bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation applications of niche modeling: native and naturalized ferns may compete for limited Hawaiian dryland habitat
Authors: Edwards-Calma Krystalyn , Jiménez Laura , Zenil-Ferguson Rosana , Heyduk Karolina , Thomas Miles K. , Tribble Carrie M. 
Published: November 2023

AbstractPremiseCompetition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability.MethodsWe use fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantify the degree to which naturalized ferns tend to occupy native species suitable area and map remaining available habitat given land-use change.ResultsOf all native species,Doryopteris angelicahas the lowest percentage of occurrences of naturalized species in its suitable area whileD. decorahas the highest. However, allDoryopterisspp. had a higher percentage overlap—whilePellaea ternifoliahad a lower percentage overlap—than expected by chance.D. decoraandD. decipienshave the lowest proportions (<20%) of suitable area covering native habitat.DiscussionAreas characterized by shared environmental preferences of native and naturalized ferns may also decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of placed-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.
Prevalence of TEM and SHV Genes inKlebsiella pneumoniaeisolated from different Clinical specimens in Khartoum, Sudan
Authors: Hussein Saad A. S , Salih Mutassim A.M. , Adlan Hind M.E , Abdalla Abualgasim E. 
Published: November 2023

AbstractObjectiveThe aim of this study is to determine the prevalence of ESBL producingKlebsiella pneumoniaeisolated from different clinical specimens gathered from different clinics in Khartoum State.Settings and DesignThis is a descriptive cross-sectional study conducted in Khartoum State during a period from February to May 2018.Methods and MaterialsKlebsiella pneumoniaeisolated from patients attending to health-care settings with different infections, which was re-identiGied by conventional methods and screened for ESBL production by modiGied Kirby-Bauer’s method. The TEM and SHV genes were detected by PCR.ResultsOut of 100K. pneumoniaeisolates, 85% (85/100) were ESBL producing strains. The highest prevalence of ESBL production was in blood 100% (6/6) as well as stool 100% (4/4) followed by sputum 91% (21/23), wound 85% (12/14) and urine 82%(40\49) samples, while the lowest was noted in CSF 50% (2/4). The isolatedK. pneumoniaeshowed high resistance to Ceftazidime 85% followed by Cefotaxime and Cefpodoxime 80% for each and 73% for Aztreonam. Furthermore, we found that 88% of isolates were resistant to Colistin and 33% were resistant to Meropenem. TEM and SHV genes were detected in 9.4% (8/85) and 1.2% (1/85) of ESBL producing strains, respectively. However, SHV was also detected in 6.7% (1/15) of non-ESBL-producingK. pneumoniae.ConclusionsA high prevalence of ESBL-producingK. pneumoniaewas detected in this study Which is 85%. TEM and SHV genes were found in some strains of ESBL producingK. pneumoniae. The Gindings of this study alarm the physicians to take ESBL producing strains ofK. pneumoniaeunder consideration before making treatment decisions.
Transcranial ultrasound stimulation effect in the redundant and synergistic networks consistent across macaques
Authors: Gatica Marilyn , Atkinson-Clement Cyril , Mediano Pedro A. M. , Alkhawashki Mohammad , Ross James , Sallet Jèrôme , Kaiser Marcus 
Published: November 2023

AbstractLow-intensity transcranial ultrasound stimulation (TUS) is a non-invasive technique that safely alters neural activity, reaching deep brain areas with good spatial accuracy. We investigated the effects of TUS at the level of macaque using a recent metric, the synergy minus redundancy rank gradient, that quantifies different kinds of causal neural information processing. We analyzed this high-order quantity on the fMRI data after TUS in two targets: the supplementary motor area (SMA-TUS) and the frontal polar cortex (FPC-TUS). The TUS produced specific changes at the limbic network at FPC-TUS and the motor network at SMA-TUS and altered, in both targets, the sensorimotor, temporal, and frontal networks, consistent across macaques. Moreover, there was a reduction in the structural and functional coupling after both stimulations. Finally, the TUS changed the intrinsic high-order network topology, decreasing the modular organization of the redundancy at SMA-TUS and increasing the synergistic integration at FPC-TUS.
Genetic Influences on Educational Attainment Through the Lens of the Evolving Swedish Welfare State: A cross-level gene-environment interaction study based on polygenic indices and longitudinal register data
Authors: Pettersson Oskar 
Published: November 2023

AbstractGene-environment interaction with regards to educational attainment has received increasing attention during the last few years. However, the potential interdependence between different types of environments in gene-environment interaction models has mostly been neglected. Using high-quality register data for an extensive panel of Swedish twins, born during most of the twentieth century, this study explores how genetic propensities for educational attainment, as measured by a polygenic index, interact with both macro-level institutional and sociopolitical context, and with socioeconomic background. The analyses, which combine between-family and causally robust within-family models, suggest that the average association between genetic propensities and educational attainment has increased in Sweden during the twentieth century, along with the expansion of the educational system and decreased economic inequality. There is also evidence of a positive interaction between genetic propensities and socioeconomic background, but only in the oldest cohorts in the sample, and that were born before the Swedish welfare state had been fully established. This implies that micro-level gene-environment interactions can be significantly dependent on macro-level context, an insight that has arguably not yet been given sufficient attention in the literature. Acknowledging limitations of polygenic indices, and the arbitrariness of the genetic lottery, the results may nevertheless indicate a development towards higher equality of opportunity in Sweden during the twentieth century.
Sufficient COVID-19 quarantine and testing on international travelers from China
Authors: Bojja Dinesh , Zuo Scott , Townsend Jeffrey P. 
Published: November 2023

AbstractObjectivesRemoval of zero-COVID restrictions in China led to a surge in COVID-19 cases. In response, countries imposed restrictions on Chinese travelers. However, border policies may not provide substantial benefits and their assessment depends on accurate prevalence data.MethodsWe analyzed quarantines and testing sufficient to prevent additional in-country transmission for February 13–19, 2023 based on World Health Organization (WHO) and self-reported infection rates to estimate prevalence.ResultsHere we have shown that self-reported prevalence data indicated more stringent border restrictions compared to WHO-published prevalence statistics. No travel restrictions were required for Singapore for infections to not be greater than in complete border closure, while a 1-day quarantine, 2-day quarantine, and a 3-day quarantine were indicated for England, Germany, and Scotland respectively. A 10-day quarantine, 11-day quarantine, and 13-day quarantine were required for Italy, Japan, and France, respectively, to prevent an increase in the number of within-country infections due to travel, while South Korea required a complete border shutdown.ConclusionsOur results demonstrated the necessity for accurate and timely reporting of pandemic statistics to prevent an increase in viral spread. Through the minimum-quarantine analysis, countries can use science to determine policy, minimize international friction, and improve the cost-efficiency of interventions.
Cross-sectional associations between prenatal maternal per- and poly-fluoroalkyl substances and bioactive lipids in three Environmental influences on Child Health Outcomes (ECHO) cohorts
Authors: Suthar Himal , Manea Tomás , Pak Dominic , Woodbury Megan , Eick Stephanie M. , Cathey Amber , Watkins Deborah J. , Strakovsky Rita S. , Ryva Brad A. , Pennathur Subramaniam , Zeng Lixia , Weller David , Park June-Soo , Smith Sabrina , DeMicco Erin , Padula Amy , Fry Rebecca C. , Mukherjee Bhramar , Aguiar Andrea , Geiger Sarah Dee , Ng Shukhan , Huerta-Montanez Gredia , Vélez-Vega Carmen , Rosario Zaira , Cordero Jose F. , Zimmerman Emily , Woodruff Tracey J. , Morello-Frosch Rachel , Schantz Susan L. , Meeker John D. , Alshawabkeh Akram , Aung Max T. 
Published: November 2023

ABSTRACTBackgroundPer- and poly-fluoroalkyl substances (PFAS) exposure can occur through ingestion of contaminated food and water, and inhalation of indoor air contaminated with these chemicals from consumer and industrial products. Prenatal PFAS exposures may confer risk for pregnancy-related outcomes such as hypertensive and metabolic disorders, preterm birth, and impaired fetal development through intermediate metabolic and inflammation pathways.ObjectiveEstimate associations between maternal pregnancy PFAS exposure (individually and as a mixture) and bioactive lipids.MethodsOur study included pregnant women in the Environmental influences on Child Health Outcomes Program: Chemicals in our Bodies cohort (CiOB, n=73), Illinois Kids Developmental Study (IKIDS, n=287), and the ECHO-PROTECT cohort (n=54). We measured twelve PFAS in serum and 50 plasma bioactive lipids (parent fatty acids and eicosanoids derived from cytochrome p450, lipoxygenase, and cyclooxygenase) during pregnancy (median 17 gestational weeks). Pairwise associations across cohorts were estimated using linear mixed models and meta-analysis. Associations between the PFAS mixture and individual bioactive lipids were estimated using quantile g-computation.ResultsPFDeA, PFOA, and PFUdA were associated (p<0.05) with changes in bioactive lipid levels in all three enzymatic pathways (cyclooxygenase [n=6 signatures]; cytochrome p450 [n=5 signatures]; lipoxygenase [n=7 signatures]) in at least one combined cohort analysis. The strongest signature indicated that a doubling in PFOA corresponded with a 24.3% increase (95% CI [7.3%, 43.9%]) in PGD2 (cyclooxygenase pathway) in the combined cohort. In the mixtures analysis, we observed nine positive signals across all pathways associated with the PFAS mixture. The strongest signature indicated that a quartile increase in the PFAS mixture was associated with a 34% increase in PGD2 (95% CI [8%, 66%]), with PFOS contributing most to the increase.ConclusionsBioactive lipids were revealed as biomarkers of PFAS exposure and could provide mechanistic insights into PFAS’ influence on pregnancy outcomes, informing more precise risk estimation and prevention strategies.
Role of Cardiorespiratory Fitness and Mitochondrial Energetics in Reduced Walk Speed of Older Adults with Diabetes in the Study of Muscle, Mobility and Aging (SOMMA)
Authors: Ramos Sofhia V. , Distefano Giovanna , Lui Li-Yung , Cawthon Peggy M. , Kramer Philip , Sipula Ian J. , Bello Fiona M. , Mau Theresa , Jurczak Michael J. , Molina Anthony J. , Kershaw Erin E. , Marcinek David J. , Toledo Frederico G.S. , Newman Anne B. , Hepple Russell T. , Kritchevsky Stephen B. , Goodpaster Bret H. , Cummings Steven R. , Coen Paul M. 
Published: November 2023

ABSTRACTRationaleCardiorespiratory fitness and mitochondrial energetics are associated with reduced walking speed in older adults. The impact of cardiorespiratory fitness and mitochondrial energetics on walking speed in older adults with diabetes has not been clearly defined.ObjectiveTo examine differences in cardiorespiratory fitness and skeletal muscle mitochondrial energetics between older adults with and without diabetes. We also assessed the contribution of cardiorespiratory fitness and skeletal muscle mitochondrial energetics to slower walking speed in older adults with diabetes.FindingsParticipants with diabetes had lower cardiorespiratory fitness and mitochondrial energetics when compared to those without diabetes, following adjustments for covariates including BMI, chronic comorbid health conditions, and physical activity. 4-m and 400-m walking speeds were slower in those with diabetes. Mitochondrial oxidative capacity alone or combined with cardiorespiratory fitness mediated ∼20-70% of the difference in walk speed between older adults with and without diabetes. Further adjustments of BMI and co-morbidities further explained the group differences in walk speed.ConclusionsSkeletal muscle mitochondrial energetics and cardiorespiratory fitness contribute to slower walking speeds in older adults with diabetes. Cardiorespiratory fitness and mitochondrial energetics may be therapeutic targets to maintain or improve mobility in older adults with diabetes.ARTICLE HIGHLIGHTSWhy did we undertake this study?To determine if mitochondrial energetics and cardiorespiratory fitness contribute to slower walking speed in older adults with diabetes.What is the specific question(s) we wanted to answer?Are mitochondrial energetics and cardiorespiratory fitness in older adults with diabetes lower than those without diabetes? How does mitochondrial energetics and cardiorespiratory fitness impact walking speed in older adults with diabetes?What did we find?Mitochondrial energetics and cardiorespiratory fitness were lower in older adults with diabetes compared to those without diabetes, and energetics, and cardiorespiratory fitness, contributed to slower walking speed in those with diabetes.What are the implications of our findings?Cardiorespiratory fitness and mitochondrial energetics may be key therapeutic targets to maintain or improve mobility in older adults with diabetes.Graphical Abstract
Curating Retrospective Multimodal and Longitudinal Data for Community Cohorts at Risk for Lung Cancer
Authors: Li Thomas Z. , Xu Kaiwen , Chada Neil C. , Chen Heidi , Knight Michael , Antic Sanja , Sandler Kim L. , Maldonado Fabien , Landman Bennett A. , Lasko Thomas A. 
Published: November 2023

AbstractLarge community cohorts are useful for lung cancer research, allowing for the development and validation of predictive models. A robust methodology for (1) identifying lung cancer and pulmonary nodules from electronic health record (EHRs) as well as (2) associating longitudinal data with these conditions is needed to optimally curate cohorts at scale from clinical data. Both objectives present the challenge of labeling noisy multimodal data while minimizing assumptions about the data structure specific to any institution. In this study, we leveraged (1) SNOMED concepts to develop ICD-based decision rules for building a cohort that captured lung cancer and pulmonary nodules and (2) clinical knowledge to define time windows for collecting longitudinal imaging and clinical concepts. We curated three cohorts with clinical concepts and repeated imaging for subjects with pulmonary nodules from our Vanderbilt University Medical Center. Our approach achieved an estimated sensitivity 0.930 (95% CI: [0.879, 0.969]), specificity of 0.996 (95% CI: [0.989, 1.00]), positive predictive value of 0.979 (95% CI: [0.959, 1.000]), and negative predictive value of 0.987 (95% CI: [0.976, 0.994]). for distinguishing lung cancer from subjects with SPNs. This work represents a strategy for high-throughput curation of multi-modal longitudinal cohorts at risk for lung cancer from routinely collected EHRs.
Meta-analysis of RNA sequencing data from 534 skin samples shows substantial IL-17 effects in non-lesional psoriatic skin
Authors: Solvin Åshild Øksnevad , Chawla Konika , Jenssen Marita , Olsen Lene Christin , Furberg Anne-Sofie , Danielsen Kjersti , Saunes Marit , Hveem Kristian , Sætrom Pål , Løset Mari 
Published: November 2023

ABSTRACTPsoriasis is a common chronic inflammatory skin disease characterized by disturbed interactions between infiltrating immune cells and keratinocytes. To enhance our understanding of the underlying molecular and cellular mechanisms driving psoriasis pathobiology, and to identify potential biomarkers for disease severity, we conducted RNA sequencing of skin biopsies from 75 patients with psoriasis vulgaris and 46 non-psoriatic controls. To increase the robustness of the results, we meta-analysed our data with four publicly available datasets, bringing the total number of samples to 534. By comparing lesional psoriatic (PP) to healthy control (NN) skin, we identified 2269 differentially expressed genes (DEGs) (|log2FC|>1.0, FDR <0.1), and 58 DEGs when comparing non-lesional psoriatic (PN) to NN skin. We also identified 54 DEGs associated with disease severity (PASI ≥10 vs. PASI <10). Cellular deconvolution analysis showed that differentiated keratinocytes emerged as the most prominent cell type among the DEGs in PP/NN. Functional enrichment analysis in PN/NN revealed several IL-17 related pathways and confirmed a previously reported ‘pre-inflammatory signature’ across all psoriatic skin. This study provides insights into the psoriasis transcriptome and identifies a severity-specific signature, which may serve as candidate for future studies aimed at identifying psoriasis biomarkers and predicting disease progression.
Accelerated biological aging six decades after prenatal famine exposure
Authors: Cheng Mengling , Conley Dalton , Kuipers Tom , Li Chihua , Ryan Calen , Taubert Jazmin , Wang Shuang , Wang Tian , Zhou Jiayi , Schmitz Lauren L. , Tobi Elmar W. , Heijmans Bas , Lumey L.H. , Belsky Daniel W. 
Published: November 2023

AbstractTo test the hypothesis that early-life adversity accelerates the pace of biological aging, we analyzed data from the Dutch Hunger Winter Families Study (DHWFS, N=951). DHWFS is a natural-experiment birth-cohort study of survivors of in-utero exposure to famine conditions caused by the German occupation of the Western Netherlands in Winter 1944-5, matched controls, and their siblings. We conducted DNA methylation analysis of blood samples collected when the survivors were aged 58 to quantify biological aging using the DunedinPACE, GrimAge, and PhenoAge epigenetic clocks. Famine survivors had faster DunedinPACE, as compared with controls. This effect was strongest among women. Results were similar for GrimAge, although effect-sizes were smaller. We observed no differences in PhenoAge between survivors and controls. Famine effects were not accounted for by blood-cell composition and were similar for individuals exposed early and later in gestation. Findings suggest in-utero undernutrition may accelerate biological aging in later life.Significance StatementEnvironmental conditions during gestation are hypothesized to shape health across the life course. The Dutch Hunger Winter, a famine caused by a German blockade of the Western Netherlands in late 1944 and ended by the allied liberation of the Netherlands in Spring 1945, has been studied as a “natural experiment” in which the timing of a child’s conception determined their exposure to severe under-nutrition during gestation. We applied this natural-experiment design to test effects of in-utero adversity on midlife biological aging, as measured by epigenetic clocks. We found that individuals with in-utero famine exposure had a faster pace of biological aging six decades later. The environmental conditions surrounding pregnancy have potential to shape aging trajectories for the next generation.
Plasma proteome signature of canine acute haemorrhagic diarrhoea syndrome (AHDS)
Authors: Huber Lukas , Kuropka Benno , Doulidis Pavlos G. , Baszler Elisabeth , Martin Lukas , Rosu Anda , Kulmer Lisa , Ramos Carolina Frizzo , Rodríguez-Rojas Alexandro , Burgener Iwan A. 
Published: November 2023

AbstractAcute haemorrhagic diarrhoea is a common complaint in dogs. In addition to causes like intestinal parasites, dietary indiscretion, intestinal foreign bodies, canine parvovirus infection, or hypoadrenocorticism, acute haemorrhagic diarrhoea syndrome (AHDS) is an important and sometimes life-threatening differential diagnosis. There is some evidence supporting the link betweenClostridium perfringenstoxins and AHDS. These toxins may be partially responsible for the epithelial cell injury, but the pathogenesis of AHDS is still not fully understood. Recent studies have suggested that severe damage to the intestinal mucosa and associated barrier dysfunction can trigger chronic gastrointestinal illnesses. Besides bloodwork and classical markers for AHDS such as protein loss and intestinal bacterial dysbiosis, we focused mainly on the plasma-proteome to identify systemic pathological alterations during this disease and searched for potential biomarkers to improve the diagnosis. To accomplish the goals, we used liquid chromatography-mass spectrometry. We compared the proteomic profiles of 20 dogs with AHDS to 20 age-, breed-, and sex-matched control dogs. All dogs were examined, and several blood work parameters were determined and compared, including plasma biochemistry and cell counts. We identified and quantified 207 plasmatic proteins, from which dozens showed significantly altered levels in AHDS. Serpina3, Lipopolysaccharide-binding protein, several Ig-like domain-containing proteins, Glyceraldehyde-3-phosphate dehydrogenase and Serum amyloid A were more abundant in plasma from AHDS affected dogs. In contrast, other proteins such as Paraoxonase, Selenoprotein, Amine oxidases, and Apolipoprotein C-IV were significantly less abundant. Many of the identified and quantified proteins are known to be associated with inflammation. Other proteins like Serpina3 and RPLP1 have a relevant role in oncogenesis. Some proteins and their roles have not yet been described in dogs with diarrhoea. Our study opens new avenues that could contribute to the understanding of the aetiology and pathophysiology of AHDS.