bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between extreme species richness and Holocene persistence of forest-steppe grasslands in Transylvania, Romania
Authors: Novák Jan , Šamonil Pavel , Roleček Jan 
Published: January 2024

AbstractThe most species-rich grasslands worldwide are known from the Carpathian Mts and their periphery in East-Central Europe. They occur in forest-steppe regions, transitional between temperate forest and arid steppe biomes. Their climate, largely suitable for forests, raises questions about the origin of these grasslands. Have they been forested in the past, or locally maintained through a disturbance regime? We addressed these questions to contribute to the broader understanding of Holocene dynamics of open habitats in temperate Europe. We employed soil charcoal analysis and soil morphology to reconstruct past representation of woody species with fine spatial resolution. Our study area was Romanian Transylvania, a region renowned for a well-developed forest-steppe. Six soil profiles along a climatic gradient were assessed: four in forest-steppe grasslands, two in grasslands in adjacent forest region. The results revealed profound differences between forest-steppe and forest grasslands. Forest-steppe profiles showed Phaeozems with low specific anthracomass and continuous dominance byJuniperus, suggesting a long-term presence of grasslands. Forest profiles showed Luvisols with higher anthracomass and abundant charcoal of broad-leaved trees, indicating establishment after deforestation. The high radiocarbon ages of charcoals in basal soil horizons point to a glacial origin of soils and the link of forest-steppe grasslands to glacial forests. Siberian hemiboreal forests and related grasslands may be modern analogues of the reconstructed ecosystems, sharing many species with present day forest-steppe. We highlight the role of disturbances such as fire, herbivore grazing, and human activities in shaping the forest-steppe over time, contributing to the formation of today’s richest grasslands.
Fundamental constraints on the evolution of vertebrate life histories
Authors: Brooks George C. , Uyeda Josef C. , Bone Nicholas , Conrad Hailey M. , Mull Christopher G. , Kindsvater Holly K. 
Published: January 2024

ABSTRACTVertebrate life histories evolve in response to selection imposed by abiotic and biotic environmental conditions while being limited by genetic, developmental, physiological, demographic, and phylogenetic processes that constrain adaptation. Despite the well-recognized shifts in selective pressures accompanying transitions among environments, identifying the conditions driving innovation and the consequences for life-history evolution remain an outstanding question. Here, we compare the traits of aquatic and terrestrial vertebrates to infer shifts in demographic and evolutionary constraints that explain differences in life-history optimization. Specifically, our results emphasize the reduced potential for life-history diversification on land, especially that of reproductive strategies. Moreover, our study reveals differences between the evolution of viviparity in the two realms. Transitions from egg laying to live birth represents a major shift across life-history space for aquatic organisms, whereas terrestrial egg-laying organisms evolve live birth without drastic changes in life-history strategy. Whilst trade-offs in the allocation of resources place fundamental constraints on the way life histories can vary, ecological setting influences the position of species within the viable phenotypic space available for adaptive evolution.
The Gut Microbiome Controls Liver Tumors via the Vagus Nerve
Authors: Bauer Kylynda C. , Trehan Rajiv , Ruf Benjamin , Myojin Yuta , Benmebarek Mohamed-Reda , Ma Chi , Seifert Matthias , Nur Amran , Qi Jonathan , Huang Patrick , Soliman Marlaine , Green Benjamin L. , Wabitsch Simon , Springer Danielle A. , Rodriguez-Matos Francisco J. , Ghabra Shadin , Gregory Stephanie N. , Matta Jennifer , Dawson Brian , Golino Jihye , Xie Changqing , Dzutsev Amiran , Trinchieri Giorgio , Korangy Firouzeh , Greten Tim F. 
Published: January 2024

AbstractLiver cancer ranks amongst the deadliest cancers. Nerves have emerged as an understudied regulator of tumor progression. The parasympathetic vagus nerve influences systemic immunity via acetylcholine (ACh). Whether cholinergic neuroimmune interactions influence hepatocellular carcinoma (HCC) remains uncertain. Liver denervation via hepatic vagotomy (HV) significantly reduced liver tumor burden, while pharmacological enhancement of parasympathetic tone promoted tumor growth. Cholinergic disruption in Rag1KO mice revealed that cholinergic regulation requires adaptive immunity. Further scRNA-seq and in vitro studies indicated that vagal ACh dampens CD8+ T cell activity via muscarinic ACh receptor (AChR) CHRM3. Depletion of CD8+ T cells abrogated HV outcomes and selective deletion ofChrm3on CD8+T cells inhibited liver tumor growth. Beyond tumor-specific outcomes, vagotomy improved cancer-associated fatigue and anxiety-like behavior. As microbiota transplantation from HCC donors was sufficient to impair behavior, we investigated putative microbiota-neuroimmune crosstalk. Tumor, rather than vagotomy, robustly altered fecal bacterial composition, increasing Desulfovibrionales and Clostridial taxa. Strikingly, in tumor-free mice, vagotomy permitted HCC-associated microbiota to activate hepatic CD8+ T cells. These findings reveal that gut bacteria influence behavior and liver anti-tumor immunity via a dynamic and pharmaceutically targetable, vagus-liver axis.
Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources
Authors: Liu Zhihao , Chen Minghao , Hu Jingmin , Wang Yonghong , Chen Yu 
Published: January 2024

AbstractCells choose between alternative pathways in metabolic networks under diverse environmental conditions, but the principles governing the choice are insufficiently understood, especially in response to dynamically changing conditions. Here we observed that a lactic acid bacteriumBacillus coagulansdisplayed homolactic fermentation on glucose or trehalose as the sole carbon source, but transitioned from homolactic to heterolactic fermentation during the hierarchical utilization of glucose and trehalose when growing on the mixture. We simulated the observation by dynamic minimization of reallocation of proteome (dMORP) using an enzyme-constrained genome-scale metabolic model ofB. coagulans, which coincided with our omics data. Moreover, we evolved strains to co-utilize mixed carbon sources and repress the choice of heterolactic fermentation, and the dynamics after co-utilization of carbon sources could also be captured by dMORP. Altogether, the findings suggest that upon rapid environmental changes bacteria tend to minimize proteome reallocation and accordingly adjust metabolism, and dMORP would be useful in simulating and understanding cellular dynamics.
CACIMAR: Cross-species Analysis of Cell Identities, Markers, Regulations and Interactions Using Single-cell RNA Sequencing Data
Authors: Jiang Junyao , Li Jinlian , Xu Xueli , Huang Sunan , Jiang Fan , Liang Yanran , Wang Jie 
Published: January 2024

AbstractTranscriptomic analysis across species is increasingly used to reveal conserved gene regulations which implicate crucial regulators. Cross-species analysis of single-cell RNA sequencing (scRNA-seq) data provides new opportunities to identify the cellular and molecular conservations especially for cell types and cell type-specific gene regulations. However, few methods have been developed to analyze cross-species scRNA-seq data to uncover both molecular and cellular conservation patterns. Here, we built a tool called CACIMAR, which can perform cross-species analysis of cell identities, markers, regulations and interactions using scRNA-seq profiles. Based on the weighted sum models of the conserved features, we developed different conservation scores to measure the conservation of cell types, regulatory networks and intercellular interactions. Using publicly available scRNA-seq data on retinal regeneration in mice and zebrafish, we demonstrated four main functions of CACIMAR. First, CACIMAR allows to identify evolutionarily conserved cell types, including poorly conserved cell types. Second, the tool facilitates the identification of evolutionarily conserved or species-specific marker genes. Third, CACIMAR enables the identification of conserved intracellular regulations, including cell type-specific regulatory subnetworks and regulators. Lastly, CACIMAR provides a unique feature on the identification of conserved intercellular interactions. Overall, CACIMAR facilitates the identification of evolutionarily conserved cell types, marker genes, intracellular regulations and intercellular interactions, providing insights on the cellular and molecular mechanisms of species evolution.
IDENTIFICATION OF KEY GENES ASSOCIATED WITH PCOS (POLY CYSTIC OVARIAN SYNDROME) AND ENDOMETRIAL/OVARIAN CANCER THROUGH BIOINFORMATICS
Authors: Raulo Karishma , Qazi Sahar 
Published: January 2024

ABSTRACTBackgroundPCOS, a common endocrine disorder, is linked to increased risks of endometrial cancer (EC) and ovarian cancer (OC). Our study utilizes bioinformatics analysis to identify shared gene signatures and elucidate biological processes between EC/OC and PCOS.Materials and MethodsGene expression profiles for PCOS (GSE199225), endometrial cancer (GSE215413), and ovarian cancer (GSE174670) were obtained from the GEO database. Hub genes were identified through functional enrichment analysis and protein-protein interaction. Drug identification analyses were employed to find drugs targeting the hub genes.ResultKey hub genes linking PCOS and EC includes RECQL4, RAD54L, ATR, CHTF18, WDHD1, CDT1, PLK1, PKMYT1, RAD18, and RPL3; for PCOS and OC, they include HMOX1, TXNRD1, NQO1, GCLC, GSTP1, PRDX1, SOD1, GPX3, BOP1, and BYSL.Gene Ontology analysis revealed DNA Metabolic Processes in PCOS and EC, while in PCOS and OC, it identified the Removal of Superoxide Radicals. KEGG Pathway analysis highlighted Cell cycle in PCOS and EC and Hepatocellular carcinoma in PCOS and OC. Potential drugs for PCOS and EC include quercetin, calcitriol, and testosterone; for PCOS and OC, eugenol and 1-chloro-2,4-dinitrobenzene are identified.ConclusionThese findings offer insights into potential therapeutic targets and pathways linking PCOS with EC and OC, enhancing our understanding of the molecular mechanisms involved in these associations.
A comparison of knowledge-based dose prediction approaches to assessing head and neck radiotherapy plan quality
Authors: Leone Alexandra O. , Gronberg Mary , Gay Skylar S. , Govyadinov Pavel A. , Beadle Beth M. , Lim Tze Y. , Whitaker Thomas J. , Hoffman Karen , Court Laurence E. , Cao Wenhua 
Published: January 2024

AbstractPURPOSERecent studies demonstrate deep learning dose prediction algorithms may produce results like those of traditional knowledge-based planning tools. In this exploratory study, we compared 2D DVH-based knowledge-based planning tools and 3D deep learning-based approaches to assessing radiotherapy plan quality.METHODSPre-validated 2D and 3D dose prediction models were applied to 58 patients with head and neck cancer treated under RTOG 0522 obtained from The Cancer Imaging Archive (TCIA). The 2D model was used to predict dose-volume histogram bands for seven organs at risk (OARs; brainstem, spinal cord, oral cavity, larynx, mandible, right parotid, and left parotid). A 3D dose prediction model was used to predict 3D dose distributions, based on computed tomography images, OAR contours, planning target volumes and prescriptions. The mean and D1% to the seven OARs for the 2D and 3D dose prediction models were compared. Further post predictive analysis was done to quantify the predicted 3D dose sparing for all normal tissues.RESULTSThe two models predicted similar dose sparing to the OARs, with a mean difference of 1.4±5.5 Gy across all evaluated dose metrics. When looking at the sparing of non-OAR normal tissue regions, the 3D model predicted a mean dose reduction to normal tissue regions of 6.4±3.0 Gy when compared with the clinical dose.CONCLUSION2D and 3D dose predictions are comparable at predicting dose reductions to OARs. The 3D approach allows for dose visualization, which may support further sparing of normal tissues not typically drawn as OARs on head and neck plans.
An Open-label Clinical Study of Brief Submaximal Cardiopulmonary Testing in Pre-surgical Evaluation: Feasibility of implementation
Authors: Carr Zyad J. , Agarkov Daniel , Li Judy , Charchaflieh Jean , Brenes-Bastos Andres , Freund Jonah , Zafar Jill , Schonberger Robert B. , Heerdt Paul 
Published: January 2024

AbstractObjectivesWe tested the logistic feasibility of integrating brief submaximal cardiopulmonary exercise testing (smCPET) in a pre-surgical evaluation (PSE) clinic.DesignProspective open-label clinical device trial.SettingPre-surgical evaluation clinic.Participants43 participants who met criteria of i) age>60 years old, ii) revised cardiac risk index of<2, iii) self-reported metabolic equivalents (METs) of>4.6 (i.e. ability to climb 2 flights of stairs), and iv) presenting for noncardiac surgery.InterventionsPre-intervention self-reported METs, Duke Activity Status Index (DASI) surveys, smCPET trial, Borg survey of perceived exertion, and post-intervention survey.Measurements: Feasibility endpoints were 1) operational efficiency as measured by length of time of experimental session<20 minutes, 2) no more than moderate perceived physical exertion as quantified by a modified Borg survey of perceived exertion of<7 in the absence of observed complications, 3) high participant satisfaction with smCPET task execution, represented as a score of>8, and 4) high patient satisfaction with scheduling of smCPET testing, represented as a score of>8.ResultsSession time was 16.9 minutes (±6.8). Post-test modified Borg survey was 5.35 (±1.8), corresponding to moderate perceived exertion. Satisfaction [on a scale of 1 (worst) to 10 (best)] regarding ease of smCPET tasks was 9.6 (±0.7) and mean patient satisfaction with smCPET scheduling was 9.5 (±1.5). Operational efficiency was achieved after 10-15 experimental sessions.ConclusionsOur findings suggest that smCPET integration in a PSE clinic; 1) is time efficient 2) shows high participant satisfaction with task, and 3) rapidly achieved operational efficiency.Trial RegistrationClinicalTrials.govRegistration: #NCT05743673. Principal Investigator: Zyad J. Carr, M.D. Date of Registration: 5-12-2023.Strengths and limitations of this studyWe examined patient-and logistic-centered acceptance of study procedures within the environment of a high-volume preoperative surgical evaluation clinic.Study procedures were well tolerated, and participants readily accepted submaximal cardiopulmonary exercise testing with high satisfaction with device use, scheduling, and perceived exertion.User operational efficiency developed over 10-15 sessions of use.This feasibility study met our proposed endpoints but is comprised of a small sample of participants, limiting its generalizability to larger populations.
Safety Monitoring of Bivalent COVID-19 mRNA Vaccines Among Recipients 6 months and Older in the United States
Authors: Lloyd Patricia C. , Smith Elizabeth R. , Gruber Joann F. , Ondari Michelle , Wong Hui Lee , Hu Mao , Clarke Tainya C. , McEvoy Rowan , Amend Kandace L. , Beachler Daniel C. , McMahill-Walraven Cheryl N , Seeger John D. , Secora Alex , Djibo Djeneba Audrey , Song Jennifer , Selvam Nandini , DeShazo Jonathan P. , Clifford Robin , Abente Eugenio , Chillarige Yoganand , Forshee Richard A. , Anderson Steven A. , Shoaibi Azadeh 
Published: January 2024

AbstractActive monitoring of health outcomes after COVID-19 vaccination provides early detection of rare outcomes post-licensure.ObjectiveTo evaluate health outcomes following bivalent COVID-19 Pfizer-BioNTech (BNT162b2) and Moderna (mRNA-1273.222) vaccination among individuals 6 months and older in the United States.DesignMonthly monitoring of health outcomes from August 2022 to July 2023 in four administrative claims databases. Descriptive analyses monitored vaccine uptake, outcome counts and coadministration of bivalent COVID-19 and influenza vaccines. Sequential analyses tested for elevated risk of each outcome in a prespecified post-vaccination risk interval, or a period of hypothesized elevation based on clinical guidance, compared to a historical baseline.Participants and ExposuresPersons 6 months and older who received a bivalent COVID-19 BNT162b2 or mRNA-1273.222 vaccine during the study period, with continuous enrollment in a medical insurance plan from the start of an outcome-specific clean interval to the COVID-19 vaccination date. Vaccines were identified using product-specific codes from medical coding systems.Health OutcomesTwenty outcomes were monitored in BNT162b2 vaccine recipients 6 months-4 years, and mRNA-1273.222 vaccine recipients 6 months-5 years. Twenty-one outcomes were monitored in BNT162b2 vaccine recipients 5-17 years and mRNA-1273.222 vaccine recipients 6-17 years. Eighteen outcomes were monitored in persons 18 years and older for both mRNA vaccines.ResultsOverall, 13.9 million individuals 6 months and older received a single bivalent COVID-19 mRNA vaccine. The statistical threshold for a signal was met for two outcomes in one database: anaphylaxis following bivalent BNT162b2 and mRNA-1273.222 vaccines in persons 18-64 years and myocarditis/pericarditis following bivalent BNT162b2 vaccines in individuals 18-35 years. There were no signals identified in young children.ConclusionsResults were consistent with prior observations from published studies on COVID-19 vaccine safety. This study supports the safety profile of bivalent COVID-19 mRNA vaccines and the conclusion that the benefits of vaccination outweigh the risks.
Evaluating the Diagnostic and Treatment Recommendation Capabilities of GPT-4 Vision in Dermatology
Authors: Pillai Abhinav , Joseph Sharon Parappally , Kreutz Jason , Trabousi Danya , Gandhi Maharshi , Hardin Jori 
Published: January 2024

AbstractBackgroundThe integration of artificial intelligence (AI) in dermatology presents a promising frontier for enhancing diagnostic accuracy and treatment planning. However, general purpose AI models require rigorous evaluation before being applied to real-world medical cases.ObjectiveThis project specifically evaluates GPT-4V’s performance in accurately diagnosing and generating treatment plans for common dermatological conditions, comparing its assessment of textual versus image data and its performance with multimodal inputs. Beyond the immediate scope, this study contributes to the broader trajectory of integrating AI in healthcare, highlighting the limitations of these technologies, as well as their potential to enhance efficiency, and education within medical training and practice.MethodsA dataset of 102 images representing nine common dermatological conditions was compiled from open-access websites. Fifty-four images were ultimately selected by two board-certified dermatologists as being representative and typical of the common conditions. Additionally, nine clinical scenarios corresponding to these conditions were developed. GPT-4V’s diagnostic capabilities were assessed in three setups: Image Prompt (image-based), Scenario Prompt (text-based), and Image and Scenario Prompt (combining both modalities). The model’s performance was evaluated based on diagnostic accuracy, differential diagnosis, and treatment recommendations.ResultsIn the Image Prompt setup, GPT-4V correctly identified the primary diagnosis for 29 of 54 images. The Scenario Prompt setup showed a higher accuracy rate of 89% in identifying the primary diagnosis. The multimodal Image and Scenario Prompt setup also achieved an 89% accuracy rate. However, a notable bias towards textual data over visual data was observed. Treatment recommendations were evaluated by the same two dermatologists, using a modified Entrustment Scale, showing competent but not expert-level performance.ConclusionGPT-4V demonstrates promising capabilities in dermatological diagnosis and treatment recommendations, particularly in text-based scenarios. However, its performance in image-based diagnosis and integration of multimodal data highlights areas for improvement. The study underscores the potential of AI in augmenting dermatological practice, emphasizing the need for further development, and fine-tuning of such models to ensure their efficacy and reliability in clinical settings.
Global heterogeneity of latitudinal patterns in herbivory between native and exotic plants
Authors: Guo Yaolin , Parepa Madalin , Wang Hui , Wang Min , Wu Jihua , Li Bo , Ju Rui-Ting , Bossdorf Oliver 
Published: January 2024

AbstractLatitudinal gradient of herbivory that differs between native and exotic plants has been an open issue. It is expected that a latitudinal gradient of herbivory will be evident for native plants; this gradient in exotic plants may lag behind native plants in terms of co-evolution with local abiotic and biotic factors in introduced area. Our study aims to elucidate the difference in latitudinal gradient of herbivory between native and exotic plants globally, while exploring the underlying mechanisms driving the latitudinal gradient of herbivory with biotic and abiotic factors. To achieve this, we analyzed herbivory data from 94 studies and calculated 862 herbivory effect sizes (zr) to quantitatively characterize the intensity of latitudinal herbivory gradient. For each herbivory data, we matched the corresponding plant identity (native/exotic), herbivore feeding guilds and climate data to reveal the contribution of these factors tozr. Our findings demonstrate a significant decrease in the latitudinal gradients of with increasing latitude for native plants, a pattern not observed for exotic plants. The heterogeneity in latitudinal gradients of herbivory between native and exotic plants is mediated by herbivore feeding guilds. There is a significant influence of climatic factors on the latitudinal gradient of herbivory for native plants, but not for exotic plants. Overall, our results underscore a general heterogeneity in global macroecological herbivory patterns between native and exotic plants, and highlight the role of biotic and abiotic factors in explaining these global-scale differences.