bluuebunny/crossref_metadata_2025_split huggingface dataset:
Songbirds avoid the oxidative stress costs of high blood glucose levels
Authors: Vágási Csongor I. , Vincze Orsolya , Adámková Marie , Kauzálová Tereza , Lendvai Ádám Z. , Pătra□ Laura , Pénzes Janka , Pap Péter L. , Albrecht Tomáš , Tomášek Oldřich 
Published: May 2023

ABSTRACTChronically high blood glucose levels (hyperglycaemia) can compromise healthy ageing and lifespan at the individual level. Elevated oxidative stress can play a central role in hyperglycaemia-induced pathologies. Nevertheless, the lifespan of birds shows no species-level association with blood glucose. This suggests that the potential pathologies of high blood glucose levels can be avoided by adaptations in oxidative physiology at the macroevolutionary scale. However, this hypothesis remains unexplored. Here, we examined this hypothesis using comparative analyses controlled for phylogeny, allometry and fecundity based on data from 51 songbird species (681 individuals with blood glucose and 1021 individuals with oxidative state data). We measured blood glucose at baseline and after stress stimulus and computed glucose stress reactivity as the magnitude of change between the two time points. We also measured three parameters of non-enzymatic antioxidants (uric acid, total antioxidants and glutathione) and a marker of oxidative lipid damage (malondialdehyde). We found no clear evidence for blood glucose concentration being correlated with either antioxidant or lipid damage levels at the macroevolutionary scale, as opposed to the hypothesis postulating that high blood glucose levels entail oxidative costs. The only exception was the moderate evidence for species with a stronger stress-induced increase in blood glucose concentration evolving moderately lower investment into antioxidant defence (uric acid and glutathione). Neither baseline nor stress-induced glucose levels were associated with oxidative physiology. Our findings support the hypothesis that birds evolved adaptations preventing the (glyc)oxidative costs of high blood glucose observed at the within-species level. Such adaptations may explain the decoupled evolution of glycaemia and lifespan in birds and possibly the paradoxical combination of long lifespan and high blood glucose levels relative to mammals.Summary statementHigh blood glucose levels can harm organisms by causing oxidative stress. We show that, at the macroevolutionary level, songbirds defy this expectation, as their glucose levels and oxidative physiology are uncoupled.
Activity and abundance of nitrous oxide consuming bacteria inPlatismatia glaucacryptogamic lichen in boreal Finnish spruce forest
Authors: Abagnale Vincenzo , Palacin-Lizarbe Carlos , Paul Dhiraj , Kerttula Johanna , Siljanen Henri M.P. 
Published: May 2023

AbstractThe boreal spruce forest soil can assimilate atmospheric N2O through symbiotic relationships with mycorrhizae or with bacteria, especially during spring and autumn, when aerobic microsites to soil can form. In cold soils with large field capacity (FCD), high humidity and absence of fertilisation, a balance between absorption and emission of nitrous oxide and dinitrogen was observed to be close to zero, and even to assume negative values in some cases, thus suggesting that forest soils absorb more N2O than they emit. Furthermore, in the presence of cryptogamic coverings of mosses and lichens, the absorption value was observed to be greater than in forests with less coverage; although the main role in N2O absorption is played by soil and root system. However, the role played by epiphytic organisms in N2O absorption in the boreal forests has not been uncovered yet. We studied, N2O dynamics of the lichen,Platismatia glauca, showing that N2O is consumed especially at lower incubation temperatures. The quantitative analysis with real-time PCR of nitrous oxide reductase gene fragment nosZ, showed that enzyme is present in the lichen and the gene is more transcribed under lower incubation temperature. The presented results unveil that cryptogamic covers consume nitrous oxide (with values between 0.1 and 0.4 ng N2O-C/g (ww)/h) at the atmospheric concentration via complete dissimilatory denitrification when nitrogen is limited.
Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources
Authors: Ferraille Thibaut , Kerbiriou Christian , Bigard Charlotte , Claireau Fabien , Thompson John D. 
Published: May 2023

AbstractStrategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM) are frequently used for the elaboration of spatially exhaustive biodiversity diagnostics. Despite the paradigm of “garbage in - garbage out” that emphasises the importance of testing the suitability of data for SDM and priority conservation areas, the assessment of database sources remains relatively rare. In addition, the lack of practical recommendations for the use of open-access databases by SEA stakeholders remains a problem. The aim of this study is to explore the quality of data sources that can be used in SEA to assess priority conservation areas in SEA. The study used data for nine taxonomic groups (commonly used in inventories for environmental impact assessment) and three databases available to SEA stakeholders. Three local administrative entities in very different socio-ecological contexts were used to examine three main issues : (i) the suitability of local versus regional or country databases for assessing conservation priorities, (ii) differences among taxonomic groups or territories in terms of the suitability of databases, (iii) the importance of the quality of databases for the application of SDM to assess priority conservation areas. Our study provides several clear messages for potential users of open- access databases. First, the need for prudence in the interpretation of biodiversity maps. Second, the collection of individual databases at the country scale is necessary to complete local data and ensure the suitability of SDM in a local context. Third, a data driven approach can lead to the use of notably different species communities to identify priority conservation areas when compared to the community in the original database. Finally, we propose a workflow to guide SEA stakeholders through the process of data rationalization and use in conservation planning.
Lipoteichoic acid biosynthesis byStaphylococcus aureusis controlled by the MspA protein through competitive interference
Authors: Bonini Dora , Duggan Seána , Alnahari Alaa , Brignoli Tarcisio , Strahl Henrik , Massey Ruth C. 
Published: May 2023

ABSTRACTStaphylococcus aureusproduces a plethora of virulence factors critical to its ability to establish an infection and cause disease. We have previously characterised a small membrane protein, MspA, which has pleiotropic affects on virulence and contributes toS. aureuspathogenicityin vivo. Here we report thatmspAinactivation triggers overaccumulation of the essential cell wall component lipoteichoic acid (LTA) which, in turn, decreases autolytic activity and leads to increased cell size due to a delay in cell separation. We show that MspA directly interacts with the LTA synthesis enzymes UgtP, LtaA and LtaS, and competitively interferes with the association between LtaA and LtaS. While complementation of themspAmutant with wild-typemspAreduces the amount of LTA, expression of a mutated version of MspA that does not interfere with the interactions between LtaA and LtaS does not. We suggest that MspA contributes to maintaining a physiological level of LTA in the cell wall by interacting with the LTA synthetic enzymes. In conclusion, this study uncovers the critical role of the MspA protein in regulating cell envelope biosynthesis and pathogenicity.IMPORTANCETheS. aureuscell envelope, comprising of the cytoplasmic membrane, a thick peptidoglycan layer and the anionic polymers lipoteichoic acid and wall teichoic acids, is fundamental for bacterial growth and division, as well as being the main interface between the pathogen and the host. It has become increasingly apparent that the synthesis and turnover of cell envelope components also affect the virulence ofS. aureus. In this study, we show that MspA, a novel effector ofS. aureusvirulence, contributes to the maintenance of normal levels of lipoteichoic acid in the cell wall, with implications on cell cycle and size. These findings further our understanding of the connections between envelope synthesis and pathogenicity and suggests MspA as a novel a target for therapeutic intervention.
Single-cell transcriptome landscape of circulating CD4+T cell populations in human autoimmune diseases
Authors: Yasumizu Yoshiaki , Takeuchi Daiki , Morimoto Reo , Takeshima Yusuke , Okuno Tatsusada , Kinoshita Makoto , Morita Takayoshi , Kato Yasuhiro , Wang Min , Motooka Daisuke , Okuzaki Daisuke , Nakamura Yamami , Mikami Norihisa , Arai Masaya , Zhang Xuan , Kumanogoh Atsushi , Mochizuki Hideki , Ohkura Naganari , Sakaguchi Shimon 
Published: May 2023

AbstractCD4+T cells are a key mediator of various autoimmune diseases; however, how they contribute to disease development remains obscure primarily because of their cellular heterogeneity. Here, we evaluated CD4+T cell subpopulations by decomposition-based transcriptome characterization together with canonical clustering strategies. This approach identified 12 independent transcriptional gene programs governing whole CD4+T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell data sets of over 1.8M peripheral CD4+T cells from 953 individuals by projecting cells onto the reference and cataloged cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+T cell subpopulations involved in autoimmune disease.
Discordance between gut-derived appetite hormones and energy intake in humans
Authors: Hengist Aaron , Sciarrillo Christina M. , Guo Juen , Walter Mary , Hall Kevin D. 
Published: May 2023

SUMMARYGut-derived hormones affect appetite and are thought to play an important role in body weight regulation. Dietary macronutrient composition can influence gut-derived appetite hormone concentrations, thereby providing theoretical basis for why some diets might facilitate weight loss better than others. We investigated postprandial gut-derived appetite hormones in 20 inpatient adults after 2 weeks of eating either a low carbohydrate (LC) or a low fat (LF) diet followed by the alternate diet in random order. A LC meal resulted in significantly greater postprandial GLP-1, GIP, and PYY but lower ghrelin compared to an isocaloric LF meal (allp≤0.02). However, differences in gut-derived appetite hormones were incommensurate with subsequent ad libitum energy intake over the rest of the day, which was 551±103 kcal (p<0.0001) greater with the LC as compared to the LF diet. The effects of gut-derived appetite hormones on ad libitum energy intake can be dominated by other diet-related factors, at least in the short-term.Graphical Abstract
Estimating county-level flu vaccination in the United States
Authors: Tiu Andrew , Bansal Shweta 
Published: May 2023

AbstractIn the United States, influenza vaccines are an important part of public health efforts to blunt the effects of seasonal influenza epidemics. This in turn emphasizes the importance of understanding the spatial distribution of influenza vaccination coverage. Despite this, high quality data at a fine spatial scale and spanning a multitude of recent flu seasons are not readily available. To address this gap, we develop county-level counts of vaccination across five recent, consecutive flu seasons and fit a series of regression models to these data that account for bias. We find that the spatial distribution of our bias-corrected vaccination coverage estimates is generally consistent from season to season, with the highest coverage in the Northeast and Midwest but is spatially heterogeneous within states. We also observe a negative relationship between a county’s vaccination coverage and social vulnerability. Our findings stress the importance of quantifying flu vaccination coverage at a fine spatial scale, as relying on state or region-level estimates misses key heterogeneities.
Glucocorticoid-driven gene expression in circulating monocytes and neutrophils in health and severe inflammation
Authors: Molendijk Arthur , Koenderman Leo 
Published: May 2023

SUMMARYGlucocorticoids (GCs) are used as anti-inflammatory and immunosuppressive drugs in many immune mediated diseases, but their use in sepsis and shock is controversial. This is caused in part by a lack of information regarding the responding cell types and GC-regulated genesin vivo. We used public blood transcriptomic datasets and GC-induced query genes to obtain 2 robust gene expression correlation signatures of GC induction, either in the absence or in the presence of severe inflammation. GC signature 1 originated from circadian cortisol with biases for gene expression in NK cells and neutrophils. GC signature 2 originated from GC in severe inflammation, mainly with biases for gene expression in monocytes and neutrophils. Many genes upregulated by GC treatment in septic shock and burn shock were also present as high-ranking genes in GC signatures, which pointed to their direct regulation by GC. Robust GC signatures were also obtained from dataset collections of monocytes and neutrophils, separately, and predicted cellular effects. Additionally, gene induction by GC was put into a wider framework of gene expression in circulating monocytes and neutrophils in health and systemic inflammation. We present and interpret a large number of GC-regulated genes in different blood cells and tissues, and select 2 whole blood transcriptomic biomarker gene sets, GC-1 and GC-2, for monitoring cortisol action in health, and in severe inflammation, respectively. GC signature 2 was found in sepsis and many other inflammatory diseases, both from treatment with GC, and from endogenous GC.
Rapid Online Assessment of Reading (ROAR): Evaluation of an Online Tool for Screening Reading Skills in a Developmental-Behavioral Pediatrics Clinic
Authors: Barrington Elizabeth P. , Sarkisian Sadie Mae , Feldman Heidi M. , Yeatman Jason D. 
Published: May 2023

ABSTRACTObjectiveReading difficulties frequently co-occur with other neurodevelopmental/behavioral conditions. It is difficult to assess reading routinely in Developmental-Behavioral Pediatrics (DBP) clinical practice due to time/resource constraints. Rapid Online Assessment of Reading (ROAR) is a gamified assessment that children take in a web-browser without adult supervision. This study’s purpose was to evaluate ROAR as a screening tool for reading difficulties in a DBP clinic.MethodPatients, ages 6-14 years, attending a DBP clinic, were invited to participate. Children took ROAR and completed the Woodcock-Johnson Letter-Word Identification (LWID) and Word Attack (WA). Basic Reading Skills (BRS), a standardized aggregate score of LWID and WA, was used as the gold standard assessment. The strength of association between age-adjusted standard score on ROAR and BRS was calculated. BRS scores < 90 (bottom quartile of sample) were deemed poor reader. Receiver Operating Characteristic (ROC) curve analysis was used to assess the quality of ROAR as a screening test.ResultsA total of 41 children, 78% boys, mean age 9.5 years (SD 2.0 years), completed the study. The correlation of ROAR standard score with BRS was r = 0.66, p<0.001. ROC curve classification analysis with ROAR scores accurately classified poor readers with an area under the curve (AUC) of 0.90.ConclusionROAR is a useful screening tool for children to take before attending a DBP clinic to identify children at high risk for reading difficulties. Assessment of the tool during a busy clinic was challenging and a larger replication is warranted.
Reconciling the efficacy and effectiveness of masking on epidemic outcomes
Authors: Yang Wan , Shaman Jeffrey 
Published: May 2023

AbstractMask wearing in public settings has been broadly implemented as a means to mitigate the COVID-19 pandemic. However, the reported effectiveness of masking has been much lower than laboratory measures of efficacy, and this large discrepancy has cast doubt on the utility of masking. Here, we develop an agent-based model that comprehensively accounts for individual masking behaviors and infectious disease dynamics, and test the impact of masking on epidemic outcomes. Using realistic inputs of mask efficacy and contact data at the individual level, the model reproduces the lower effectiveness as reported in randomized controlled trials. Model results demonstrate that transmission within households, where masks are rarely used, can substantially lower effectiveness, and reveal the interaction of nonlinear epidemic dynamics, control measures (e.g., masking and social distancing), and potential measurement biases. Overall, model results show that, at the individual level, consistent masking can reduce the risk of first infection, and, over time, reduce the frequency of repeated infection. At the population level, masking can provide direct protection to mask wearers, as well as indirect protection to non-wearers, collectively reducing epidemic intensity. These findings suggest it is prudent for individuals to use masks during an epidemic, and for policy makers to recognize the less-than-ideal effectiveness of masking when devising public health interventions.Significance statementDuring the COVID-19 pandemic, mask wearing in public settings has been a key control measure. However, the low effectiveness reported for masking has cast doubt on its validity. Here, we develop an agent-based model to interrogate influencing factors. Using realistic inputs of mask efficacy and contact data, the model reproduces the lower effectiveness reported in real-world settings. Testing shows that transmission within-household where masks are rarely used can substantially lower effectiveness. Nonetheless, the model results support the effectiveness of masking at both the individual and population levels, albeit at less-than-ideal levels. Overall, these findings indicate it is prudent for individuals to use masks during an epidemic, and for policy makers to recognize the less-than-ideal effectiveness of masking when devising interventions.
Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development
Authors: Darbellay Fabrice , Ramisch Anna , Lopez-Delisle Lucille , Kosicki Michael , Visel Axel , Andrey Guillaume 
Published: May 2023

AbstractThe precisely orchestrated differentiation of chondrocytes during skeleton development is a critical determinant of human height and body shape and disruptions of this process can cause severe skeletal abnormalities. The ultimate size and shape of each of over 200 bones depends on the intricate spatiotemporal regulation of chondrogenic and chondrocyte differentiation genes, but the genomic architecture coordinating these events remains poorly defined. Here we provide a comprehensive map of transcriptional enhancers specifically active in chondrocytes and show that they provide a mechanistic framework through which noncoding genetic variants can influence human stature. We isolated limb and trunk fetal chondrocytes from mice with aCol2a1fluorescent regulatory sensor and used RNA-seq to identify 780 genes that are specifically expressed during chondrogenesis. To create cell type-specific enhancer maps, we performed ATAC-seq to map open chromatin regions and ChIP-seq for H3K27ac, an enhancer-associated histone modification, and identified 2’704 putative chondrogenic enhancer regions. Most (74%) of these enhancers showedpan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. We found that chondrogenic enhancers are enriched for the binding of several chondrogenic transcription factors including SOX9. Finally, we find that genetic variation overlapping chondrogenic enhancers explains a higher fraction of the heritability of human adult height than the one overlapping non-chondrogenic enhancers. This data provides a comprehensive mapping of the chondrogenic enhancer repertoire, paving the way to interpreting the role of non-coding sequence polymorphisms in phenotypic variation and bone diseases.
A global LC-MS2-based methodology to identify and quantify anionic phospholipids in plant samples
Authors: Genva Manon , Fougère Louise , Bahammou Delphine , Mongrand Sébastien , Boutté Yohann , Fouillen Laetitia 
Published: May 2023

SummaryAnionic phospholipids (PS, PA, PI, PIPs) are low abundant phospholipids with impactful functions in cell signaling, membrane trafficking and cell differentiation processes. They can be quickly metabolized and can transiently accumulate at define spots within the cell or an organ to respond to physiological or environmental stimuli. As even a small change in their composition profile will produce a significant effect on biological processes, it is crucial to develop a sensitive and optimized analytical method to accurately detect and quantify them. While thin layer chromatography (TLC) separation coupled with gas chromatography (GC) detection methods already exist, they do not allow for precise, sensitive and accurate quantification of all anionic phospholipid species. Here we developed a method based on high performance liquid chromatography (HPLC) combined with two-dimensional mass spectrometry (MS2) by MRM mode to detect and quantify all molecular species and classes of anionic phospholipids in one-shot. This method is based on a derivatization step by methylation that greatly enhances the ionization, the separation of each peaks, the peak resolution as well as the limit of detection and quantification for each individual molecular species, and more particularly for PA and PS. Our method universally works in various plant samples. Remarkably, we identified that PS is enriched with very long chain fatty acids in the roots but not in aerial organs ofArabidopsis thaliana. Our work thus paves the way to new studies on how the composition of anionic lipids is finely tuned during plant development and environmental responses.Significance StatementWhile anionic phospholipids have key functions in plant cellular processes, their low concentration in biological samples and their low stability during the analysis complicate their quantification. Here, we present the first one-shot analytical method for the profiling and quantification of all anionic phospholipid classes and species from plant tissues with unprecedented sensitivity. This method open the way to future studies requiring a fine quantification of anionic phospholipids to understand their role in plant cell processes.