cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3ffbg79fh
title: Data from: Effect of pH regulation by microbes on corrosion behaviour of duplex stainless steel 2205 in acidic artificial seawater environment

description: Sulphate reducing bacteria (SRB) can regulate environmental pH because of
 their metabolism. Since local acidification results in pitting corrosion,
 the potential capacity of pH regulation by SRB would have important
 consequences for electrochemical aspects of the bio-corrosion process.
 This study focussed on identifying the effect of pH on the corrosion of
 duplex stainless steel (DSS) 2205 in a nutrient rich artificial seawater
 medium containing SRB species, Desulfovibrio vulgaris. DSS samples were
 exposed to the medium for 13 days at 37 0C at pH ranging from 4.0 to 7.4.
 The open circuit potential value (OCP), sulphide level, pH and number of
 bacteria in the medium were recorded daily. Electrochemical impedance
 spectroscopy (EIS) and potential dynamic polarization were used to study
 the properties of the films and corrosion behaviour of the material.
 Inductively coupled plasma mass spectrometry (ICPMS) was used to measure
 the concentration of cations Cr, Fe, Ni, Mo, Mn in the experimental
 solution after 13 days. Scanning electron microscopy (SEM) and Energy
 Dispersive X-Ray Spectroscopy (EDX) were used for surface analysis. The
 results showed the pH changed from acidic values set at the beginning of
 the experiment to approximately pH 7.5 after 5 days due to bacterial
 metabolism. After 13 days, the highest iron concentration was in the
 solution that was initially at pH 4 accompanied by pitting on the
 stainless steel. Sulphide was present on all specimens but with more
 sulphide corrosion products at pH 4. The results of this study suggest
 that the corrosion process for the first few days exposure at low pH was
 driven by pH in solution rather than by bacteria. The increasing pH during
 the course of the experiment slowed down the corrosion process of
 materials originally at low pH. The nature and mechanism of SRB attack on
 duplex stainless steel at different acidic environments are discussed.
description: The data was collected by experiments. The
 data was processed manually by excel and ZsimWin software.
DOI: 10.5061/dryad.wh70rxwjx
title: Expression and comparison of unigene in the transcriptome in Siniperca chuatsi

description: Muscle from 3-month old individuals of different sizes was used for
 transcriptome analysis. After screening, 39005 unigenes were annotated
 into four databases, including Nr (38833, 52.9%), Swissprot (337479,
 46.0%), COG (10926, 14.8%) and KEGG (19791, 26.9%). Finally, the
 results was annotated by Nr database which
 defined the maximum number of unigenes.
DOI: 10.5061/dryad.8w9ghx3j1
title: Data from: Functional and phylogenetic diversity explain different components of diversity effects on biomass production

description: The Anthropocene is defined by human-driven environmental change, with one
 consequence being the modern dramatic decline in biodiversity globally.
 This is especially worrisome given the long-acknowledged causal linkage
 between biodiversity and ecosystem functioning and the delivery of
 ecosystem services. However, the exact mechanisms driving biodiversity-
 ecosystem function (BEF) relationships remain unclear, specifically the
 linkages between species differences, measured by trait and phylogenetic
 distances, and how interactions, such as competitive inequality and stable
 coexistence via niche partitioning, influence these relationships. Using
 complementary plant biodiversity experiments, a synthetic-assembled one
 that combined species in different phylogenetic distance treatments with a
 semi- natural functional group removal experiment, we assessed how species
 differences influence the mechanisms underpinning BEF relationships. We
 calculated the net biodiversity effect (ΔY) of biomass production and
 partitioned it into two additive parts: the complementarity and selection
 effects at species and functional group level to test how phylogenetic
 diversity and functional diversity capture the influences of the
 complementarity and selection effects. For both experiments, we found that
 phylogenetic and functional diversity explained biodiversity effects
 through similar mechanisms, with a positive relationship with the
 complementarity effect, and a negative relationship with the selection
 effect. However, we found that the selection effect was best predicted by
 a negative relationship with functional dispersion (FDis) of height where
 the selection effect was strongest in plots with similarly tall species
 and weakest with a greater diversity of heights, while higher
 complementary effects were best explained by increasing phylogenetic
 diversity (i.e., high MPDa). Our work revealed that the mechanisms
 underpinning biodiversity-ecosystem function relationships are dependent
 on species differences and how these differences influence competitive
 inequalities and niche differences.
DOI: 10.5066/p19tlxvg
title: Topographic, multispectral, and GPS data collected during uncrewed aircraft system (UAS) operations at Marsh Island, New Bedford, Massachusetts

description: Small Uncrewed Aircraft Systems (sUAS) were used to collect aerial remote sensing data over Marsh Island, a salt marsh restoration site along New Bedford Harbor, Massachusetts. Remediation of the site will involve direct hydrological and geochemical monitoring of the system alongside the UAS remote sensing data. Baseline conditions were evaluated in October 2023, and future data collections will be used to monitor landscape changes. USGS personnel used UAS to collect natural (RGB) color images, multispectral images, and lidar. Additional ground control and check points were taken for quality control. These data were processed to produce a series of high resolution lidar point clouds (LPC), digital elevation models (surface and terrain), and natural-color and multispectral reflectance image orthomosaics.
DOI: 10.5061/dryad.j0zpc86b7
title: Data from: Male rock lizards may compensate reproductive costs of an immune challenge affecting sexual signals

description: Sexual signals can be evolutionarily stable if they are condition
 dependent or costly to the signaler. One of these costs may be the
 trade-off between maintaining the immune system and the elaboration of
 ornaments. Experimental immune challenges in captivity show a reduction in
 the expression of sexual signals, but it is not clear whether these
 detrimental effects are important in nature and, more importantly, whether
 they have reproductive consequences. We designed a field experiment to
 challenge the immune system of wild male Carpetan rock lizards,
 Iberolacerta cyreni, with a bacterial antigen (LPS). The immune challenge
 decreased relative reflectance of UV structural and melanin-dependent
 sexual coloration in the throat and the lateral ocelli, whereas the
 carotenoid-dependent dorsal green coloration was not affected. Immune
 activation also decreased proportions of ergosterol and
 cholesta-5,7-dien-3-ol in femoral secretions. These results support a
 trade-off between the immune system and both visual and chemical sexual
 ornaments. Moreover, reproductive success of males, estimated with DNA
 microsatellites, depended on the expression of some color and chemical
 traits. However, the immune challenge did not cause overall differences in
 reproductive success, although it increased with body size/age in control
 but not in challenged males. This suggests the use of alternative
 reproductive strategies (e.g. forced matings) in challenged males,
 particularly in smaller ones. These males might consider that their
 survival probabilities are low and increase reproductive effort as a form
 of terminal investment in spite of their "low-quality" sexual
 signals and potential survival costs.
description: See paper for more information
description: Spreadsheet contains male data, female data, paternity assign.
 CERVUS Output. Includes key to variable names.
DOI: 10.5061/dryad.51c59zw58
title: Gowardia zebrina sp. nov., a new species in a little-known genus of arctic-alpine lichens (Parmeliaceae)

description: The fruticose lichen genus Gowardia (Parmeliaceae) was recently segregated
 from Alectoria based on phylogeny, morphology, secondary chemistry,
 ecology and distribution. As currently circumscribed, Gowardia comprises
 two wide-ranging species of arctic-alpine regions. Here we describe a
 third species, G. zebrina sp. nov., apparently endemic to subalpine
 regions in mountainous northwestern North America. Gowardia zebrina
 differs from other species in the genus by its combined subpendent habit,
 uniformly capillary branches, predominantly isotomic branching,
 pale-and-dark banding of the terminal branches, and epiphytic ecology.
 Morphological examination of North American herbarium specimens filed
 under A. nigricans suggests the existence of several additional
 undescribed species of Gowardia. A brief overview of morphological
 diversity in these species is given, shedding new light on the question of
 whether Gowardia should be subsumed under Alectoria, as some have
 suggested, or is more appropriately recognized as a distinct genus.
description: Phylogenetic study was based on sequences of nuclear ribosomal
 ITS regions from 29 specimens, including four specimens from the genus
 <em>Alectoria</em> and 24 specimens from
 <em>Gowardia</em>. <em>Bryocaulon divergens</em>
 (Ach.) Kärnefelt belongs to the Alectorioid clade
 <em>sensu</em> Divakar et al. (2015) together with
 <em>Alectoria</em> and <em>Gowardia</em> and was
 used as an outgroup. Seven new ITS sequences were generated for this
 study. The remaining sequence data were obtained from the NCBI GenBank
 (www.ncbi.nlm.nih.gov/genbank/), including all available ITS sequences of <em>Gowardia</em>. The ITS sequences were aligned with MUSCLE v.3.8.31 (Edgar 2004) using EMBL-EBI’s freely available web service (http://www.ebi.ac.uk/Tools/msa/ muscle/). Phylogenetic relationships were inferred using maximum likelihood (ML) as optimality criteria. The ML analysis was performed in RAxML v.8.1.15 (Stamatikis 2104) located at CSC – IT Center for Science (http://www.csc.fi/english). We divided the data set into three partitions (ITS1 region, 5,8S gene, ITS2 region) and used a GTRGAMMA model because GTR is the only substitution model implemented in RAxML. Nodal support was estimated with 1000 bootstrap replicates using the rapid bootstrap algorithm.
DOI: 10.15468/dl.yhu5we
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sepioloidea pacifica",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 44 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002343-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8ppr
title: Data from: Antibacterial activity of graphene oxide nanosheet against multi drug resistant superbugs isolated from infected patients

description: Graphene oxide (GO) is a derivative of graphene nanosheet which is the
 most promising material of the decade in biomedical research. In
 particular, it has been known as an antimicrobial nanomaterial with good
 biocompatibility. In this study, we have synthesized and characterize GO
 and checked its antimicrobial property against different Gram-negative and
 Gram-positive multi drug resistant (MDR) hospital superbugs grown in solid
 agar-based nutrient plates with and without human serum through the
 utilization of agar well diffusion method, live/dead fluorescent staining
 and genotoxicity analysis. The main focus of the antimicrobial activity
 analysis is to distinguish the killing performance of GO in artificial and
 blood containing media because after injection into the bloodstream the
 activity of GO may be modified by adsorption of blood proteins or other
 biomolecules. No significant changes in antibacterial activity were found
 in these two different conditions. We also compare the bactericidal
 capability of GO with some commonly administrated antibiotics and in all
 cases the degree of inhibition is found to be higher. The data presented
 here are novel and show that GO is an effective bactericidal agents
 against different superbugs and can be used as a future antibacterial
 agent.
description: <b>Spectroscopic Characterization of GO</b> 1.The diluted aqueous solutions of GO were taken in crystal cuvette and placed in Hitachi (U-2001, Tokyo, Japan) for UV-vis measurement. The cuvettes were out of all kinds of finger print and spot to get accurate result. DI water was used as reference for all the tests. 2. Ringaku Mini Flex, 600, Japan was used to analyze XRD at 40 mA and 40 kV within the range of 2<b>θ</b> = 5–50° using Copper K-α radiation. 3. In Raman spectroscopy an invia laser-Raman spectrometer (The Renishaw, UK) containing 514 argon ion laser was run. 4. Nicolet NEXUS 470 was applied to obtain FTIR spectra of graphite and GO. KBr was used to prepare sample pellets for the experiment. 5. The TGA was conducted by Shimadzu TG 50 instrument, Japan at 10 °C min <sup>-1</sup> heating rate between 25-700°C temperature range.  All the experiments were conducted several times util get the best results. All the data were collected form the machines by CD and export to my computer. Finally the graphs were  prepared by microsoft excel and put to the manuscript.  
description: Everything is ready to use.
DOI: 10.5061/dryad.v41ns1rsd
title: A SLC1A3 variant associated with hemiplegic migraine and acetazolamide-responsive MRS changes

description: Familial hemiplegic migraine (FHM) is a group of rare familial disorders
 caused, in most cases, by mutations
 in CACNA1A and ATP1A2.1 Heterozygous
 mutations in solute carrier family 1 member 3 (SLC1A3), encoding glial
 glutamate transporter, are associated with episodic ataxia type 6
 (EA6).2,–5 In addition to episodic ataxia (EA), alternating
 hemiplegia and hemiplegic migraine have been reported twice in patients
 with EA6.2,4 Mutations in SLC1A3 are very rare;
 screenings in cohorts of EA and alternating hemiplegia have yielded either
 negative results3,6,–8 or variants of unclear
 significance.e-1--e-3 Herein, we characterize a patient featuring
 sporadic hemiplegic migraine (SHM) responsive to acetazolamide (ACZ) and
 mild cerebellar atrophy associated with a new variant
 in SLC1A3. We also report the utility of proton magnetic
 resonance spectroscopy (MRS) for this condition.
DOI: 10.5061/dryad.tx95x69tx
title: Using patterns in prey DNA digestion rates to quantify predator diets

description: Dietary metabarcoding – the process of taxonomic identification of food
 species from DNA in consumer guts or feces – has been rapidly adopted by
 ecologists to gain insights into biocontrol, invasive species, and the
 structure of food webs. However, an outstanding issue with metabarcoding
 is the semi-quantitative nature of the data it provides: because
 metabarcoding is likely to produce false positives for some prey more
 often than for other prey, we cannot infer relative frequencies of prey in
 the diet. To correct for this, we can adjust detected prey frequencies
 using DNA detectability half-lives unique to each predator-prey
 combination. Because the feeding experiments required to deduce these
 half-lives are time- and resource-intensive, our ability to weight the
 frequency of observations using their detectability has thus far been
 limited to systems with just a few prey. Here, we present a meta-analysis
 of 24 spider prey DNA half-lives and show that these half-lives are
 predictable given predator and prey mass, predator family, temperature,
 and DNA amplicon length. We further provide a new technique for weighting
 observations with half-lives, which allows not just for the ranking of
 prey in the diet, but reveals the proportion of the diet each prey
 comprises. Lastly, we apply this method to published dietary metabarcoding
 data to calculate half-lives and proportion of the predator’s diet for 35
 prey families, demonstrating that this technique can generate improved
 understanding of diets in real, diverse systems.
description: See README file.
DOI: 10.5061/dryad.rxwdbrv58
title: Quantitative genetics of wing morphology in the parasitoid wasp Nasonia vitripennis: hosts increase sibling similarity

description: The central aim of evolutionary biology is to understand patterns of
 genetic variation between species and within populations. To quantify the
 genetic variation underlying intraspecific differences, estimating
 quantitative genetic parameters of traits is essential. In Pterygota, wing
 morphology is an important trait affecting flight ability. Moreover,
 gregarious parasitoids such as Nasonia vitripennis oviposit multiple eggs
 in the same host, and siblings thus share a common environment during
 their development. Here we estimate the genetic parameters of wing
 morphology in the outbred HVRx population of N. vit-ripennis, using a
 sire-dam model adapted to haplodiploids and disentangled additive genetic
 effects and host effects. The results show that the wing size traits have
 low heritability (h2~0.1), while most wing shape traits have roughly twice
 the heritability compared to wing size traits. However, the estimates
 in-creased to h2~0.6 for wing size traits when omitt ing the host effect
 from the statistical model, while no meaningful increases were observed
 for wing shape traits. Overall, host effects contributed ~50% of the
 variation in wing size traits. This indicates that hosts have a large
 effect on wing size traits, about five-fold more than genetics. Moreover,
 bivariate analyses were conducted to derive the genetic relationships
 among traits. Overall, we demonstrate the evo-lutionary potential for
 morphological traits in the N. vitripennis HVRx outbred population and
 report the host effects on wing morphology. Our findings can contribute to
 a further dissection of the genetics underlying wing morphology in N.
 vitripennis, with relevance for gregarious parasitoids and possible other
 insects as well.
DOI: 10.5061/dryad.866t1g1nb
title: Paired human macrophage RNA sequencing data

description: Allele-specific expression (ASE) analysis, which quantifies the relative
 expression of two alleles in a diploid individual, is a powerful tool for
 identifying cis-regulated gene expression variations that underlie
 phenotypic differences among individuals. Existing methods for gene-level
 ASE detection analyze one individual at a time, therefore failing to
 account for shared information across individuals. Failure to accommodate
 such shared information not only reduces power, but also makes it
 difficult to interpret results across individuals. However, when only RNA
 sequencing (RNA-seq) data are available, ASE detection across individuals
 is challenging because the data often include individuals that are either
 heterozygous or homozygous for the unobserved cis-regulatory SNP, leading
 to sample heterogeneity as only those heterozygous individuals are
 informative for ASE, whereas those homozygous individuals have balanced
 expression. To simultaneously model multi-individual information and
 account for such heterogeneity, we developed ASEP, a mixture model with
 subject-specific random effect to account for multi-SNP correlations
 within the same gene. ASEP only requires RNA-seq data, and is able to
 detect gene-level ASE under one condition and differential ASE between two
 conditions (e.g., pre- versus post- treatment). Extensive simulations
 demonstrated the convincing performance of ASEP under a wide range of
 scenarios. We applied ASEP to a human kidney RNA-seq dataset, identified
 ASE genes and validated our results with two published eQTL studies. We
 further applied ASEP to a human macrophage RNA-seq dataset, identified
 genes showing evidence of differential ASE between M0 and M1 macrophages,
 and confirmed our findings by results from cardiometabolic trait-relevant
 genome-wide association studies. To the best of our knowledge, ASEP is the
 first method for gene-level ASE detection at the population level that
 only requires the use of RNA-seq data. With the growing adoption of
 RNA-seq, we believe ASEP will be well-suited for various ASE studies for
 human diseases.
description: Raw RNA
 sequencing data were aligned to the hg19 human reference genome using STAR
 and mapping bias was removal using WASP. The genetic variants were called
 using mpileup and variants with base quality score lower than 20 were
 removed. ANNOVAR was used to annotate the genetic variants and SNPs mapped
 to exonic regions were kept in analyses.
DOI: 10.5061/dryad.wpzgmsbhw
title: Neuronal activity in sensory cortex predicts the specificity of learning

description: Learning to avoid dangerous signals while preserving normal responses to
 safe stimuli is essential for everyday behavior and survival. Following
 identical experiences, subjects exhibit fear specificity ranging from high
 (specializing fear to only the dangerous stimulus) to low (generalizing
 fear to safe stimuli), yet the neuronal basis of fear specificity remains
 unknown. Here, we identified the neuronal code that underlies
 inter-subject variability in fear specificity using longitudinal imaging
 of neuronal activity before and after differential fear conditioning in
 the auditory cortex of mice. Neuronal activity prior to, but not after
 learning predicted the level of specificity following fear conditioning
 across subjects. Stimulus representation in auditory cortex was
 reorganized following conditioning. However, the reorganized neuronal
 activity did not relate to the specificity of learning. These results
 present a novel neuronal code that determines individual patterns in
 learning. Keywords: fear conditioning, auditory cortex, sensory systems,
 learning, computational model, imaging, sensory cortex, tuning curve,
 neurobiology, population coding.
description: All imaging sessions were carried out inside a single-walled acoustic isolation booth (Industrial Acoustics). Mice were placed in the imaging setup, and the head plate was secured to a custom base (eMachine Shop) serving to immobilize the head. Mice were gradually habituated to head-fixing over 3 – 5 days, 3 – 4 weeks after surgery and before imaging commenced. Imaging took place in mice aged 17.5 – 19.6 weeks (min: 12.9, max: 27.1 weeks). We recorded changes in fluorescence of GCaMP6s/m caused by fluctuations in calcium concentration in transfected neurons of awake, head-fixed mice, using two-photon microscopy (Ultima <i>in vivo</i> multiphoton microscope, Bruker). The laser (940 nm, Chameleon Ti-Sapphire) power at the brain surface was kept below 30 mW. Recordings were made at 512 x 512 pixels and 13-bit resolution at ~30 frames per second. Stimuli were generated at a sampling rate of 400 kHz using Matlab (MathWorks, USA)  and consisted of 100-ms long tone pips in the 5−32-kHz frequency range and presented at 60 – 80 dB SPL. In a single recording session, each frequency was repeated 15 – 25 times in a <i>pseudo</i>-random order with a 4-s inter-stimulus interval.
description: This dataset consists of all data necessary to reproduce figures
 from the manuscript. Please read the README file. Code supplied is written
 in Matlab. Data is supplied in Matlab files (.mat)