matrix in head- and neck-related procedures is limited. To inform patient care decisions, this study evaluated healthcare resource utilization (HCRU) in US adults undergoing head- and neck-related procedures using AlloDerm.

Methods:
A retrospective claims analysis was conducted using MarketScan Commercial and Medicare Supplemental Databases (study period: October 1, 2015, to March 31, 2022; index period: November 1, 2015, to March 1, 2022). Adults aged 18 years or older with (1) medical claims for AlloDerm and a skin substitute on the same day during the index period, (2) a head/neck procedure diagnostic code, and (3) 30 or more days of continuous enrollment before and after first AlloDerm use index date. Descriptive statistics were used to describe surgery types and 30-day follow-up reoperations, graft complications, and all-cause HCRU.

Results:
Among 431 patients (51.7% women), mean (SD) age was 52.2 (15.8) years. AlloDerm was most used with oral cavity reconstruction (35.3%), septal perforation repair/rhinoplasty (16.5%), and parotidectomy (13.0%). Most procedures were performed in outpatient settings (hospital, 90.0%; ambulatory surgical center, 8.6%). Over 30 days, less than 1% of patients (4 of 431) required reoperation with AlloDerm; 0.5% (2 of 431) had graft-related complications. Most (75.6%) patients had an outpatient visit; few had an emergency room visit (7.9%) or inpatient claim (3.0%).

Conclusions:
Real-world evidence indicates that AlloDerm is used in head- and neck-related procedures in US adults, particularly oral reconstruction. Postprocedure complications and reoperations are uncommon during the follow-up period.
Arginyltransferase1 drives a mitochondria-dependent program to induce cell death
Authors: Kumar Akhilesh , O’Shea Corin R. , Yadav Vikas K. , Kandasamy Ganapathi , Moorthy Balaji T. , Ambrose Evan A. , Mulati Aliya , Fontanesi Flavia , Zhang Fangliang 
Published: November 2024

AbstractCell death regulation is essential for stress adaptation and/or signal response. Past studies have shown that eukaryotic cell death is mediated by an evolutionarily conserved enzyme, arginyltransferase1 (Ate1). The downregulation of Ate1, as seen in many types of cancer, prominently increases cellular tolerance to a variety of stressing conditions. Conversely, in yeast and mammalian cells, Ate1 is elevated under acute oxidative stress conditions and this change appears to be essential for triggering cell death. However, studies of Ate1 were conventionally focused on its function in inducing protein degradation via the N-end rule pathway in the cytosol, leading to an incomplete understanding of the role of Ate1 in cell death. Our recent investigation shows that Ate1 dually exists in the cytosol and mitochondria, the latter of which has an established role in cell death initiation. Here, by using budding yeast as a model organism, we found that mitochondrial translocation of Ate1 is promoted by the presence of oxidative stressors and is essential for inducing cell death with characteristics of apoptosis. Also, we found that Ate1-induced cell death is dependent on the formation of the mitochondrial permeability pore and at least partly dependent on the action of mitochondria-contained factors including the apoptosis-inducing factor, but is not directly dependent on mitochondrial electron transport chain activity or its derived reactive oxygen species (ROS). Furthermore, our evidence suggests that, contrary to widespread assumptions, the cytosolic protein degradation pathways including ubiquitin-proteasome, autophagy, or endoplasmic reticulum (ER) stress response has little or negligible impacts on Ate1-induced cell death. We conclude that Ate1 controls the mitochondria-dependent cell death pathway.
Heat shock factor 2 positively regulates oncogenic herpesvirus gene expression by remodeling the chromatin landscape
Authors: Cutrone Lorenza , Djupenström Hedvig , Peltonen Jasmin , Klimova Elena Martinez , Corso Simona , Giordano Silvia , Sistonen Lea , Gramolelli Silvia 
Published: November 2024

AbstractHuman gamma-herpesviruses, Kaposi’s sarcoma herpesvirus (KSHV) and Epstein-Barr virus (EBV) are causally associated to a wide range of cancers. While the default infection program for these viruses is latent, sporadic lytic reactivation supports virus dissemination and oncogenesis. Despite its relevance, the repertoire of host factors governing the transition from latent to lytic phase is not yet complete, leaving much of this complex process unresolved. Here, we show that heat shock factor 2 (HSF2), a transcription factor involved in regulation of acute stress responses and specific cell differentiation processes, promotes gamma-herpesvirus lytic gene expression. In lymphatic endothelial cells infected with KSHV and gastric cancer cells positive for EBV, ectopic HSF2 enhances the expression of lytic genes, while knocking down HSF2 significantly decreases their expression. Mechanistically, HSF2 overexpression results in decreased levels of repressive chromatin histone marks, at the promoters of the master regulators of the oncogenic lytic cascade, KSHV ORF50 and EBV BZLF1. Our results demonstrate that endogenous HSF2 binds to the ORF50 promoter in latent cells and sustains a transcriptionally permissive state. In contrast, in lytic cells, HSF2 occupancy at the ORF50 promoter is lost in conjunction with its proteasomal degradation. These findings establish HSF2 as a conserved regulator of gamma-herpesvirus lytic gene expression in latency and offer new functional insights on the cellular role of HSF2 at target promoters.
How to Predict Effective Drug Combinations - Moving beyond Synergy Scores
Authors: Eckhart Lea , Lenhof Kerstin , Herrmann Lutz , Rolli Lisa-Marie , Lenhof Hans-Peter 
Published: November 2024

AbstractTo improve our understanding of multi-drug therapies, cancer cell line panels screened with drug combinations are frequently studied using machine learning (ML). ML models trained on such data typically focus on predicting synergy scores, which support drug development and repurposing efforts but have limitations when deriving personalized treatment recommendations. To simulate a more realistic personalized treatment scenario, we pioneer ML models that predict the relative growth inhibition (instead of synergy scores), and that can be applied to previously unseen cell lines. Our approach is highly flexible: it enables the reconstruction of dose-response curves and matrices, as well as various measures of drug sensitivity (and synergy) from model predictions, which can finally even be used to derive cell line-specific prioritizations of both mono- and combination therapies.
Local High-Protein, Plant-Based Ready-to-Use Therapeutic Food Enhances Recovery from Malnutrition in Rats
Authors: Bechoff Aurélie , Akomo Peter , Muleya Molly , Tsaousis Anastasios D. , Nikolaou Charoula Konstantia , Utume Laura , Schneider Aviv , Khalaf Mona , Reifen Ram , Monsonego-Ornan Efrat 
Published: November 2024

AbstractInfant child malnutrition is a major public health issue. We conducted a preclinical study with young rats to mimic the conditions of child malnutrition (combined wasting and stunting) and evaluate recovery using a novel plant-based ready-to-use-therapeutic food (RUTF) formulation.Three-week old female Sprague Dawley rats were assigned to six treatments groups in a 6-week experiment. The treatments included: 1) control balanced diet (CT), 2) A protein-deficient diet to induce malnutrition (MN), 3) and 4) A control balanced diet followed by either commercial RUTF (CT-PM) or a locally produced plant-based RUTF (CT-ChSMS), and 5) and 6) a protein deficient diet followed by either commercial RUTF (MN-PM) or locally produced plant based RUTF (MN-ChSMS), respectively. In treatments 3-6, rats were initially fed either a control-balanced or protein-deficient diet for 3 weeks, followed by 3 weeks of either the commercial or the locally plant-based RUTF.Results showed that rats in the CT-ChSMS group exhibited growth and weight comparable to CT group, while those in the MN-PM group showed no significant improvement compared to the MN group. Notably, rats in the MN-ChSMS group demonstrated significant catch-up growth, whereas those in the MN-PM group did not.Additionally, consumption of ChSMS and PM RUTFs differed significantly. ChSMS RUTF which contained 14% protein over total energy with better amino-acid composition and a higher Protein Digestibility-Corrected Amino Acid Score (PDCAAS), resulted in significantly greater weight gain and length compared to PM RUTF, which contained 10% protein over total energy. These findings indicate that a locally produced, culturally acceptable and affordable plant-based RUTF formulated with high protein quality and quantity may be effective in treating acute and chronic malnutrition in children.
Mechanical stresses govern myoblast fusion and myotube growth
Authors: Le Toquin Yoann , Dubey Sushil , Ardaševa Aleksandra , Balasubramaniam Lakshmi , Delaune Emilie , Morin Valérie , Doostmohammadi Amin , Marcelle Christophe , Ladoux Benoît 
Published: November 2024

AbstractMyoblast fusion into myotubes is critical for muscle formation, growth and repair. While the cellular and molecular mechanisms regulating myoblast fusion are increasingly understood, the role of biomechanics in this process remains largely unexplored. Here, we reveal that a dynamic feedback loop between evolving cell mechanics and cell-generated stresses shape the fusion of primary myoblastsin vitro. Applying principles from active nematics, we show that myoblast and myotube patterning follows physical rules similar to liquid crystal organization. Remarkably, fusion predominantly occurs at comet-shaped topological defects in cellular alignment, which we identified as regions of high compressive stress. We further find that this stress-driven organization depends on extracellular matrix (ECM) deposition, which mirrors the nematic order of the cell population. Our integrated data, supported by active nematics-based mathematical modeling, accurately predict self-organization patterns and mechanical stresses that regulate myoblast fusion. By revealing the essential role of biomechanics and ECM interplay in myogenesis, this work establishes a foundational framework for understanding biomechanical principles in morphogenesis.
Introducing SPROUT (Semi-automated Parcellation of Region Outputs Using Thresholding): an adaptable computer vision tool to generate 3D segmentations
Authors: He Yichen , Camaiti Marco , Roberts Lucy E. , Mulqueeney James M. , Didziokas Marius , Goswami Anjali 
Published: November 2024

AbstractThe increased availability of 3D image data requires improving the efficiency of digital segmentation, currently relying on manual labelling, especially when separating structures into multiple components. Automated and semi-automated methods to streamline segmentation have been developed, such as deep learning and smart interpolation, but require pre-labelled data, and specialized hardware and software. Deep learning models in particular often require the manual creation of extensive training data, particularly for complex multi-class segmentations. Here, we introduce SPROUT, a novel, semi-automated computer vision method providing a time-efficient and user-friendly pipeline for segmenting and parcellating image data. SPROUT generates seeds (representing parts of an object) based on specified density thresholds and erosion of connected components, to achieve element separation. Seeds are grown to obtain fully-parcellated segmentations. We compare SPROUT’s performance to that of smart interpolation and apply it to diverse datasets to demonstrate the utility and versatility of this open-source 3D segmentation method.
Receptor polarization through localized activity and global sensitization
Authors: Goetz Andrew , Dixit Purushottam D. 
Published: November 2024

AbstractEukaryotic cellschemosenseconcentration gradients of extracellular ligands using membrane-bound receptors that polarize their activity. Receptors from several chemosensing families are preferentially degraded after activation and undergo significant lateral diffusion, both of which may blunt their polarization. To explore the combined role of these two seemingly detrimental phenomena on active receptor polarization, we use a reaction/diffusion model. The model elucidates a counterintuitive principle that governs receptor polarization under external gradients: Localized Activity and Global Sensitization (LAGS). In LAGS, receptor activity is localized through receptor degradation or ligand unbinding. In contrast, uniform sensitivity to ligands is maintained over the plasma membrane through lateral receptor diffusion. Surprisingly, increasing preferential degradation of active receptors and increasing lateral diffusion of all receptors both sharpen active receptor polarization. Additionally, when combined with receptor oligomerization, an increase in preferential degradation allows cells to sense relative ligand gradients over a larger range of background ligand concentrations. An analytical model identifies parameter regimes that dictate which processes dominate receptor polarization. A survey of kinetic parameters suggests that receptor polarization in many mammalian pathways can be modeled using LAGS.
Pairwise interactions and serial bottlenecks help explain species composition in a multi-species microbial community
Authors: Lele Kasturi , Wolfe Benjamin E. , Uricchio Lawrence H. 
Published: November 2024

AbstractCharacterizing the processes that drive microbial community assembly remains a key challenge in ecology. Several recent studies have argued that pairwise interactions may be insufficient to explain co-occurrence patterns in complex microbial communities, but most such studies have focused on synthetic communities not found in nature or microbes grown in contexts that differ widely from their natural environment. Moreover, most models of pairwise interactions rely on equilibrium assumptions that are not relevant to all natural communities, such as gut microbiomes or species in fluctuating environments. Microbes from fermented foods can be cultured in their natural abiotic environment in the lab and typically have moderate species complexity, making them tractable systems for studying community assembly processes. In this study, we investigated whether multi-species co-occurrence patterns can be predicted from pairwise interactions for microbes isolated from sourdough starters. Interaction parameters inferred from pairwise growth trajectories were suggestive of widespread coexistence between pairs of microbes in our species’ pool. In communities of up to nine species, most species’ presence and relative abundance could be reliably predicted based on a model of pairwise interactions. The inclusion of nonequilibrium demography in our model further improved the accuracy of our pairwise model. Our work contributes to the broader debate on the processes underlying community assembly by showing that pairwise interactions are predictive of community structure in a system of moderate species complexity.
Inositol-Requiring Enzyme 1 pathway and autophagy drive sequential response of endothelial cells to febrile range hyperthermia
Authors: Vorbe Julie , Massey Florence , Rocher Corinne , Morales Océane , Brikci Nihal , Le Borgne Marie , Caligiuri Giuseppina , Nicoletti Antonino , Franck Grégory , Illiano Stéphane 
Published: November 2024

AbstractContextFever is an evolutionarily conserved and adaptive response during infections. However, prolonged fever has numerous systemic metabolic and functional side effects. In the heart, prolonged fever associated with infection is linked to fatal adverse effects, particularly involving impaired coronary circulation. Yet, the direct relationship between elevated temperature and coronary microcirculation dysfunction, remains to be fully demonstrated. In this study, we aimed to explore the specific responses of human coronary artery endothelial cells (HCAECs) to fever-range hyperthermia.MethodHCAECs were cultured at either 37°C or 40°C for up to 24 hours. Transcriptomic and proteomic profiles were obtained through microarray and mass spectrometry after 6, 12, and 24 hours of exposure. Key signaling pathways, upstream regulators, and candidate mechanisms were identified and validated at the mRNA and protein levels using mechanistic approaches.ResultsProlonged hyperthermia compromised HCAEC function, evidenced by cell detachment, loss of junctions, and increased permeability. HCAECs rapidly activated the unfolded protein response (UPR), including IRE1α activation andXBP1splicing. Additionally, autophagic flux was significantly elevated, participating in the degradation of junction proteins. Pharmacological inhibition of IRE1α reduced the autophagic burden, protected against cell detachment, and preserved junction integrity over time.ConclusionOur findings reveal that in response to fever-range hyperthermia, the IRE1α-autophagy axis regulates the survival and function of coronary endothelial cells. This mechanism could play a key role in modulating endothelial responses during infection and contribute to the pathological outcomes of fever. Furthermore, it may be relevant in local inflammatory conditions with elevated temperatures.
Structure-Based Design of Covalent Nanobody Binders for a Thermostable Green Fluorescence Protein
Authors: Yue Zhihao , Li Yanfang , Cai Hongmin , Yao Hebang , Li Dianfan , Ni Aimin , Li Tingting 
Published: November 2024

AbstractGreen fluorescence protein (GFP) lights up almost every aspects of life sciences. An ultra thermostable GFP (TGP), engineered from a coral GFP, offers potential advantages over traditional jellyfish-derived GFP due to its high stability. However, owing to its later discovery, TGP lacks the extensive toolsets available for GFP, such as heavy chain-only antibody binders known as nanobodies. In this study, we have structurally characterized TGP in complex with Sb92, a synthetic nanobody identified from a previous in vitro screening, revealing its precise three-dimensional epitope. This structural insight, alongside the previously characterized Sb44-TGP complex, have allowed us to rationally design disulfide bonds between antigen and antibody for tighter interactions. Using biochemical analyses, we identify two bridged complexes (TGP A18C-Sb44 V100C, TGP E118C-Sb92 S57C), with the TGP-Sb92 disulfide pair showing high resistance to reducing agents. Our study expands the toolkit available for TGP and should encourage its wider applications.