cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cnp5hqc4q
title: Neutrophil-mediated oxidative stress and albumin structural damage predict COVID-19-associated mortality

description: This work reports that COVID-19-induced oxidative stress inflicts
 structural damages to human serum albumin (HSA) and is linked with
 mortality outcome in critically ill patients. Analyzing blood samples from
 patients and healthy individuals, the paper provides evidence that
 neutrophils are major sources of oxidative stress in blood and that
 hydrogen peroxide is highly accumulated in plasmas of non-survivors. The
 electron paramagnetic resonance spectra of spin-labeled fatty acids
 (SLFAs) bound with HSA in whole blood of control, survivor, and
 non-survivor subjects (n=10–11) were analyzed to probe structural damages
 to the protein. Non-survivors’ HSA showed dramatically altered biophysical
 parameters that reflect remarkably fluid protein microenvironments.
 Following loading/unloading of 16-DSA, the results show that the transport
 function of HSA may be impaired in severe patients. Stratified at the
 means, Kaplan–Meier survival analysis indicated that lower values of S/W
 ratio and accumulated H2O2 in plasma significantly predicted in-hospital
 mortality.
description: All patients were recruited
 from Kasr Alainy Cairo University Hospital/ICU-facility at the Internal
 Medicine Quarantine Hospital. Supportive therapy, including supplemental
 oxygen and symptomatic treatment, was administered as required. Patients
 with moderate to severe hypoxia (defined as requiring fraction of inspired
 oxygen [FiO2]≥40%) were transferred to intensive care for further
 management including invasive mechanical ventilation when necessary.
 Patients recruited in the current study were divided into two arms based
 on future mortality outcome: those who survived the past 15 days following
 blood samples collection (Sev-R) and those who died within 15 days of
 samples collection (Sev-D). Details of samples collection and handlings
 are described in details in the published manuscript.
description: The dataset includes source data for all experimental results. A
 few missing values are to be found in the excel sheets. Missing data due
 to insufficient sample size (blood volume received) or processing
 errors. The
 readme file contains an explanation of each of the variables in the
 dataset, its measurement units, and the way it was calculated from the
 primary data. N/A = values not available. Information on how the
 measurements were done can be found in the associated manuscript
 referenced above.
DOI: 10.5061/dryad.76hdr7swm
title: Using cancer risk algorithms to improve risk estimates and referral decisions

description: Background: Cancer risk algorithms were introduced to clinical
 practice in the last decade, but they remain underused.
 We investigated whether GPs change their referral decisions in
 response to an unnamed algorithm, if decisions improve, and if changing
 decisions depends on having information about the algorithm and on whether
 GPs overestimated or underestimated risk. Methods: 157 UK General
 Practitioners (GPs) were presented with 20 vignettes describing patients
 with possible colorectal cancer symptoms. GPs gave their risk estimates
 and inclination to refer. They then saw the risk score of an unnamed
 algorithm and could update their responses. Half of the sample was given
 information about the algorithm’s derivation, validation, and accuracy. At
 the end, we measured their algorithm disposition. We analysed the data
 using multilevel regressions with random intercepts by GP and vignette.
 Results: We find that, after receiving the algorithm’s estimate,
 GPs’ inclination to refer changes 26% of the time and their decisions
 switch entirely 3% of the time. Decisions become more consistent with the
 NICE 3% referral threshold (OR 1.45 [1.27,
 1.65], p&lt;.001). The algorithm’s impact is greatest when
 GPs have underestimated risk. Information about the algorithm does not
 have a discernible effect on decisions but it results in a more positive
 GP disposition towards the algorithm. GPs’ risk estimates become better
 calibrated over time, i.e., move closer to the algorithm. 
 Conclusions: Cancer risk algorithms have the potential to improve
 cancer referral decisions. Their use as learning tools to improve risk
 estimates is promising and should be further investigated. 
description: All data were collected online using the Qualtrics platform. The
 data were analysed using STATA 17.0 and R (version 4.0.3).
DOI: 10.5061/dryad.9s4mw6mgg
title: Plant circadian clock control of Medicago truncatula nodulation involving regulation of Nodule Cysteine-Rich genes

description: Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized
 polyploid cells within root nodules, which undergo tightly regulated
 metabolic activity. By carrying out expression analysis of transcripts
 over time in Medicago truncatula nodules we found that the circadian clock
 enables coordinated control of metabolic and regulatory processes linked
 to nitrogen fixation. This involves the circadian clock-associated
 transcriptional factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants
 being affected in nodulation. Rhythmic transcripts in root nodules include
 a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the
 LHY-bound conserved Evening Element in their promoters. Until now, studies
 have suggested that NCRs act to regulate bacteroid differentiation and
 keep the rhizobial population in check. However, these conclusions came
 from the study of a few members of this very large gene family that has
 complex diversified spatio-temporal expression. We suggest that rhythmic
 expression of NCRs may be important for temporal coordination of bacterial
 activity with the rhythms of the plant host, in order to ensure optimal
 symbiosis.
description: See Achom et al. (2022) Journal of Experimental Botany.
description: All
 Supplementary Datasets have full legends within the xlsx files.
 Supplementary Dataset
 S1. <em>Medicago truncatula</em> A17 transcript IDs detected
 in 40 day-old A17 nodules and information on their oscillating
 behavior. 
 Supplementary Dataset
 S2. <em>Medicago truncatula</em> A17 transcript IDs detected
 in 40 day-old A17 roots and information on their oscillating
 behavior. 
 Supplementary Dataset S3.
 Expression of circadian clock gene transcripts detected in 40 day-old A17
 nodules and information on their oscillating
 behavior.
 Supplementary Dataset S4. Pathway
 and protein term enrichment in oscillating gene
 clusters. 
 Supplementary Dataset S5.
 Analysis of
 the <em>lhy-1</em> and <em>lhy-2</em> mutants. Supplementary Dataset S6. Genes annotated as NCRs in <em>Medicago truncatula</em> A17 and information on their expression levels, oscillating behaviour and presence of motifs.  Supplementary Dataset S7. Motif analysis in NCRs and cycling genes.
DOI: 10.5061/dryad.h44j0zpk0
title: Reproductive strategies affect telomere dynamics across the life course

description: Because parental care has a heritable basis, the benefits of receiving
 increased parental provisioning early in life are genetically linked to
 the costs of providing increased parental provisioning at adulthood.
 Reproductive strategies thus result in distinct cost-benefit syndromes
 across the life course that may shape individual health and ageing
 trajectories. Here we used an artificial selection approach in Japanese
 quail (Coturnix japonica) to test how reproductive strategies affect
 telomere length, a biomarker of somatic state, at different life stages.
 We show that males, but not females, from lines selected for low maternal
 investment (i.e. developing in a relatively small egg) had shorter
 telomeres at birth. These patterns were still weakly present at the end of
 the juvenile growth period. In contrast, significantly shorter telomeres
 were found in reproductively active adult birds from the high investment
 lines, suggesting that telomere attrition was accelerated in these
 individuals once they had become reproductively active. Our study shows
 that reproductive strategies differentially affect telomere dynamics
 across the life course, highlighting the role of cross-generational
 constraints in shaping individual ageing trajectories.
DOI: 10.5061/dryad.dr7sqv9z6
title: Precipitation manipulation and terrestrial carbon cycling: the roles of treatment magnitude, experimental duration, and local climate

description: Aim: Precipitation manipulation experiments have shown diverse terrestrial
 carbon (C) cycling responses when the ecosystem is subjected to different
 magnitudes of altered precipitation, various experimental durations, or
 heterogeneity in local climate. However, how these factors combine to
 affect C cycle responses to changes in precipitation remains unclear.
 Location: Global. Time period: 1990–2019. Major taxa studied: Terrestrial
 ecosystems. Methods: Using observations from 230 published studies in
 which precipitation was manipulated and terrestrial C cycling variables
 were measured, we conducted a global meta-analysis to investigate
 responses of diverse C cycle processes to altered precipitation, including
 gross ecosystem productivity, ecosystem respiration, net ecosystem
 productivity, ecosystem carbon use efficiency, net primary productivity,
 aboveground and belowground net primary productivity, aboveground and
 belowground biomass, shoot:root ratio, soil respiration, and soil
 microbial biomass C. Results:  We found that C cycling responses
 correlated linearly and positively with the magnitude of precipitation
 treatments. We also detected that the responses of net primary
 productivity (NPP) and its aboveground component (ANPP) to altered
 precipitation weakened with experimental duration. Furthermore, gross
 ecosystem productivity, ecosystem respiration, and net ecosystem
 productivity had larger responses to precipitation treatments of greater
 magnitude over shorter time periods. The response of soil respiration, a
 key component of the C budget in most terrestrial ecosystems, particularly
 depended on the local climate. Local temperature and precipitation not
 only influenced the magnitude of the response of soil respiration to
 altered precipitation but also affected its sensitivity to the magnitude
 of the precipitation treatments, with higher sensitivities in the response
 of soil respiration to treatment magnitude at drier and colder sites. Main
 conclusions:  Our findings highlight the importance of
 the interactions between the magnitude of precipitation treatments, their
 duration, and local climate in the response of ecosystem C cycling to
 altered precipitation, which is critical to better understanding and
 projecting ecosystem C processes and functioning under changing
 precipitation regimes.
description: We conducted a meta-analysis using 1775 paired observations from
 global precipitation manipulation experiments to synthesize the effects of
 changes in precipitation on a diverse array of C cycle
 processes.
DOI: 10.5061/dryad.j3tx95xdg
title: Translation Inhibitory Elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition

description: During embryogenesis, Hox mRNA translation is tightly regulated by a
 sophisticated molecular mechanism that combines two RNA regulons located
 in their 5’UTR. First, an Internal Ribosome Entry Site (IRES) enables
 cap-independent translation. The second regulon is a Translation
 Inhibitory Element or TIE, which ensures concomitant cap-dependent
 translation inhibition. In this study, we deciphered the molecular
 mechanisms of mouse Hoxa3 and a11 TIE elements. Both TIEs possess an
 upstream Open Reading Frame (uORF) that is critical to inhibit
 cap-dependent translation. However, the molecular mechanisms used are
 different. In TIE a3, we identify a uORF which inhibits cap-dependent
 translation and we show the requirement of the non-canonical initiation
 factor eIF2D for this process. The mode of action of TIE a11 is different,
 it also contains a uORF but it is a minimal uORF formed by an uAUG
 followed immediately by a stop codon, namely a ‘start-stop’. The 
 ‘start-stop’ sequence is species-specific and in mice, is located upstream
 of a highly stable stem loop structure which stalls the 80S ribosome and
 thereby inhibits cap-dependent translation of Hox a11 main ORF.
DOI: 10.5061/dryad.h18931zkp
title: Environmental range per unit space determines a unimodal pattern of species richness along a heterogeneity gradient

description: Although many studies have focused on the effects of the environment and
 area on local patterns of species richness, few studies have demonstrated
 how to reconcile the availability of more niches with smaller habitat
 areas in heterogeneous localities. Here, the environmental range that a
 species prefers was defined as a niche; a space was defined as an
 available space if the environmental range of the space matches a niche;
 and the metric “environmental range per unit space (ERUS)” was presented
 to describe the heterogeneity of localities. Because the spaces with
 stressful environmental ranges, outside the niche, increased with
 increasing heterogeneity, available spaces did not continue to
 indefinitely increase, but the proportion of available spaces in spaces
 was low at high heterogeneous localities. Consequently, the probability of
 species occurring in their respective available spaces was unimodal. Due
 to the presence of large spaces in homogenous localities and more spaces
 in heterogeneous localities, the interval distances between nonadjacent
 spaces were large in these localities. Together, the changes in the number
 and proportion of available spaces and distance between spaces determined
 the unimodal probability of species dispersing into their respective
 available spaces. Thus, the probability of species coexisting was unimodal
 because it is important for coexisting species to grow in their respective
 available spaces. The probability of population extinction increased with
 increasing heterogeneity because the available spaces became narrower. In
 this way, the ERUS strongly influence species richness: a unimodal
 richness along the heterogeneity gradient occurred in suitable, suboptimal
 and stressful environments, and a unimodal algae richness occurred in a
 lake and river. These results challenge the viewpoint that richness
 increases with heterogeneity, providing information about the conservation
 of richness in very homogeneous and heterogeneous regions, and
 highlighting the importance of balancing the roles of environment and
 space in understanding and predicting richness.
DOI: 10.5061/dryad.rjdfn2zbb
title: Supplement to: Sex and race differences in the risk of ischemic stroke associated with fasting blood glucose in REGARDS

description: Background: To investigate sex and race differences in the
 association between fasting blood glucose (FBG) and risk of ischemic
 stroke (IS). Methods: This prospective longitudinal cohort
 study included adults age ≥45 years at
 baseline in the Reasons for Geographic And Racial Differences in
 Stroke Study, followed for a median of 11.4 years. The exposure
 was baseline FBG (mg/dL); suspected IS events were
 ascertained by phone every 6 months and were physician-adjudicated. Cox
 proportional hazards were used to assess the adjusted sex/race-specific
 associations between FBG (by category and as a restricted cubic spline)
 and incident IS. Results: Of 20,338 participants, mean
 age was 64.5(SD 9.3) years, 38.7% were Black, 55.4% were women, 16.2% were
 using diabetes medications, and 954 IS events occurred. Compared to FBG
 &lt;100, FBG ≥150 was associated with 59% higher hazards of IS (95%CI
 1.21-2.08) and 61% higher hazards of IS among those on diabetes
 medications (95%CI 1.12-2.31). The association between FBG and IS varied
 by race/sex (HR, FBG ≥ 150 vs. FBG &lt;100: White women
 2.05 (95% CI 1.23-3.42), Black women 1.71
 (95%CI 1.10-2.66), Black men 1.24 (95%CI 0.75-2.06),
 White men 1.46 (95%CI 0.93-2.28), pFBG*race/sex=0.004). Analyses
 using FBG splines suggest that sex was the major contributor to
 differences by race/sex subgroups. Conclusions: Sex differences in the
 strength and shape of the association between FBG and IS are likely
 driving the significant differences in the association between FBG and IS
 across race/sex subgroups. These findings should be explored further and
 may inform tailored stroke prevention guidelines.
DOI: 10.5061/dryad.rbnzs7hbg
title: Phloem flow modeling

description: Seasonal changes in climate are accompanied by shifts in carbon allocation
 and phenological changes in woody angiosperms, the timing of which can
 have broad implications for species distributions, interactions, and
 ecosystem processes. During critical transitions from autumn to winter and
 winter to spring, physiological and anatomical changes within the phloem
 could impose a physical limit on the ability of woody angiosperms to
 transport carbon and signals. There is a paucity of literature that
 addresses tree (floral or foliar) phenology, seasonal phloem anatomy and
 seasonal phloem physiology together, so our knowledge of how carbon
 transport could fluctuate seasonally, especially in temperate climates is
 limited. We review phloem phenology focusing on how sieve element anatomy
 and phloem sap flow could affect carbon availability throughout the year
 with a focus on winter. To investigate whether flow is possible in the
 winter, we constructed a simple model of phloem sap flow and investigated
 how changes to the sap concentration, pressure gradient and sieve plate
 pores could influence flow during the winter.  Our model
 suggests that phloem transport in some species could occur year-round,
 even in winter, but current methods for measuring all the parameters
 surrounding phloem sap flow make it difficult to test this hypothesis. We
 highlight outstanding questions that remain about phloem functionality in
 the winter and emphasize the need for new methods to address gaps in our
 knowledge about phloem function.
description: Model code to generate Figure 2. See readme and comments within
 the code for explanations.
DOI: 10.6076/d12s3m
title: Accuracy in near-perfect virus phylogenies

description: Phylogenetic trees from real-world data often include short edges with
 very few substitutions per site, which can lead to partially resolved
 trees and poor accuracy. Theory indicates that the number of sites needed
 to accurately reconstruct a fully resolved tree grows at a rate
 proportional to the inverse square of the length of the shortest edge.
 However, when inferred trees are partially resolved due to short edges,
 "accuracy" should be defined as the rate of discovering
 false splits (clades on a rooted tree) relative to the actual number
 found. Thus, accuracy can be high even if short edges are common.
 Specifically, in a "near-perfect" parameter space in which trees
 are large, the tree length ξ (the sum of all edge lengths), is small, and
 rate variation is minimal, the expected false positive rate is less than
 ξ/3; the exact value depends on tree shape and sequence length. This
 expected false positive rate is far below the false negative rate for
 small $\xi$ and often well below 5% even when some assumptions are
 relaxed. We show this result analytically for maximum parsimony and
 explore its extension to maximum likelihood using theory and simulations.
 For hypothesis testing, we show that measures of split
 "support" that rely on bootstrap resampling
 consistently imply weaker support than that implied by the false positive
 rates in near-perfect trees. The near-perfect parameter space closely fits
 several empirical studies of human virus diversification during outbreaks
 and epidemics, including Ebolavirus, Zika virus, and SARS-CoV-2,
 reflecting low substitution rates relative to high transmission/sampling
 rates in these viruses.
DOI: 10.5061/dryad.sbcc2fr6j
title: Statistical analysis code for output from a model used to simulate foot-and-mouth disease dynamics in the United Kingdom

description: Epidemics can sometimes be managed through reductions of host density,
 such as social distancing for human diseases, reducing plant density
 through cultural and genetic means, and host culling for epizootics. These
 approaches allow for a certain density of hosts to remain within a
 targeted area. By contrast, total ring depopulation is often used as a
 management strategy for emerging infectious diseases in livestock. In this
 study, we explore the trade-offs of a density-based culling strategy to
 determine if fewer livestock farms can be culled within rings while
 maintaining a decrease in disease transmission. To do so, we evaluated a
 farm-density-based ring culling strategy to control foot-and-mouth disease
 (FMD) in the United Kingdom. This strategy may allow for some farms within
 rings around infected premises (IPs) to escape depopulation, with the aim
 to prevent over-culling during outbreaks. Using a spatially-explicit,
 stochastic, state-transition simulation algorithm originally developed by
 Keeling et al. 2001 to model FMD spread in the United Kingdom, we
 simulated this reduced-farm-density, or “target density” strategy. We
 modeled FMD disease spread in four counties in the UK (Aberdeenshire,
 Cumbria, Devon, and North Yorkshire) that have different farm
 demographies. We ran 740,000 simulations in a full-factorial analysis of
 epidemic impact measurements (i.e. culled animals, culled farms, epidemic
 length) and cull strategy parameters (i.e. target farm density, daily farm
 cull capacity, cull radius). We found that all of the cull strategy
 parameters were drivers of epidemic impact. We found that outbreaks in
 Cumbria had higher epidemic impacts and were more likely to take off
 compared with other counties with more outbreaks being likely to take off
 in Cumbria. Most importantly, in all counties, our proposed target density
 strategy was more effective at combatting FMD compared with traditional
 ‘total ring depopulation’ when considering average culled animals and
 culled farms. The differences in epidemic impact between the counties are
 likely driven by farm demography, especially differences in cattle and
 farm density. This target density strategy can be applied to many
 different systems, including other livestock and agricultural systems, to
 reduce host density as opposed to over-culling hosts.