bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unusual Case of Primary Hepatic Squamous Carcinoma on 18F-FDG PET/CT
Authors: Li Wei , Liu Zhidong , Zhang Rusen 
Published: November 2023

AbstractPrimary hepatic squamous carcinoma is an extremely rare liver tumor type with high malignancy and poor prognosis. We present18F-FDG PET/CT findings of primary squamous carcinoma of the liver in a 65-year-old man, who was admitted to the hospital with subxiphoid pain in the epigastric region radiating to the left lower back for 2 months.18F-FDG PET/CT demonstrated a large heterogeneous mild enhancing mass in the left lobe of the liver, with intense circumferential18F-FDG activity.
Surgeon views on firearm safety counseling in clinical practice: A cross-sectional survey
Authors: Kirkendoll Shelbie D. , Silver Casey M. , Stey Anne M. , Nathens Avery B. , Jackson Kathryn , Campbell Brendan T. 
Published: November 2023

BACKGROUND
Firearms are commonplace in the United States, and one proposed strategy to decrease risk of firearm injury is to have physicians counsel their patients about safe firearm ownership. Current rates of firearm safety counseling by surgeons who care for injured people are unknown.

METHODS
This study used an anonymous cross-sectional survey derived from previously published survey instruments and was piloted (n = 13) at the annual meeting of the American Association for the Surgery of Trauma (2022). The finalized survey was distributed using a quick response code during two sessions at the 2022 American College of Surgeons Clinical Congress. Eligible participants included the surgeons and surgical trainees who attended these sessions.

RESULTS
One hundred fourteen individuals completed the survey (20% response rate), and a majority were male (n = 71 [62.3%]), attending surgeons (n = 108 [94.7%]), and specialized in acute care surgery (n = 72 [63.2%]). Few participants (n = 43 [37.7%]) reported counseling patients on firearm safety as part of their routine clinical practice; however, the majority (n = 102 [89.5%]) believed that surgeons should provide firearm safety counseling. Counseling rates did not vary significantly by age, sex, surgical specialty, or region of practice, but attitudes toward counseling did differ by firearm safety counseling practices (p = 0.03) and region of practice (0.04). Noted barriers to counseling included lack of time (n = 47 [41.2%]), perceived lack of training (n = 43 [37.7%]), and lack of firearm knowledge/experience (n = 36 [31.6%]).

CONCLUSION
Most surgeon respondents did not provide firearm safety counseling to their patients despite the fact the majority believed they should. This suggests that counseling interventions that do not solely rely on surgeons for implementation could increase the number of patients who receive firearm safety guidance during clinical encounters.

LEVEL OF EVIDENCE
Prognostic and Epidemiological; Level III.
Comparison of Automated Spike Detection Software in Detecting Epileptiform Abnormalities on Scalp-EEG of Genetic Generalized Epilepsy Patients
Authors: Janmohamed Mubeen , Nhu Duong , Shakathreh Lubna , Gonen Ofer , Kuhlman Levin , Gilligan Amanda , Tan Chang Wei , Perucca Piero , O'Brien Terence J. , Kwan Patrick 
Published: November 2023

Purpose:
Despite availability of commercial EEG software for automated epileptiform detection, validation on real-world EEG datasets is lacking. Performance evaluation of two software packages on a large EEG dataset of patients with genetic generalized epilepsy was performed.

Methods:
Three epileptologists labelled IEDs manually of EEGs from three centres. All Interictal epileptiform discharge (IED) markings predicted by two commercial software (Encevis 1.11 and Persyst 14) were reviewed individually to assess for suspicious missed markings and were integrated into the reference standard if overlooked during manual annotation during a second phase. Sensitivity, precision, specificity, and F1-score were used to assess the performance of the software packages against the adjusted reference standard.

Results:
One hundred and twenty-five routine scalp EEG recordings from different subjects were included (total recording time, 310.7 hours). The total epileptiform discharge reference count was 5,907 (including spikes and fragments). Encevis demonstrated a mean sensitivity for detection of IEDs of 0.46 (SD 0.32), mean precision of 0.37 (SD 0.31), and mean F1-score of 0.43 (SD 0.23). Using the default medium setting, the sensitivity of Persyst was 0.67 (SD 0.31), with a precision of 0.49 (SD 0.33) and F1-score of 0.51 (SD 0.25). Mean specificity representing non-IED window identification and classification was 0.973 (SD 0.08) for Encevis and 0.968 (SD 0.07) for Persyst.

Conclusions:
Automated software shows a high degree of specificity for detection of nonepileptiform background. Sensitivity and precision for IED detection is lower, but may be acceptable for initial screening in the clinical and research setting. Clinical caution and continuous expert human oversight are recommended with all EEG recordings before a diagnostic interpretation is provided based on the output of the software.
Dynamic gene expression analysis reveals distinct severity phases of immune and cellular dysregulation in COVID-19
Authors: An Andy Y. , Baghela Arjun , Zhang Peter , Blimkie Travis M. , Gauthier Jeff , Kaufmann Daniel E. , Acton Erica , Lee Amy H.Y. , Levesque Roger C. , Hancock Robert E.W. 
Published: November 2023

AbstractBackgroundCOVID-19 patients experience dynamic changes in immune and cellular function over time with potential clinical implications. However, there is insufficient research investigating, on a gene expression level, the mechanisms that become activated or suppressed over time as patients deteriorate or recover, which can inform use of repurposed and novel drugs as therapies.ObjectiveTo investigate longitudinal changes in gene expression profiles throughout the COVID-19 disease timeline.MethodsThree-hundred whole blood samples from 128 adult patients were collected during hospitalization from COVID-19, with up to five samples per patient. Transcriptome sequencing (RNA-Seq), differential gene expression analysis and pathway enrichment was performed. Drug-gene set enrichment analysis was used to identify FDA-approved medications that could inhibit critical genes and proteins at each disease phase. Prognostic gene-expression signatures were generated using machine learning to distinguish 3 disease stages.ResultsSamples were longitudinally grouped by clinical criteria and gene expression into six disease phases: Mild, Moderate, Severe, Critical, Recovery, and Discharge. Distinct mechanisms with differing trajectories during COVID-19 hospitalization were apparent. Antiviral responses peaked early in COVID-19, while heme metabolism pathways became active much later during disease. Adaptive immune dysfunction, inflammation, and metabolic derangements were most pronounced during phases with higher disease severity, while hemostatic abnormalities were elevated early and persisted throughout the disease course. Drug-gene set enrichment analysis predicted repurposed medications for potential use, including platelet inhibitors in early disease, antidiabetic medications for patients with increased disease severity, and dasatinib throughout the disease course. Disease phases could be categorized using specific gene signatures for prognosis and treatment selection. Disease phases were also highly correlated to previously developed sepsis endotypes, indicating that severity and disease timing were significant contributors to heterogeneity observed in sepsis and COVID-19.ConclusionsHigher temporal resolution of longitudinal mechanisms in COVID-19 revealed multiple immune and cellular changes that were activated at different phases of COVID-19. Understanding how a patient’s gene expression profile changes over time can permit more accurate risk stratification of patients and provide time-dependent personalized treatments with repurposed medications. This creates an opportunity for timely intervention before patients transition to a more severe phase, potentially accelerating patients to recovery.
ASSESSMENT AND CHARACTERIZATION OF COVID-19 RELATED COGNITIVE DECLINE: RESULTS FROM A NATURAL EXPERIMENT
Authors: Sekendiz Zennur , Clouston Sean A. P. , Morozova Olga , Carr Melissa A. , Fontana Ashley , Mehta Nikhil , Ali Alina , Jiang Eugene , Luft Benjamin 
Published: November 2023

AbstractBackgroundCognitive impairment is the most common and disabling manifestation of post-acute sequelae of SARS-CoV-2. There is an urgent need for the application of more stringent methods for evaluating cognitive outcomes in research studies.ObjectiveTo determine whether cognitive decline emerges with the onset of COVID-19 and whether it is more pronounced in patients with Post-Acute Sequelae of SARS-CoV-2 or severe COVID-19.MethodsThis longitudinal cohort study compared the cognitive performance of 276 patients with COVID-19 to that of 217 controls across four neuroinflammation or vascular disease-sensitive domains of cognition using data collected both before and after the pandemic starting in 2015.ResultsThe mean age of the COVID-19 group was 56.04±6.6 years, while that of the control group was 58.1±7.3 years. Longitudinal models indicated a significant decline in cognitive throughput ((β=-0.168,P=.001) following COVID-19, after adjustment for pre-COVID-19 functioning, demographics, and medical factors. The effect sizes were large; the observed changes in throughput were equivalent to 10.6 years of normal aging and a 59.8% increase in the burden of mild cognitive impairment. Cognitive decline worsened with coronavirus disease 2019 severity and was concentrated in participants reporting post-acute sequelae of SARS-CoV-2.ConclusionCOVID-19 was most likely associated with the observed cognitive decline, which was worse among patients with PASC or severe COVID-19. Monitoring patients with post-acute sequelae of SARS-CoV-2 for declines in the domains of processing speed and visual working memory and determining the long-term prognosis of this decline are therefore warranted.
Lower Physical Activity Modifies the Association between Perceived Fatigability and Executive Function but not Memory: The Study of Muscle, Mobility and Aging (SOMMA)
Authors: Schumacher Benjamin T. , Rosano Caterina , Qiao Yujia (Susanna) , Rosso Andrea L. , Cawthon Peggy M. , Moored Kyle D. , Cummings Steven R. , Kritchevsky Stephen B. , Glynn Nancy W. 
Published: November 2023

ABSTRACTOBJECTIVEEmerging evidence shows that perceived fatigability—the quantification of vulnerability to fatigue in relation to specific intensity and duration of activities—may be associated with cognitive function. We sought to quantify associations with multiple domains of cognitive function and the role of physical activity (PA).METHODSSOMMA participants completed the Pittsburgh Fatigability Scale (PFS) Physical and Mental subscales (each range 0–50; higher scores=greater fatigability) and three cognitive function assessments [Digit Symbol Substitution Test (DSST), executive function; Montreal Cognitive Assessment (MoCA), general function; and California Verbal Learning Test (CVLT), memory]. Linear regression quantified associations cross-sectionally between each PFS subscale and cognitive assessment scores adjusting for covariates. Effect modification by volume and intensity of accelerometer-measured PA was assessed.RESULTSIn 873 participants (59.2% women; age 76.3±5.0; 85% White), mean PFS Physical, Mental, and DSST scores were 15.8±8.7, 7.7±7.8, and 55.4±13.7. After adjustments, for each 4-point higher PFS Physical and 3-point higher PFS Mental, participants had nearly one fewer correct DSST items [β coefficient and 95% confidence interval for PFS Physical: -0.69 (-1.09, - 0.29); PFS Mental: -0.64 (-0.97, -0.30)]. Volume and intensity of PA modified the association of PFS Mental and DSST (Pinteractions<0.01). All associations were strongest in those with the lowest volume and intensity of PA. PFS was not associated with MoCA or CVLT.DISCUSSIONGreater perceived fatigability may be associated with poorer executive function, but not memory. Individuals with greater perceived fatigability, particularly those less active, might benefit from interventions that reduce fatigability and may beneficially influence cognitive function.
Fending for oneself or partnering up: Competition between mixo- and heterotrophic ciliates under dynamic resource supply
Authors: Flöder Sabine , Klauschies Toni , Klaassen Moritz , Stoffers Tjardo , Lambrecht Max , Moorthi Stefanie 
Published: November 2023

AbstractThe outcome of species competition strongly depends on the traits of the competitors and associated trade-offs, as well as on environmental variability. Here we investigate the relevance of consumer trait variation for species coexistence in a ciliate consumer – microalgal prey system under fluctuating regimes of resource supply. We focus on consumer competition and feeding traits, and specifically on the consumer’s ability to overcome periods of resource limitation by mixotrophy, i.e. the ability of photosynthetic carbon fixation via algal symbionts in addition to phagotrophy. In a 48-day chemostat experiment, we investigated competitive interactions of different heterotrophic and mixotrophic ciliates of the generaEuplotesandColepsunder different resource regimes, providing prey either continuously or in pulses under constant or fluctuating light, entailing periods of resource depletion in fluctuating environments, but overall providing the same amount of prey and light. Although ultimate competition results remained unaffected, population dynamics of mixotrophic and heterotrophic ciliates were significantly altered by resource supply mode. However, the effects differed among species combinations and changed over time. Whether mixotrophs or heterotrophs dominated in competition strongly depended on the genera of the competing species and thus species-specific differences in the minimum resource requirements that are associated with feeding on shared prey, nutrient uptake, light harvesting and access to additional resources such as bacteria. Potential differences in the curvature of the species’ resource-dependent growth functions may have further mediated the species-specific responses to the different resource supply modes. In addition, while the presence of a heterotrophic competitor may have a direct negative effect on the growth rate of a mixotrophic species through grazing on a shared prey species, its presence may also have an indirect positive effect on the growth rate of the mixotroph by reducing competition between the autotroph and mixotroph for shared nutrients and light. Our study thus demonstrates that complex trophic interactions determine the outcome of competition, which can only be understood by taking on a multidimensional trait perspective.
Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective
Authors: Peona Valentina , Martelossi Jacopo , Almojil Dareen , Bocharkina Julia , Brännström Ioana , Brown Max , Cang Alice , Valenzuela Tomas Carrasco , DeVries Jon , Doellman Meredith , Elsner Daniel , Espindola Hernandez Pamela , Friis Montoya Guillermo , Gaspar Bence , Zagorski Danijela , Hałakuc Paweł , Ivanovska Beti , Laumer Christopher , Lehmann Robert , Boštjančić Ljudevit Luka , Mashoodh Rahia , Mazzoleni Sofia , Mouton Alice , Janke Maria Nilsson , Pei Yifan , Potente Giacomo , Provataris Panagiotis , Pardos José Ramón , Raut Ravindra , Sbaffi Tomasa , Schwarz Florian , Stapley Jessica , Stevens Lewis , Sultana Nusrat , Symonova Radka , Tahami Mohadeseh , Urzì Alice , Yang Heidi , Yusuf Abdullah , Pecoraro Carlo , Suh Alexander 
Published: November 2023

AbstractThe advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. However, manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd sourcing efforts could offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. Here, we present an example of such crowd sourcing effort developed through both in-person and online courses built around a collaborative peer-reviewed teaching process that can be used as teaching reference guide for similar projects. The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs: A hidden treasure awaits discovery within non-model organisms.
Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set
Authors: Kristensen Nikolaj Pagh , Dionisio Edoardo , Bentzen Amalie Kai , Tamhane Tripti , Kemming Janine Sophie , Nos Grigorii , Voss Lasse Frank , Hansen Ulla Kring , Lauer Georg Michael , Hadrup Sine Reker 
Published: November 2023

AbstractKnowledge of widely recognized T-cell epitopes against common virus infections are vital for immune monitoring and characterization of relevant antigen-specific CD8 T cells and their antigen receptors. We therefore aimed to establish a concise and validated epitope panel for monitoring human virus-specific immunity complete with data on both prevalence of recognition and reactivity in humans. To achieve this, we first establish TCR downregulation, and loss of peptide major histocompatibility (pMHC) multimer-binding, as an early and sensitive marker of T cell reactivity after peptide stimulation. We next applied TCR downregulation in a high-throughput assay by monitoring binding, and loss of binding (i.e. reactivity), to libraries of DNA-barcode labelled pMHC multimers in paired unstimulated/stimulated samples. This novel method allowed us to access T-cell responses in 48 donors towards 929 epitopes recorded in the Immune Epitope Database (IEDB) encompassing 29 virus common infections and 25 different HLA alleles. This yielded a concise panel of 137 virus epitopes, many of which were underrepresented in the public domain, recognized by T cells in peripheral blood. 84% of these epitopes exhibited prevalent reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, non-reactive responses correlated with naïve and immunosenescence phenotypes. This study represents the largest effort to unbiasedly assess T-cell recognition and reactivity to common virus infections in healthy individuals providing a minimal epitope panel for monitoring adaptive immune responses in humans.Significance StatementCD8 T-cell epitopes are widely available in public databases yet many are not recognized in the general population. Here we undertook an exhaustive screening process using “state-of-the-art” methods to assess both T-cell recognition and reactivity against common virus infections, which holds significant implications for shaping T-cell immunity and disease protection. We identify 137 commonly recognized epitopes from common virus infections to which T cell responses are expected to occur in human donors. Importantly, several of the verified epitopes were underreported in public databases compared to their observed prevalence of recognition and high cellular frequency making this an important reference dataset and resource for immunologists studying antigen-specific T cells across different immunopathologies and contexts including autoimmunity, infectious disease and cancer immunotherapy.
Can biocrust moss hide from climate change? Fine-scale habitat sheltering improves summer-stress resistance inSyntrichia caninervis
Authors: Clark Theresa A. , Russell Alexander , Greenwood Joshua L. , Devitt Dale , Stanton Daniel , Stark Lloyd R. 
Published: November 2023

ABSTRACTPremiseMosses provide many ecosystem functions and are the most vulnerable of biocrust organisms to climate change due to their sensitive water relations stressed by summer aridity. Given their small size, moss stress resistance may be more dependent on fine-scale habitat than macroscale (climate and community), but this sheltering role of habitat (i.e. habitat buffering) has never been compared to macroclimate and may have important implications for predicting critical biocrust refugia in changing climates.MethodsWe located three populations of a keystone biocrust moss,Syntrichia caninervis, spanning 1200-m of altitude comprising three plant communities (elevation-plant zones) in the Mojave Desert. We stratified 96 microsites along three habitat aridity gradients: elevation-zone, topography (aspect), and microhabitat (shrub proximity). We estimated summer photosynthetic stress (Fv/Fm) and aridity exposure (macroclimate, irradiance, and shade).ResultsMicrosite aridity exposure varied greatly revealing exposed and buffered microhabitats in all elevation-zones. Moss stress did not differ by elevation zone despite the extensive macroclimate gradient, failing to support the high-elevation refugia hypothesis. Instead, stress was lowest on N-facing slopes and microhabitats with higher shrub shading, while the importance of (and interactions between) topography, irradiance, and shade varied by elevation zone.ConclusionsWe demonstrate fine-scale habitat buffering is physiologically more protective than high-elevation climate, and thus, may allow some mosses to hide from the brunt of climate change in widespread microrefugia throughout their current ranges. Our findings support a scale-focused vulnerability paradigm: microrefugia may be more important than macrorefugia for bolstering biocrust moss resistance to summer climate stress.