bluuebunny/crossref_metadata_2025_split huggingface dataset:
The spatial-temporal effect of air pollution on GP visits and hospital admissions by ethnicity in the United Kingdom: An individual-level analysis
Authors: Al Ahad Mary Abed 
Published: September 2022

AbstractBackgroundAir pollution has been associated with increased rates of hospital admissions and general-practitioner (GP) visits. Yet, more research is to be done to reveal the spatial-temporal dimension of this association and whether ethnic minorities experience greater effects from exposure to air pollution compared to the rest of population. This study investigates the spatial-temporal effect of air pollution on GP visits and hospital admissions by ethnicity in the United-Kingdom (UK).MethodsWe used individual-level longitudinal data from the “UK Household Longitudinal Study” including 46,442 adult individuals who provided 140,466 responses across five years (2015-2019). This data was linked to yearly concentrations of NO2, SO2, and particulate-matter (PM10, PM2.5) pollution using the Lower-Super-Output-Area (LSOA) of residence for each individual. We distinguished between spatial (between areas) and temporal (across time within each area) effects of air pollution on GP visits and hospital admissions and we used multilevel mixed-effects ordered logistic models for analysis.ResultsResults showed higher odds of outpatient hospital admissions with increasing concentrations of NO2 (OR=1.009; 95%CI=1.006-1.013), SO2 (OR=1.063; 95%CI=1.030-1.097), PM10 (OR=1.013; 95%CI=1.006-1.021), and PM2.5 (OR=1.022; 95%CI=1.012-1.032) pollutants. Higher odds of GP visits were also observed with increasing concentrations of NO2 (OR=1.011; 95%CI=1.007-1.015) and SO2 (OR=1.123; 95%CI=1.087-1.160) pollutants. Decomposing air pollution into between (spatial: across LSOAs) and within (temporal: across years within each LSOA) effects, showed significant between effects for air pollution on GP visits and hospital admissions, but not within effects. We observed no differences between ethnic minorities and British-white for the association between air pollution and hospital admissions and GP visits.ConclusionUsing individual-level longitudinal data, our study supports the presence of a spatial-temporal association between air pollution and hospital admissions and GP visits. However, ethnic minorities do not seem to experience greater health-related effects from exposure to air pollution compared to the rest of population.
Comparisons Between GPS-based and Self-reported Life-space Mobility in Older Adults
Authors: Bai Chen , Zapata Ruben , Karnati Yashaswi , Smail Emily , Hajduk Alexandra M. , Gill Thomas M. , Ranka Sanjay , Manini Todd M. , Mardini Mamoun T. 
Published: September 2022

AbstractAssessments of Life-space Mobility (LSM) evaluate the locations of movement and their frequency over a period of time to understand mobility patterns. Advancements in and miniaturization of GPS sensors in mobile devices like smartwatches could facilitate objective and high-resolution assessment of life-space mobility. The purpose of this study was to compare self-reported measures to GPS-based LSM extracted from 27 participants (44.4% female, aged 65+ years) who wore a smartwatch for 1-2 weeks at two different site locations (Connecticut and Florida). GPS features (e.g., excursion size/span) were compared to self-reported LSM with and without an indicator for needing assistance. Although correlations between self-reported measures and GPS-based LSM were positive, none were statistically significant. The correlations improved slightly when needing assistance was included, but statistical significance was achieved only for excursion size (r=0.40, P=0.04). The poor correlations between GPS-based and self-reported indicators suggest that they capture different dimensions of life-space mobility.
Super resolution ultrasound imaging Using deep learning based micro-bubbles localization
Authors: Long Feixiao , Zhang Weiguang 
Published: September 2022

AbstractSuper resolution ultrasound imaging has shown its potential to detect minor structures of tissues beyond the limit of diffraction and achieve sub-wavelength resolution through localizing and tracking the ultrasound contrast agents, such as micro-bubbles. Normally, one important step of super resolution ultrasound imaging, micro-bubbles localization is implemented through conventional computer vision techniques, such as local maxima detection etc. However, these classical techniques are generally time consuming and need fine-tuning multiple parameters to achieve the optimal results. Hence, in the manuscript, a deep learning based micro-bubbles localization is proposed, trying to replace or simplify the complex operations of classical methods. The efficiency of our proposed models is preliminarily proved through 2022 ultra-SR challenge.
Bitter taste receptor-stimulated nitric oxide innate immune responses are reduced by loss of CFTR function in nasal epithelial cells and macrophages
Authors: Carey Ryan M. , Palmer James N. , Adappa Nithin D. , Lee Robert J. 
Published: September 2022

AbstractBitter taste receptors (T2Rs) are G protein-coupled receptors identified on the tongue but expressed all over the body, including in airway cilia and macrophages, where T2Rs serve an immune role. T2R isoforms detect bitter metabolites (quinolones and acyl-homoserine lactones) secreted by gram negative bacteria, includingPseudomonas aeruginosa, a major pathogen in cystic fibrosis (CF). T2R activation by bitter bacterial products triggers calcium-dependent nitric oxide (NO) production. In airway cells, the NO increases mucociliary clearance and has direct antibacterial properties. In macrophages, the same pathway enhances phagocytosis. Because prior studies linked CF with reduced NO, we hypothesized that CF cells may have reduced T2R/NO responses. Using qPCR, immunofluorescence, and live cell imaging of air-liquid interface cultures, we found primary nasal epithelial cells from both CF and non-CF patients exhibited similar T2R expression, localization, and calcium signals. However, CF cells exhibited reduced NO production also observed in immortalized CFBE41o-CF cells and non-CF 16HBE cells CRISPR modified with CF-causing mutations in the CF transmembrane conductance regulator (CFTR). NO was restored by VX-770/VX-809 corrector/potentiator pre-treatment, suggesting reduced NO in CF cells is due to loss of CFTR function. In nasal cells, reduced NO correlated with reduced ciliary and antibacterial responses. In primary human macrophages, inhibition of CFTR reduced NO production and phagocytosis during T2R stimulation. Together, these data suggest an intrinsic deficiency in T2R/NO signaling caused by loss of CFTR function that may contribute to intrinsic susceptibilities of CF patients toP. aeruginosaand other gram-negative bacteria that activate T2Rs.
GRETA: an R package for mapping in silico genetic interaction and essentiality networks
Authors: Takemon Yuka , Marra Marco A. 
Published: September 2022

AbstractSummaryMapping genetic interaction and essentiality networks in human cell lines have been used to identify vulnerabilities of cells carrying specific genetic alterations and to associate novel functions to genes, respectively. In vitro and in vivo genetic screens to decipher these networks are resource-intensive, limiting the throughput of samples that can be analyzed. In this application note, we provide an R package we call Genetic inteRaction and EssentialiTy mApper (GRETA). GRETA is an accessible tool for in silico genetic interaction screens and essentiality network analyses using publicly available data, requiring only basic R programming knowledge.Availability and implementationThe R package, GRETA, is licensed under GNU General Public License v3.0 and freely available at https://github.com/ytakemon/GRETA and https://doi.org/10.5281/zenodo.6940757, with documentation and tutorial. A Singularity container is also available at https://cloud.sylabs.io/library/ytakemon/greta/greta.Contactmmarra@bcgsc.caSupplemental informationSupplemental materials are available at Bioinformatics online.Issue sectionSystems biology
Palbociclib interferes with replication origin firing in a pRb independent manner
Authors: Kim Su-Jung , Maric Chrystelle , Briu Lina-Marie , Fauchereau Fabien , Baldacci Giuseppe , Debatisse Michelle , Koundrioukoff Stéphane , Cadoret Jean-Charles 
Published: September 2022

AbstractOver the last decade, CDK4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have emerged as promising anticancer drugs. Numerous studies have demonstrated that CDK4/6 inhibitors efficiently block the pRb-E2F pathway and induce cell cycle arrest in pRb-proficient cells. Based on these studies, the inhibitors have been approved by the FDA for treatment of advanced hormonal receptor (HR) positive breast cancers in combination with hormonal therapy. However, some evidence has recently shown unexpected effects of the inhibitors, promoting needs to understand more about the mechanism of inhibitors beyond pRb. Our study demonstrates here how palbociclib impairs the origin firing in the DNA replication process in pRb-deficient cell lines. Strikingly, despite the absence of pRb, cells treated with palbociclib synthesize less DNA without any induced cell cycle arrest. Furthermore, palbociclib treatment disturbs the temporal program of DNA replication and reduces the density of replication forks. Cells treated with palbociclib show a defect in the loading of proteins of the Pre-initiation complex (Pre-IC) on chromatin, indicating a reduced initiation of DNA replication. Our findings highlight hidden effects of palbociclib on the dynamics of DNA replication and on its cytotoxic consequences on cell viability in the absence of pRb. This study provides a potential therapeutic application of palbociclib to target genomic instability towards pRb deficient patients.Significance StatementPalbociclib is a promising anticancer drug for pRb-proficient cell, particularly for hormonal receptor positive breast cancer, that induces the cell cycle arrest. But what about pRb deficient cell lines ? Our results show that Palbociclib disturb the DNA replication process inducing a replicative stress, an increase of DNA damages and leading to a significant decrease in cell viability. Palbociclib impairs the DNA synthesis reducing the number of active origins with the decrease of availability of the pre-initiation complexes. We believe that the demonstration of this effect of palbociclib on pRb-deficient cells may be a new therapeutic entry point in combination with other treatments for these types of cancer. Replicative stress can be one of weaknesses of pRb defficient cancer cells.
From southern Africa and beyond: historical biogeography of a monocotyledonous bulbous geophyte
Authors: Howard Cody Coyotee , Nanyeni Leevi , Mollel Neduvoto , Chuba David , Zuntini Alexandre R. , Malakasi Panagiota , Harvey Timothy S. , Cellinese Nico 
Published: September 2022

AbstractAimWithin sub-Saharan Africa, plants inhabiting more seasonal and arid landscapes showcase unique distributional patterns that hint at fascinating evolutionary histories. The Ledebouriinae (Scilloideae, Asparagaceae) are widespread throughout such climates in sub-Saharan Africa, and Madagascar, the Middle East, India, and Sri Lanka. Long-distance dispersal has been hypothesized as leading to such a widespread distribution; however, low taxon sampling and taxonomic uncertainties have made uncovering the history of the Ledebouriinae difficult. Here, using the most comprehensive sampling of the lineage to date, we hypothesize that both vicariance and dispersal events impacted the biogeographical history of these bulbous monocots within and outside of Africa.LocationSub-Saharan Africa, Madagascar, AsiaTaxonLedebouriinae (Scilloideae, Asparagaceae)MethodsWe infer age estimates using penalized likelihood as implemented in treePL. Capitalizing on our broad geographic sampling, we use ‘BioGeoBEARS’ to reconstruct ancestral ranges and investigate the role of vicariance and dispersal.ResultsOur results suggest the Ledebouriinae originated within the past ∼30 myr in southeastern sub-Saharan Africa, with the major subclades arising soon thereafter. Although long-distance dispersal cannot be fully ruled out, our results lead us to hypothesize vicariance was the major process responsible for the current distribution ofLedebouriain Eurasia. We recover two distinctLedebouriagroups that overlap in eastern Africa, but are divided into mostly northern and southern clades with divergent biogeographical histories, and each showing an independent dispersal to Madagascar. A similar north-south split is seen inDrimiopsis. Additionally, we recover a complex biogeographic history in the predominantly sub-Saharan AfricanLedebouriaclade, with a rapid radiation estimated at ∼14 mya.Main conclusionsWe recover evidence to suggest that the expansion of seasonal rainfall and aridity in sub-Saharan Africa, coupled with orogeny, may have fostered the diversification of the Ledebouriinae and many subclades. Miocene-driven aridification may have caused fragmentation of a once widespread distribution that led to their occurrence in Eurasia.
Rethinking the functions of peacock’s display and lek organisation in native populations of Indian PeafowlPavo cristatus
Authors: Paranjpe Dhanashree Ashok , Mahimkar Vedanti Rajiv , Dange Priyanka 
Published: September 2022

AbstractMales of Indian Peafowl are known for their extravagant courtship display used to attract mates. The displays are seen in absence of potential mates as well. This study investigates various contexts in which display behaviours are shown by Indian peafowl. Upto 70% of displays were observed in absence of potential mates. High frequency of displays in presence of other males and longer display bouts during the month of May when mating rarely happens, indicated that display behaviours might have a role to play in male-male competition or territory defence in addition to the female mate choice. The males establish and maintain their courtship display territories throughout the breeding season. Earlier studies assume that the choice of location does not depend on any resources as the species has a lek mating system. How these display sites are chosen is still a question. In this study, we investigated factors that might be important for the selection of display sites in a free-ranging Indian Peafowl population. It was observed that display sites were more concentrated within a radius of 300 meters of the food provisioning site and/ or a water resource while the number of display sites decreased considerably beyond the 300 m radius of food and water resources. Overall, the selection of display sites is non-random and highlights the importance of resources in the choice of display territories. The spatial organisation of leks in our study indicate that the mating system in Indian peafowl may be resource-based lek.
The effect of grey wolf (Canis lupus) and human disturbance on the activity of big game species in the Bükk Hills, Hungary
Authors: Szabó Zsófia , Gombkötő Péter , Aranyi Sándor Csaba , Patkó László , Gigler Dóra , Barta Zoltán 
Published: September 2022

AbstractThe recent return of wolves to the Hungarian forests escalates conflicts among stakeholders. Hunting management agencies communicate that the presence of wolves may change the behaviour of big game species leading to difficulties for hunting organization and logistics. Here, we take a data driven approach to explore the activity of wolves and big game species. For this purpose we analysed camera trap data, collected in the Bükk National Park, Hungary. To estimate avoidance among wolves, humans and games we calculated a non-parametric activity overlap coefficient (Δ4) and used a machine learning (XGBoost) model. Our results show that game species have higher overlap coefficient with wolf (Δ4 = 0.83-0.89) than with human activity (Δ4 = 0.26-0.52), because predators and games are active in the same periods of the day, mainly night and dawn, and human activity mainly takes place during daytime. We could detect the refugee effects in the case of all game species. Our XGBoost analyses only found a moderate negative effect of wolf on red deer occurrence, while human activity had higher importance value and lowered the occurrence of all three game species investigated. Our results may thus indicate that human disturbance might be more important in shaping game activity than the presence of the grey wolf in Hungary.
Mouse Memory CD8 T cell subsets defined by Tissue Resident Memory (TRM) Integrin Expression Exhibit Distinct Metabolic Profiles
Authors: Sportiello Mike , Poindexter Alexis , Reilly Emma C. , Geber Adam , Emo Kris Lambert , Jones Taylor N. , Topham David J. 
Published: September 2022

AbstractTissue-resident memory CD8 T cells (TRM) principally reside in peripheral non-lymphoid tissues such as lung and skin and confer protection against a variety of illnesses ranging from infections to cancers. The functions of different memory CD8 T cell subsets have been linked with distinct metabolic pathways and differ from other CD8 T cell subsets. For example, skin-derived memory T cells undergo fatty acid oxidation and oxidative phosphorylation to a greater degree than circulating memory and naïve cells. Lung TRMcells defined by the cell surface expression of integrins exist as distinct subsets that differ in gene expression and function. We hypothesize that TRMsubsets with different integrin profiles will utilize unique metabolic programs. To test this, differential expression and pathway analysis were conducted on RNAseq datasets from mouse lung TRMyielding significant differences related to metabolism. Next, metabolic models were constructed and the predictions were interrogated using functional metabolite uptake assays. The levels of oxidative phosphorylation, mitochondrial mass, and neutral lipids were measured. Furthermore, to investigate the potential relationships to TRMdevelopment, T-cell differentiation studies were conductedin vitrowith varying concentrations of metabolites. These demonstrated that lipid conditions impact T cell survival, and that glucose concentration impacts the expression of canonical TRMmarker CD49a, with no effect on central memory-like T-cell marker CCR7. In summary, it is demonstrated that mouse resident memory T cells subsets defined by integrin-expression in the lung have unique metabolic profiles and that nutrient abundance can alter differentiation.
Shape-shifting microgel automata controlled by DNA sequence instructions
Authors: Shi Ruohong , Chen Kuan-Lin , Fern Joshua , Deng Siming , Liu Yixin , Scalise Dominic , Huang Qi , Cowan Noah J. , Gracias David H. , Schulman Rebecca 
Published: September 2022

AbstractControlling material shapes using information-bearing molecular signals is central to the creation of autonomous, reconfigurable soft devices. While physical and chemical stimuli can direct simple material swelling, bending, or folding, it has been challenging to direct multi-step shape-change programs crucial for complex, robotic tasks. Here, we demonstrate gel automata— sub-millimeter, photopatterned, highly swellable DNA gels—whose parts grow or shrink in response to easily designed DNA activator sequences, allowing for precisely controlled device articulation. We design and fabricate gel automata that reversibly transform between different letter shapes, and use neural networks to design automata that transform into every even or every odd numeral via designed reconfiguration programs. This sequential and repetitive metamorphosis of materials via chemical reorganization could dramatically advance our ability to manipulate micro-particles, cells, and tissues.One-Sentence SummaryPhotopatterned microgels follow sequences of DNA instructions to transform between complex, meaningful shapes such as letters and numerals.
Proton exchange in the nitrate vacuolar transporter AtCLCa is required for growth and nitrogen use efficiency
Authors: Hodin Julie , Lind Christof , Marmagne Anne , Espagne Christelle , Bianchi Michele Wolfe , De Angeli Alexis , Abou-Choucha Fadi , Bourge Mickaël , Chardon Fabien , Thomine Sebastien , Filleur Sophie 
Published: September 2022

ABSTRACTNitrate is a major nutrient and osmoticum for plants. To deal with its fluctuating availability in soils, plants store it into vacuoles. AtCLCa, a 2NO3-/1H+exchanger localized on the vacuole ensures this storage process. It belongs to the CLC family that includes exchangers and channels. A mutation in a glutamate residue conserved across CLC exchangers is likely responsible for the conversion of exchangers to channels. Here, we show that aclcamutant of this residue, E203, behaves as an anion channel in its native membrane. To investigate its physiological importance, we introduced theAtCLCaE203Apoint mutation in aclcaKO mutant. We first showed that theseAtCLCaE203Amutants display a growth deficit linked to water homeostasis disruption. Additionally,AtCLCaE203Aexpression is not able to complement theclcadefect in nitrate accumulation and favors higher N-assimilation at the vegetative stage. Further analyses at post-flowering stages indicated that AtCLCaE203Aresults in an increase of N uptake allocation to seeds, leading to a higher nitrogen use efficiency compared to wild-type. Altogether, these results point out the critical function of the AtCLCa exchanger on the vacuole for plant metabolism and development.
The Phosphate Deprivation Response is Mediated by an Interaction between Brassinosteroid Signaling and Zinc in Tomato
Authors: Demirer Gozde S. , Gibson Donald J. , Yue Xiaoyan , Pan Kelly , Elishav Eshel , Khandal Hitaishi , Horev Guy , Tarkowská Danuše , Cantó-Pastor Alex , Kong Shuyao , Maloof Julin , Savaldi-Goldstein Sigal , Brady Siobhan M. 
Published: September 2022

AbstractPhosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate fertilizer, on the other hand, leads to eutrophication and has a negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. Here, we show that Solanum pennellii, a wild relative of tomato, is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response, which is dependent on zinc over-accumulation. Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation.