bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells
Authors: Nguyen Dat Thanh 
Published: March 2023

AbstractMolecular quantitative trait locus (QTL) mapping of genetic variants with intermediate molecular phenotypes has proven to be a powerful approach for prioritizing genetic regulatory variants and causal genes identified by Genome-wide association studies (GWAS). Recently, this success has been extended to circular RNA (circRNA), a potential group of RNAs that can serve as markers for the diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and autoimmune diseases. However, the detection of circRNA QTL (circQTL) currently is heavily reliant on a single circRNA detection algorithm for circRNA annotation and quantification which implies limitations in both sensitivity and specificity. In this study, we show that circQTL results produced by different circRNA calling tools are extremely divergent, making difficulties in interpretation. To resolve this issue, we develop an integrative method for circQTL mapping and implement it as an automated, reproducible, and scalable, and easy-to-use framework based on Nextflow, named cscQTL. Compared to the existing approach, the new method effectively identify circQTLs with an increase of 20-100% circQTLs detected and recovered all circQTLs that are highly supported by the single method approach. We apply the new method to a dataset of human T cells and discover genetic variants that control the expression of 55 circRNAs. By collocation analysis, we further identify circBACH2 and circYY1AP1 as potential candidates for immune disease regulation. cscQTL is freely available at:https://github.com/datngu/cscQTL.
Atmospheric transport of particulate matter and particulate-bound agrochemicals from beef cattle feedlots: human health implications for downwind agricultural communities
Authors: Emert Amanda D. , Green Frank B. , Griffis-Kyle Kerry , Smith Philip N. 
Published: March 2023

AbstractBackgroundBeef cattle feedlot-derived particulate matter (PM) is a complex mixture of dust, animal waste, agrochemicals, and bioaerosols. No empirical data currently exists quantifying human exposure of PM-bound agrochemicals downwind of feedlots.ObjectivesThere were three objectives of the current study: 1) to determine spatial extent and magnitude of PM transport downwind of large beef cattle feedlot facilities, 2) to quantify occurrence of pyrethroid insecticides and anthelmintics in feedlot-derived PM, and 3) to assess cumulative human health risk of agrochemicals in agriculture-adjacent communities downwind of feedlots.MethodsAuthors investigated downwind transport (<1 to >12 km) of total suspended particulates (TSP) from three feedlots in the Southern Great Plains (SGP) of North America. PM collected on TSP filters was analyzed via UHPLC-MS/MS for six pyrethroids (bifenthrin, λ-cyhalothrin, cypermethrin, esfenvalerate, fenvalerate, and permethrin) and five macrocyclic lactones (MLs; abamectin, doramectin, eprinomectin, ivermectin, and moxidectin). An empirical distance decay model was used to determine probabilistic PM concentrations in downwind ambient air.ResultsDownwind TSP concentrations exhibited rapid decline from 0.01 - ≤1.6 km (Monte Carlo-simulated mean ± SEM; 5,049 ± 96.1 µg/m3) and subsequent stabilization >1.6 – 12.4 km (1,791 ± 9.9; µg/m3). TSP concentrations did not converge to background levels within the spatial extent of the study (12.4 km). Agrochemicals were detected downwind >LOQ at greater overall frequency (40.6%) than upwind locations (26.8%). Two pyrethroids were detected at the highest overall downwind concentrations (mean ± SEM; fenvalerate = 5.9 ± 0.8, permethrin = 1.1 ± 0.3 ng/m3), and screening-level cumulative exposure estimates indicate elevated pyrethroid risk (LOC = 1; RI = 0.173) in children (1-2 yrs) living near commercial agricultural operations in the SGP.DiscussionResults significantly expand the known distribution of feedlot-derived PM and agrochemicals, and consequently highlight exposure pathways unrecognized in residential human health assessments and feedlot risk evaluations.
Home-Cage Sipper Devices Reveal Age and Sex Differences in Ethanol Consumption Patterns
Authors: Rice RC , Baratta AM , Farris SP 
Published: March 2023

AbstractFree-choice paradigms such as two-bottle choice (2BC) are commonly used to characterize ethanol consumption and preference of rodent models used to study alcohol use disorder (AUD). However, these assays are limited by low temporal resolution that misses finer patterns of drinking behavior, including circadian drinking patterns that are known to vary with age and sex and are affected in AUD pathogenesis. Modern, cost-effective tools are becoming widely available that could elucidate these patterns, including open-source, Arduino-based home-cage sipper devices. We hypothesized that adaptation of these home-cage sipper devices would uncover distinct age- and sex-related differences in temporal drinking patterns. To test this hypothesis, we used the sipper devices in a continuous 2BC paradigm using water and ethanol (10%; v/v) for 14 days to measure drinking patterns of male and female adolescent (3-week), young adult (6-week), and mature adult (18-week) C57BL/6J mice. Daily grams of fluid consumption were manually recorded at the beginning of the dark cycle, while home-cage sipper devices continuously recorded the number of sips. Consistent with prior studies, females consumed more ethanol than males, and adolescent mice consumed the most out of any age group. Correlation analyses of manually recorded fluid consumption versus home-cage sipper activity revealed a statistically significant prediction of fluid consumption across all experimental groups. Sipper activity was able to capture subtle circadian differences between experimental groups, as well as distinct individual variation in drinking behavior among animals. Blood ethanol concentrations were significantly correlated with sipper data, suggesting that home-cage sipper devices can accurately determine individual timing of ethanol consumption. Overall, our studies show that augmenting the 2BC drinking paradigm with automated home-cage sipper devices can accurately measure ethanol consumption across sexes and age groups, revealing individual differences and temporal patterns of ethanol drinking behavior. Future studies utilizing these home-cage sipper devices will further dissect circadian patterns for age and sex relevant to the pathogenesis of AUD, as well as underlying molecular mechanisms for patterns in ethanol consumption.HighlightsFemale mice consume more ethanol than males in a continuous access paradigmAdolescent male and female mice consume more ethanol than young or mature adult miceAutomated home-cage sipper devices accurately measure ethanol consumptionDevices reveal sex- and age-dependent differences in circadian drinking patternsDevices reveal distinct individual variation in circadian drinking patterns
The immune receptor SNC1 monitors helper NLRs targeted by a bacterial effector
Authors: Wang Ming-Yu , Chen Jun-Bin , Wu Rui , Guo Hai-Long , Chen Yan , Li Zhen-Ju , Wei Lu-Yang , Liu Chuang , He Sheng-Feng , Du Mei-Da , Guo Ya-long , Peng You-Liang , Jones Jonathan DG , Weigel Detlef , Huang Jian-Hua , Zhu Wang-Sheng 
Published: March 2023

SUMMARYPlants deploy intracellular receptors to counteract pathogen effectors that suppress cell-surface receptor-mediated immunity. To what extent pathogens manipulate also immunity mediated by intracellular receptors, and how plants tackle such manipulation, remains unknown.Arabidopsis thalianaencodes three very similar ADR1 class helper NLRs (ADR1, ADR1-L1 and ADR1-L2), which play key roles in plant immunity initiated by intracellular receptors. Here, we report thatPseudomonas syringaeAvrPtoB, an effector with E3 ligase activity, can suppress ADR1-L1- and ADR1-L2-mediated cell death. ADR1, however, evades such suppression by diversification of two ubiquitination sites targeted by AvrPtoB. The intracellular sensor NLR SNC1 interacts with and guards the CCRdomains of ADR1-L1 and ADR-L2. Removal of ADR1-L1 and ADR1-L2 or delivery of AvrPtoB activates SNC1, which then signals through ADR1 to trigger immunity. Our work not only uncovers the long sought-after physiological function of SNC1 in pathogen defense, but also that reveals how plants can use dual strategies, sequence diversification and a multiple layered guard-guardee system, to counteract pathogen attack on core immunity functions.
Past, present and future in the geographical distribution of Mexican tepezmaite cycads: genusCeratozamia
Authors: Gómez-Díaz Jorge Antonio , Carvajal-Hernández César Isidro , Dáttilo Wesley 
Published: March 2023

AbstractCeratozamia morettii,C. brevifronsandC. tenuisare cycads considered endangered in montane forests in the center of Veracruz state. However, the amount of theoretical and empirical information available on the historical distribution of these species and how they could be affected in the future by the effects of climate change is still limited. Our objective was to generate information on the spatial distribution of the species since the last glacial maximum, present and future. To map the spatial distribution of species, we created a potential distribution model for each species. The spatial data used for the models included 19 bioclimatic data variables in the present, at the last glacial maximum using two models (CCSM4 and MIROC), and in the future (2080) using two models of the RCP 8.5 scenario of climate change (HadGEM2-CC and MIROC5). We found that each species occupies a unique ecoregion and climatic niche.Ceratozamia morettiiandC.tenuishave a similar pattern with an expansion of their distribution area since the last glacial maximum with the larger distribution area in the present, and with a projected reduction in their distribution under future climatic conditions. ForC. brevifrons,we also showed an increase in their distributional area since the last glacial maximum and we showed that this expansion will continue under future climatic conditions when the species will reach its maximum distributional area. Projections about the future of these endemic cycad species show changes in their habitat highlighting that temperate zone species will face imminent extinction if no effort is made to protect them. On the other hand, the tropical climate species will apparently be favored.
Egr-2 coordinates intestinal remodeling by promoting midline patterning and pharynx regeneration in planarians
Authors: Morkotinis Vasileios , Forsthoefel David J. 
Published: March 2023

AbstractRegeneration requires remodeling of pre-existing structures and their integration with new cells and tissue. Identification of injury-induced regulators of these processes is central to regenerative biology. In planarian flatworms, the intestine remodels after amputation to re-establish normal morphology and integrate with the regenerating pharynx, the centrally located feeding organ. How these events are initiated and coordinated is currently unclear. In a candidate screen for injury-induced regulators of intestinal regeneration, we found that the transcription factor Early growth response protein 2 (Egr-2) was required for collective migration and fusion of intestinal branches at the anterior midline. Even though inhibition ofegr-2by RNA interference increased dorsoventral (DV) muscle fibers at the midline between intestinal branches, bulk RNA sequencing of regenerating tissue revealed negligible dysregulation of DV-, body wall-, or intestinal-muscle-associated transcripts. Instead, the midline polarity cueslit-1and subsets of pharynx-associated transcripts were dysregulated. Bothegr-2andslit-1RNAi delayed early pharynx regeneration, consistent with reducedslit-1expression inegr-2(RNAi)regenerates in the region of pharynx specification. Furthermore, inhibition of pharynx regeneration regulatorsfoxF-1andfoxAdelayed integration with the intestine and disrupted formation of the intestine’s midline anterior branch.Our findings suggest that the pharynx plays an inductive role in initiation of intestinal remodeling, and demonstrate how injury-induced reprogramming influences subsequent tissue assembly and integration during regeneration.
Identifying environmental factors affecting the production of pea aphid dispersal morphs in field populations
Authors: Bosch Michael J , Ives Anthony R 
Published: March 2023

AbstractMany species of insects show phenotypically plastic dispersal traits in response to suboptimal environmental conditions. These polyphenetic traits can have large impacts on the population dynamics of the dispersing insects. Therefore, it is important to understand what environmental factors affect the development of dispersal traits and how these factors affect population dynamics via immigration/emigration.Pea aphids (Acyrthosiphon pisum) exhibit a polyphenetic wing dimorphism in which individuals are either winged (alate) or not (apterous). The production of alate offspring is determined by environmental cues experienced by the mother. Environmental factors associated with these cues have been intensively studied, with crowding, host plant quality, natural enemies, and fungal infection being shown to affect the production of pea aphid alates under controlled laboratory conditions. Nonetheless, environmental factors affecting alate production have rarely been studied in field populations of pea aphids.Using data from a three-year study of alate production in 5-9 alfalfa (lucerne) fields, we examined the effects of (i) pea aphid abundance, (ii) host plant maturity, (iii) temperature, (iv) predator and herbivore abundance, (v) parasitism, and (vi) entomopathic fungal incidence. In twice-weekly samples taken over the growing season, alate production ranged from 0 to 83% of the nymphal population.Pea aphid abundance, temperature, and alfalfa maturity together explained 67% of the variation in alate production. The other factors we investigated explained little variation. These results suggest there is a limited number of key environmental factors that consistently predict changes in alate production in field populations, while many factors identified in lab studies may be unimportant. Our results highlight the value of investigating factors affecting the expression of plastic traits in insect species at a broad spatiotemporal scale and under natural conditions.
Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization
Authors: Li Dean , Ge Shuwen , Liu Yandong , Pan Miaomiao , Wang Xueting , Han Guojing , Zou Sili , Liu Rui , Niu Kongyan , Zhao Chao , Liu Nan , Qu Lefeng 
Published: March 2023

ABSTRACTThe hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA transcription to result in NAD-capped RNA (NAD-RNA). NAD-RNA that intimately connects metabolite with gene expression can be developed as novel biomarkers for aging and disease. Epitranscriptome-wide profiling of NAD-RNAs involves chemo-enzymatic labeling and affinity-based enrichment; yet currently available computational analysis cannot adequately remove variations associated with capture procedures. Here, we propose a spike-in-based normalization and data-driven evaluation framework, enONE, for the omic-level analysis of NAD-capped RNAs. We demonstrate that carefully designed spike-in RNAs, together with modular normalization procedures and evaluation metrics, can lead to the optimal normalization that maximally removes unwanted variations, empowering quantitative and comparative assessment of NAD-RNAs from different datasets. Using enONE and a human aging cohort, we reveal critical features of NAD-capped RNAs that occur with normal age. enONE facilitates the discovery of NAD-capped RNAs that are responsive to physiological changes, laying a critical foundation for functional investigations into this modification.
Model-based concept to extract heart beat-to-beat variations beyond respiratory arrhythmia and baroreflex
Authors: Baranauskas Mindaugas , Stanikūnas Rytis , Kaniušas Eugenijus , Lukoševičius Arūnas 
Published: March 2023

AbstractHeart rate (HR) and its variability (HRV) reflect the autonomous nervous system (ANS) modulation, especially sympathovagal balance. This work aims to present concept of a personalizable HR model and an in silico system to identify the HR regulation parameters and subsequently capture residual heart beat-to-beat variations from individual psychophysiological recordings in humans. The model encompasses respiratory sinus arrhythmia (RSA) and baroreflex mechanisms, and uses respiration and blood pressure signals and the time instances of R peaks from an electrocardiogram as inputs. The system extracts the residual displacements of the modeled R peaks relative to the real R peaks. Three components – tonic, spontaneous, and 0.1 Hz changes – can be derived from these R peak residual displacements and can, therefore, enhance HRV analysis beyond RSA and baroreflex. Our model-based concept suggests that these residuals are not merely modeling errors. The proposed method could help to investigate additional neural regulation impulses from the higher-order brain and other influences.
UropathogenicEscherichia colipopulation structure and antimicrobial susceptibility in Norfolk, UK
Authors: Carter Cailean , Hutchison Alexandra , Rudder Steven , Trotter Elizabeth , Waters Emma , Elumogo Ngozi , Langridge Gemma C. 
Published: March 2023

SynopsisBackgroundHalf of all women have experienced a urinary tract infection (UTI) in their lifetime and this remains a persistent issue in rural counties like Norfolk, UK. In alignment globally, UropathogenicE. coli(UPEC) are the main etiological agent for UTIs in Norfolk and are increasingly difficult to treat due to multi-drug resistance (MDR).ObjectiveWe set out to identify which clonal groups and resistance genes are disseminating in the community and hospitals in Norfolk, the first study of its kind for UPEC in this region.MethodsWe collected 217 clinicalE. coliisolates causing UTIs in the community and hospital from the Clinical Microbiology laboratory at Norfolk and Norwich University Hospital. These were whole genome sequenced using the Illumina and MinION platforms forin silicomulti-locus sequence typing and antibiotic resistance determinant detection.ResultsThe isolates were composed of 74 sequence types (STs); 8 lineages represented 57% of this population: ST73, ST12, ST69, ST131, ST404, ST95, ST127, and ST1193. Importantly, primary UTI screening deemed 8% of isolates to be MDR, with high rates of resistance to ampicillin (52.1%) and trimethoprim (36.2%) in hospitals. Of concern is the probable clonal expansion of MDR groups ST131 and ST1193 in hospitals and community settings with chromosomally encodedblaCTX-M-15,blaOXA-1, and aac(6’)-Ib-cr5.ConclusionsThe burden of reported UTIs in Norfolk is largely caused by non-MDR isolates. The UPEC population is continually evolving, and monitoring samples with consideration of sources will help reduce burden of disease.
TheHypolimnas misippusgenome supports a common origin of the W chromosome in Lepidoptera
Authors: Orteu Anna , McCarthy Shane A. , Hornett Emily A. , Gemmell Matthew R. , Reynolds Louise A. , Warren Ian A. , Gordon Ian J. , Hurst Gregory D. D. , Durbin Richard , Martin Simon H. , Jiggins Chris D. 
Published: March 2023

AbstractMoths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of twoHypolimnasspecies (Hypolimnas missipusandHypolimnas bolina)and use theH. misippusassembly to explore the evolution of W chromosomes in butterflies and moths. We show that inH. misippusthe W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins.SignificanceButterflies and moths have a sex determination system in which females carry two different sex chromosomes, Z and W, while males carry two copies of the Z. The evolutionary origin of the W chromosome has been elusive, with many possible scenarios being suggested, such as the independent evolution of W chromosomes in many butterfly and moth species. Here, we present genome assemblies of twoHypolimnasbutterfly species and use one of them to shed light on the evolution of the W chromosome. We show that W chromosomes across butterflies and moths are very similar which suggests a shared common origin.
Experimental heatwaves and warming cause distinctive community responses through their interactions with a novel species
Authors: Chen Jinlin , Lewis Owen T. 
Published: March 2023

AbstractAs mean temperatures increase and heatwaves become more frequent, species are expanding their distributions to colonise new habitats. The resulting novel species interactions will simultaneously shape the temperature-driven reorganization of resident communities. The interactive effects of climate change and climate change-facilitated invasion have rarely been studied in multi-trophic communities, and are likely to differ depending on the nature of the climatic driver (i.e. climate extremes or constant warming). We recreated under laboratory conditions a host-parasitoid community typical of high-elevation rainforest sites in Queensland, Australia, comprising fourDrosophilaspecies and two associated parasitoid species. We subjected these communities to climate change in the form of either heatwaves or constant warming, in combination with an invasion treatment involving a novel host species from lower-elevation habitats. The two parasitoid species were sensitive to both warming and heatwaves, while the demographic responses ofDrosophilaspecies were highly idiosyncratic, reflecting the combined effects of thermal tolerance, parasitism, competition, and facilitation. After multiple generations, heatwaves (but not constant warming) promoted the establishment of low-elevation species in upland communities. The introduction of this invading species correlated negatively with the abundance of one of the parasitoid species, leading to cascading effects on its hosts and their competitors. Our study, therefore, reveals differing, sometimes contrasting, impacts of extreme temperatures and constant warming on community composition. It also highlights how the scale and direction of climate impacts could be further modified by range-expanding species within a bi-trophic community network.