cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm63xsjc3
title: Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

description: The sympatric existence of genetically distinct populations of the same
 species remains a puzzle in ecology. Coexisting salmonid fish populations
 are known from over 100 freshwater lakes. Most studies of sympatric
 populations have used limited numbers of genetic markers making it unclear
 if genetic divergence involves only certain parts of the genome. We return
 to the first reported case of salmonid sympatry, initially detected
 through contrasting homozygosity at a single allozyme locus (coding for
 lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna,
 Sweden. First, we verify the existence of the two coexisting demes using a
 96-SNP fluidigm array. We then apply whole-genome resequencing of pooled
 DNA to explore genome-wide diversity within and between these demes;
 nucleotide diversity is higher in Deme I than in Deme II. Furthermore,
 strong genetic divergence is observed with genome-wide FST≈0.2. Comparing
 with similar data from other lakes, this divergence is of similar
 magnitude as that between reproductively isolated populations. Individual
 whole-genome resequencing of two individuals per deme suggests higher
 inbreeding in Deme II vs. Deme I, indicating different degree of
 isolation. Finally, we located two gene-copies for LDH-A and find
 divergence between demes in a regulatory section of one of these genes.
 However, we did not find a perfect fit between the sequence data and
 previous allozyme results, and this will require further research. Our
 data demonstrates genome-wide divergence governed mostly by genetic drift
 but also by diversifying selection in coexisting populations. This type of
 hidden biodiversity needs consideration in conservation management.
description: For details please read the article
DOI: 10.6086/d1mh4b
title: Data for: Precipitation legacies amplify ecosystem nitrogen losses from nitric oxide emissions in a Pinyon-Juniper dryland

description: Climate change is increasing the variability of precipitation, altering
 the frequency of soil drying-wetting events and the distribution of
 seasonal precipitation. These changes in precipitation can alter nitrogen
 (N) cycling and stimulate nitric oxide (NO) emissions (an air pollutant at
 high concentrations), which may vary according to legacies of past
 precipitation and represent a pathway for ecosystem N loss. To identify
 whether precipitation legacies affect NO emissions, we excluded or added
 precipitation during the winter growing season in a Pinyon-Juniper dryland
 and measured in-situ NO emissions following experimental wetting. We found
 that the legacy of both excluding and adding winter precipitation
 increased NO emissions early in the following summer; cumulative NO
 emissions from the winter precipitation exclusion plots (2750 ± 972 µg
 N-NO m-2) and winter water addition plots (2449 ± 408 µg N-NO m-2) were
 higher than control plots (1506 ± 397 µg N-NO m-2). The increase in NO
 emissions with previous precipitation exclusion was associated with
 inorganic N accumulation, while the increase in NO emissions with previous
 water addition was associated with an upward trend in microbial biomass.
 Precipitation legacies can accelerate soil NO emissions and may amplify
 ecosystem N loss in response to more variable precipitation.
description: This data accompianies the mauscript entitled:
 <em>Precipitation legacies amplify ecosystem nitrogen losses from
 nitric oxide emissions in a Pinyon-Juniper dryland</em>, which is
 published as a Report in <em>Ecology</em>. The methods for
 data collection can be found within the manuscript. Briefly, NO efflux was
 measured from 24 plots within the Pinyon Flats rainfall manipulation
 experiment three time in 2020. NO emissions are made by recirculating air
 from an enclosed chamber headspace through a NO analyzer and measuring the
 change in trace gas concentrations over time. These data are in the
 "combined_fluxes.csv" document. We also measured soil inorganic
 N conctrations, soil moisture, soil microbial biomass, and ammonia
 oxidizing gene abundance in parallel to the NO efflux
 measurements.
description: Empty columns refer to samples that were lost in the data
 collection process. Most sampes are lost from the N mineralization and
 nitrification measurements, which require intact soil cores to be left in
 the field for one month. Some of these cores were removed by wildlife
 during the one month incubation, leading to missing data.
DOI: 10.15151/esrf-es-2290387023
title: PROTEINS RELATED TO PATHOGENESIS OF DISEASES, VIRAL PROTEINS, CELL DIVISION, SIGNALLING AND CHROMATIN PROCESSES

description: The outstanding research questions of our BAG (now expanded to 9 PIs) focus on proteins and their complexes involved in a variety of processes, ranging from cell homeostasis (from gene regulation to folding quality control, from energy metabolism to signal transduction) to communication and surface recognition (including trans-interactions between cell adhesion molecules, components of the extracellular matrix weaving, as well as antigen-antibody interactions for vaccine development and optimization). Key to several projects is the characterization of the mechanisms associated to enzyme function in various organisms, including bacteria, viruses, plants, animals and humans for downstream drug discovery campaigns. Emphasis is also given to research focusing on engineering protein and enzymes for future industrial applications, as well as to understand the impact of pathogenic mutations on protein structures, providing a genotype-to-molecular phenotype rationale to disease development.
DOI: 10.5061/dryad.qfttdz0j1
title: Figure data and analysis for: The effect of grain size on porewater radiolysis

description: The radiolysis of porewaters by uranium, thorium, and potassium in mineral
 grains is a recognised source of molecular hydrogen in rock- and
 sediment-hosted fluids. This radiolytic hydrogen is of geomicrobiological
 interest as a potential energy source (electron donor) for microbial
 metabolism, especially in energy-limited settings such as the marine deep
 biosphere or the subsurface of Mars. Previous efforts to predict the
 production of radiolytic hydrogen from columns of rock and sediment have
 tended to rely upon analytic models that cannot account for the
 attenuation of mineral radiation by grains larger than ~30 microns. To
 address this, we have developed a Monte Carlo method to simulate the
 physics of mineral radiation and evaluate the production of H2 as a
 function of mineral grain size and radioisotope composition. The results
 confirm that grain size is a major control on radiolytic H2 yield. For
 example, using the standard geological classification of grain sizes, we
 find that clay can produce up to an order of magnitude more H2 per unit
 time than sand. The magnitude of this effect is illustrated using
 compositional data from real geological units in order to demonstrate the
 dependence of radiolytic hydrogen flux on natural radionuclide
 concentration and bulk porosity.
DOI: 10.15151/esrf-es-2312932454
title: Self-assembly study of mixtures of biosurfactants with conventional surfactants

description: Surfactants manufacturers are actively working on replacing, partially or totally, synthetic oil-based surfactants with biobased surfactants (BS) in consumer goods, for BS are established as being less toxic, with better environmental compatibility and produced from renewable feedstock. However, home and personal care products still require surfactants formulation, optimized to obtain high-performance products. A fundamental understanding in the self-assembly properties of blends of biosurfactants with industrial surfactants is then necessary. In this proposal, we use a high throughput SAXS beamline to study the phase diagram in water under diluted conditions (&lt; 5 wt%) for mixtures of biosurfactants (sophoro-, rhamno-, cellobiose-, gluco-lipids) with industrial surfactants, negative/positive/neutral (SDS, LAS, CTAB, Pluronic P123, F127). This study will be essential for understanding BS/surfactant blends and sketch their use in commercial formulations in the field of personal care.
DOI: 10.5061/dryad.wm37pvmp3
title: Evolution of a novel female reproductive strategy in Drosophila melanogaster populations subjected to long term protein restriction

description: Reproductive output is often constrained by availability of
 macronutrients, especially protein. Long term protein restriction,
 therefore, is expected to select for traits maximizing reproduction even
 under nutritional challenge. We subjected four replicate populations of
 Drosophila melanogaster to a complete deprivation of yeast supplement,
 thereby mimicking a protein restricted ecology. Following 24 generations,
 compared to their matched controls, females from experimental populations
 showed increased reproductive output early in life, both in presence and
 absence of yeast supplement. The observed increase in reproductive output
 was without associated alterations in egg size, development time,
 pre-adult survivorship, body mass at eclosion, and lifespan of the
 females. Further, selection was ineffective on lifelong cumulative
 fecundity. However, females from experiment regime were found to have a
 significantly faster rate of reproductive senescence following the
 attainment of the reproductive peak early in life. Therefore, adaptation
 to yeast deprivation ecology in our study involved a novel reproductive
 strategy whereby females attained higher reproductive output early in life
 followed by faster reproductive aging. To the best of our knowledge, this
 is one of the cleanest demonstration of optimization of fitness by fine
 tuning of reproductive schedule during adaptation to a prolonged
 nutritional deprivation.
description: The dataset represents results from a series of assays done on a
 set of quadruply replicated laboratory populations of <em>Drosophila
 melanogaster. </em>All assays were done in the lab. The dataset was
 analysed on Statistica (version 10, Statsoft, Tulsa, OK, USA) and R
 version 4.0.2. 
description: Individual datasets are seperated in different tabs.
 Column headings are clearly written to indicate data type, treatment
 etc.
DOI: 10.15151/esrf-es-2313110628
title: High Resolution RIXS on van der Waal Antiferromagnets

description: The purpose of the inhouse is the measurements of high resolution spectra with different linear polarization for the van der Waals antiferromagnet CrPS4
DOI: 10.5061/dryad.5mkkwh76w
title: Data from: Efficacy and safety of CT-guided percutaneous fine needle aspiration and biopsy for malignant pulmonary lesions

description: Background: CT guided percutaneous transthoracic fine needle aspiration
 (FNA) and core biopsy (CB) are commonly used to characterise lung lesions.
 There is conflicting information on which method is superior and wide
 variation in reported complication rates. Objectives: Our objectives were
 to establish the efficacy and safety of percutaneous CT guided FNA and CB
 in the diagnosis of malignant lung lesions. Methods: This retrospective
 study included patients who underwent CT guided percutaneous FNA and/or CB
 for lung parenchymal lesions at Kasturba Medical College Mangalore from
 January 2013 to December 2020. Ethical clearance was obtained from the
 Institutional Ethics Committee. Efficacy was determined by the adequacy of
 samples, sensitivity, specificity and diagnostic accuracy. Safety was
 assessed using the incidence of complications. Results: 326 patients
 underwent both FNA and CB, and 49 underwent FNA alone. Adequate samples
 were obtained in 82.9% of FNA cases and 95.7% of CB cases. Considering
 biopsy as the gold standard, the sensitivity, specificity and diagnostic
 accuracy of FNA for malignancy were 95.19%, 80% and 91.27%, respectively.
 Kappa agreement between the two methods was substantial (0.767).
 Pneumothorax was the only complication observed, and was seen in 31
 patients (8.2%), of which only one required chest tube drainage. The
 incidence of pneumothorax was significantly higher in patients with
 pre-existing lung disease such as COPD/emphysema (p value 0.000), patients
 with smaller lesions (p = 0.009), and deeper lesions from the pleura (p
 &lt;0.0001). Conclusions: FNA and CB are both safe and effective
 procedures. In the absence of an onsite cytopathologist, we recommend a
 combination of both techniques.
description: Hospital based retrospective record review.
DOI: 10.15151/esrf-es-2295870826
title: Southern Germany cryo-EM BAG: Structural analysis of protein machineries using single particle cryo-EM

description: Cryogenic single-particle electron microscopy (Cryo-EM) has become the method of choice for determining the structures of large macromolecular complexes and membrane proteins – targets that have been challenging for X-ray crystallography. Exciting recent advances in cryo-EM now allow for structure determination at high resolution, of proteins in multiple states, of smaller proteins and of membrane proteins within a natural lipid environment. In this BAG, we will use the state-of-the-art cryo-EM facility at the ESRF to determine the structures of intricate protein machineries including large multi-subunit complexes, protein-nucleic acid complexes and membrane protein complexes. Our projects will contribute to a better understanding of essential cellular processes such as energy conversion and cellular respiration, nitrate and ammonium metabolism, ribosome and ribosome-associated functions, and DNA damage repair and maintenance mechanisms.
DOI: 10.5061/dryad.95x69p8md
title: Facile synthesis of magnesium-based metal-organic framework with tailored nanostructure for effective VOCs adsorption

description: A novel Mg(II) metal–organic framework (Mg-MOF) was synthesised based on
 the ligand of 2,2'-bipyridine-4,4'dicarboxylic acid (Bpdc).
 Single-crystal X-ray structural analysis confirmed that 3D-nanostructure
 Mg-MOFs formed a monoclinic system with a channel size of 15.733 Å ×
 23.736 Å. The N2 adsorption isotherm, Fourier-transform infrared
 spectroscopy, thermogravimetric analysis and high-resolution transmission
 electron microscopy were performed to characterise the thermal stability
 and purity of the Mg-MOFs. The adsorption studies on four typical volatile
 organic compounds (VOCs) emitted during wood drying showed that Mg-MOFs
 have noteworthy adsorption capacities, especially for benzene and β-pinene
 with adsorptions of 182.26 mg/g and 144.42 mg/g, respectively. In
 addition, the adsorption of Mg-MOFs mainly occurred via natural
 adsorption, specifically, multi-layer physical adsorption, accompanied by
 chemical forces, which occurred in the pores where the VOCs molecules
 combined with active sites. As an adsorbent, Mg-MOFs exhibit versatile
 behaviour for toxic-gas accumulation.
DOI: 10.5061/dryad.ns1rn8pv0
title: Hydrogen isotopes (d2H) of polyunsaturated fatty acids track bioconversion by zooplankton

description: Organisms at the base of aquatic food webs synthesize essential nutrients,
 such as omega-3 polyunsaturated fatty acids (n-3 PUFA), which are
 transferred to consumers at higher trophic levels. Many consumers,
 requiring n-3 long-chain (LC) PUFA, such as eicosapentaenoic acid (EPA)
 and docosahexaenoic acid (DHA), have limited ability to bioconvert them
 from the essential dietary precursor α-linolenic acid (ALA) and thus rely
 on dietary provision of LC-PUFA. We investigated LC-PUFA metabolism in
 freshwater zooplankton using stable hydrogen isotopes (d2H) of fatty acids
 as tracers. We conducted feeding experiments with the freshwater keystone
 grazer Daphnia to quantify changes in the d2H value of body FA in response
 to the FA composition of their food and the d2H value of the ambient
 water. The isotopic composition of LC-PUFA changed in Daphnia, depending
 on the integration of 2H from ambient water during de novo synthesis or
 bioconversion from dietary precursors, allowing us to distinguish dietary
 from bioconverted EPA in body tissue. We tested the applicability of these
 laboratory findings in a field setting by analyzing d2H values of PUFA in
 primary producers and consumers in eutrophic ponds to track EPA sources of
 zooplankton. Multilinear regression models that included conversion of ALA
 to EPA correlated better with zooplankton d2HEPA than seston d2HEPA at low
 dietary EPA supply. This study provides evidence that zooplankton can
 compensate for low dietary EPA supply by activating LC-PUFA biosynthesis
 and shows that herbivorous zooplankton play a crucial role in upgrading FA
 for higher trophic levels during low dietary EPA supply.
DOI: 10.5061/dryad.gmsbcc2p7
title: Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity

description: Global change has dramatic impacts on grassland diversity. However, little
 is known about how fast species can adapt to diversity loss and how this
 affects their responses to global change. Here, we performed a common
 garden experiment testing whether plant responses to global change are
 influenced by their selection history and the conditioning history of soil
 at different plant diversity levels. Using seeds of four grass species and
 soil samples from a 14-year-old biodiversity experiment, we grew the
 offspring of the plants either in their own soil or in soil of a different
 community, and exposed them either to drought, increased nitrogen input,
 or a combination of both. Under nitrogen addition, offspring of plants
 selected at high diversity produced more biomass than those selected at
 low diversity, while drought neutralized differences in biomass
 production. Moreover, under the influence of global change drivers, soil
 history, and to a lesser extent plant history, had species-specific
 effects on trait expression. Our results show that plant diversity
 modulates plant-soil interactions and growth strategies of plants, which
 in turn affects plant eco-evolutionary pathways. How this change affects
 species' response to global change and whether this can cause a
 feedback loop should be investigated in more detail in future studies.
DOI: 10.6084/m9.figshare.31167717
title: Effects of CO<sub>2</sub> and chloride ion interaction on the durability of one-part nickel slag geopolymer

description: To investigate the interaction between carbonation and chloride ions on the durability of single-phase nickel slag geopolymer mortar, three experimental conditions were designed: (A) chloride ion penetration followed by carbonation, (B) carbonation followed by chloride ion penetration, and (C) carbonation, chloride ion penetration, and wet-dry cycles. Macro-performance was assessed through compressive strength, pH values, and chloride ion concentration, while microstructural mechanisms were analyzed using XRD, TG-DTG, and SEM. Results showed that chloride crystallization delayed carbonation, while carbonation products enhanced resistance to chloride penetration. The synergy of carbonation and wet-dry cycles accelerated chloride transport, thickening the surface convection zone. XRD and TG-DTG analyses confirmed the formation of hydrotalcite-like phases due to the high MgO content in nickel slag. No Friedel’s salt was detected, suggesting chloride ions were captured mainly through physical adsorption of the amorphous gel phase.HighlightsCarbonation was delayed by chloride crystallization, while chloride resistance was enhanced by pre-carbonation.Chloride transport was accelerated by the synergy between carbonation and cyclic wet-dry exposure.Hydrotalcite-like phases were identified, while chloride was primarily through physical adsorption. Carbonation was delayed by chloride crystallization, while chloride resistance was enhanced by pre-carbonation. Chloride transport was accelerated by the synergy between carbonation and cyclic wet-dry exposure. Hydrotalcite-like phases were identified, while chloride was primarily through physical adsorption.
DOI: 10.6084/m9.figshare.31167717.v1
title: Effects of CO<sub>2</sub> and chloride ion interaction on the durability of one-part nickel slag geopolymer

description: To investigate the interaction between carbonation and chloride ions on the durability of single-phase nickel slag geopolymer mortar, three experimental conditions were designed: (A) chloride ion penetration followed by carbonation, (B) carbonation followed by chloride ion penetration, and (C) carbonation, chloride ion penetration, and wet-dry cycles. Macro-performance was assessed through compressive strength, pH values, and chloride ion concentration, while microstructural mechanisms were analyzed using XRD, TG-DTG, and SEM. Results showed that chloride crystallization delayed carbonation, while carbonation products enhanced resistance to chloride penetration. The synergy of carbonation and wet-dry cycles accelerated chloride transport, thickening the surface convection zone. XRD and TG-DTG analyses confirmed the formation of hydrotalcite-like phases due to the high MgO content in nickel slag. No Friedel’s salt was detected, suggesting chloride ions were captured mainly through physical adsorption of the amorphous gel phase.HighlightsCarbonation was delayed by chloride crystallization, while chloride resistance was enhanced by pre-carbonation.Chloride transport was accelerated by the synergy between carbonation and cyclic wet-dry exposure.Hydrotalcite-like phases were identified, while chloride was primarily through physical adsorption. Carbonation was delayed by chloride crystallization, while chloride resistance was enhanced by pre-carbonation. Chloride transport was accelerated by the synergy between carbonation and cyclic wet-dry exposure. Hydrotalcite-like phases were identified, while chloride was primarily through physical adsorption.
DOI: 10.5061/dryad.3n5tb2rjh
title: Data from: Drivers and cascading ecological consequences of Gambusia affinis trait variation

description: Phenotypic trait differences among populations can shape ecological
 outcomes for communities and ecosystems. However, few studies have
 mechanistically linked heritable and plastic components of trait variation
 to generalizable processes of ecology, such as trophic cascades. Here we
 assess morphological and behavioral trait variation in nine populations of
 common-garden reared western mosquitofish (Gambusia affinis) from three
 distinct ancestral predator environments (three populations per
 environment), each reared in the presence and absence of predator cues. We
 then use a pond mesocosm experiment to examine the ecological consequences
 of trait variation and density variation. Our results show significant
 among-population trait variation, but this variation was generally
 unrelated to ancestral predator environment. When traits did vary
 congruently with respect to ancestral predator environment, this trait
 variation was driven by gene-by-environment interactions. Variation in
 several mosquitofish traits altered the cascading effects of mosquitofish
 on zooplankton and primary producers, but the effect of any given trait
 was typically weaker than that of density. We note that the relatively
 stronger ecological effects of density may mask the effects of traits in
 some systems. Our example here shows that trait variation can be highly
 noncongruent with respect to a perceived selective agent, phenotypic
 change is a product of complex interactions between genes and the
 environment, and numerous interacting phenotypes generate significant but
 potentially cryptic cascading ecological change. 
description: All methods are available in the associated manuscript.
description: All metadata are available in 'Wood Metadata.pdf'.