cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2jm63xsm2
title: Hartree-Fock on a superconducting qubit quantum computer

description: The simulation of fermionic systems is among the most anticipated
 applications of quantum computing. Here, we performed several quantum
 simulations of chemistry with up to one dozen qubits, including modeling
 the isomerization mechanism of diazene. We also demonstrated
 error-mitigation strategies based on N-representability which dramatically
 improve the effective fidelity of our experiments. Our parameterized
 ansatz circuits realized the Givens rotation approach to
 non-interacting fermion evolution, which we variationally
 optimized to prepare the Hartree-Fock wavefunction. This ubiquitous
 algorithmic primitive is classically tractable to simulate, yet still
 generates highly entangled states over the computational basis, which
 allowed us to assess the performance of our hardware and establish a
 foundation for scaling up correlated quantum chemistry simulations.
description: This data was collected on the Sycamore processor from google
 used to achieve quantum supremacy.  Data was processed using python code
 in https://github.com/quantumlib/ReCirq/tree/master/recirq/hfvqe (commit: 64c78758f5c4d139af3eeada42003485fbca17d1).  
description: A readme file is contained in the upload.  All software for
 dataprocessing can be found at https://github.com/quantumlib/ReCirq.  Data stored as numpy pickled data containing the measured 1-RDMs.  The molecular datafiles can be found at (https://quantumlib.github.io/openfermioncloud/).
DOI: 10.5281/zenodo.11433368
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - JAEN - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Jaén:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5281/zenodo.11433369
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - JAEN - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Jaén:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.pg4f4qrkm
title: Data from: The genomic footprint of coastal earthquake uplift

description: Theory suggests that catastrophic earth-history events can drive rapid
 biological evolution, but empirical evidence for such processes is scarce.
 Destructive geological events such as earthquakes can represent
 large-scale natural experiments for inferring such evolutionary processes.
 We capitalised on a major prehistoric (800 y BP) geological uplift event
 affecting a southern New Zealand coastline to test for the lasting genomic
 impacts of disturbance. Genome-wide analyses of three co-distributed
 keystone kelp taxa revealed that post-earthquake recolonization drove the
 evolution of novel, large-scale intertidal spatial-genetic ‘sectors’ which
 are tightly linked to geological fault boundaries. Demographic simulations
 confirmed that, following widespread extirpation, parallel expansions into
 newly vacant habitats rapidly restructured genome-wide diversity.
 Interspecific differences in recolonization mode and tempo reflect
 differing ecological constraints relating to habitat choice and dispersal
 capacity among taxa. This study highlights the rapid and enduring
 evolutionary effects of catastrophic ecosystem disturbance, and reveals
 the key role of range expansion in reshaping spatial genetic patterns.
description: <strong>D.antarctica_popmap</strong>
 population map of <em>Durvillaea antarctica</em> used
 for de novo SNP calling in STACKS
 <strong>D.poha_popmap</strong>
 population map of <em>Durvillaea poha </em>used for
 de novo SNP calling in STACKS
 <strong>D.willana_popmap</strong>
 population map of <em>Durvillaea willana </em>used
 for de novo SNP calling in STACKS
 <strong>antarctica.snps.vcf</strong>
 contains first SNP per locus in 128 samples
 of <em>Durvillaea antarctica</em>
 <strong>poha.snps.vcf</strong>
 contains first SNP per locus in 113 samples
 of <em>Durvillaea poha</em>
 <strong>willana.snps.vcf</strong>
 contains first SNP per locus in 73 samples
 of <em>Durvillaea willana</em>
 <strong>antarctica.structure</strong>
 STRUCTURE input file for 128 samples of <em>Durvillaea
 antarctica, </em>including individuals' ID and population
 information
 <strong>poha.structure</strong>
 STRUCTURE input file for 113 samples of <em>Durvillaea
 poha, </em>including individuals' ID and population
 information
 <strong>willana.structure</strong>
 STRUCTURE input file for 73 samples of <em>Durvillaea
 willana, </em>including individuals' ID and population
 information
 <strong>antarctica.DIYABC.snp</strong>
 DIYABC SNP input file for 108 samples of <em>Durvillaea
 antarctica</em>
 <strong>poha.DIYABC.snp</strong>
 DIYABC SNP input file for 93 samples of <em>Durvillaea
 poha</em>
 <strong>antarctica_DIYABC_priors_models</strong> header file generated using DIYABC for demographic model comparison for <em>Durvillaea antarctica</em> <strong>poha_DIYABC_priors_models</strong> header file generated using DIYABC for demographic model comparison for <em>Durvillaea poha</em>
DOI: 10.6086/d1b37v
title: Care-giver identity impacts offspring development and performance in an annually social bumble bee

description: Background: The developmental fates of offspring have the potential to be
 influenced by the identity of their care-givers and by the nature of the
 care that they receive. In animals that exhibit both parental and
 alloparental care, such as the annually eusocial insects, the influence of
 care-giver identity can be directly assessed to yield mechanistic and
 evolutionary insights into the origins and elaboration of brood care.
 Here, we performed a comparative investigation of maternal and worker
 brood care in bumble bees, a pollinator group where mothers (queens) rear
 the first offspring in the nest, and then daughters (workers) assume this
 role upon their emergence. Specifically, we compared the effects of queen
 and worker brood care on offspring development and also offspring
 performance, for a set of traits related to sensory biology, learning, and
 stress resistance. Results: We found that queen-reared workers were
 smaller-bodied than worker-reared offspring, suggesting that bumble bee
 queens influence body size determination in their offspring. We also found
 that queen-reared workers were more resistant to starvation, which might
 be beneficial for early nesting success. These maternal influences could
 not be explained by feeding rate, given that we detected a similar
 offspring feeding frequency in both queens and workers. 
 Conclusion: Bumble bee queens have a unique influence on the development
 of the first offspring in the nest, which they rear, relative to
 worker-reared workers. We propose that bumble bee brood care has been
 shaped by a suite of evolutionary and ecological factors, which might
 include a maternal influence on traits that promote survival of inicipent
 colonies.
description: The complete data file contains raw data for all analyses on
 Costa et al. 2021
DOI: 10.5061/dryad.b5mkkwh9g
title: Data from: Native distribution characteristics rather than functional traits explain preadaptation of invasive species to high-UV-B environments

description: Aim: Alien species successfully colonize new ranges if they encounter
 favourable environmental conditions there and possess traits that match
 new challenges. Climate matching approaches comparing native and exotic
 ranges mostly consider temperature and precipitation niches of alien
 species, but have largely ignored UV-B radiation. UV-B fundamentally
 differs between hemispheres, with much higher levels at southern than at
 northern latitudes. Consequently, UV-B might act at the global scale and
 present a so far neglected filter that species need to overcome when
 invading high-UV-B environments. Location: We performed two multi-species
 common-garden experiments, conducted in the native European range
 (Germany) and the high-UV-B exotic range (New Zealand) to test for
 preadaptation to UV B. Methods: We used 25 herbaceous species from open
 habitats, which we exposed in each range to three UV radiation treatments:
 (i) natural sunlight, (ii) exclusion of UV-B while allowing natural UV-A,
 and (iii) exclusion of UV-B and UV-A. We additionally used plant traits
 (TRY), global distribution data (GBIF, GloNAF) and global UV-B satellite
 data (glUV) to determine species-specific characteristics as fostering
 agents of UV-B tolerance. The joint analysis of experimental and
 macroecological data allowed quantification of species plasticity and
 identification of beneficial species traits in high-UV-B environments.
 Results: Our results showed an overall limiting effect of UV-B in both
 common gardens but the UV-stress response tended to be more pronounced in
 the invaded range. Across all species, we found little evidence for
 preadaptation by functional plant traits. In contrast, preadaptation to
 climatic conditions related to the species’ native UV-B niche was of
 greater importance for plant performance in the presence of UV-B
 radiation. Main conclusions: For predicting alien species’ ability to
 expand into high-UV-B environments, macroclimatic niche characteristics of
 the species’ native range might be better predictors than functional
 traits and should be more considered in future projection models.
DOI: 10.5061/dryad.9kd51c5dp
title: Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities

description: Understanding the role of interspecific interactions in shaping ecological
 communities is one of the central goals in community ecology. In fungal
 communities, measuring interspecific interactions directly is challenging
 because these communities are composed of large numbers of species, many
 of which are unculturable. An indirect way of assessing the role of
 interspecific interactions in determining community structure is to
 identify the species co-occurrences that are not constrained by the
 environmental conditions. In this study, we investigated co-occurrences
 among root-associated fungi, asking whether fungi co-occur more or less
 strongly than expected based on the environmental conditions and the host
 plant species examined. For this purpose, we generated molecular data on
 root-associated fungi of five plant species evenly sampled along an
 elevational gradient at a high Arctic site. We analysed the data using a
 joint species distribution modelling approach that allowed us to identify
 those co-occurrences that could be explained by the environmental
 conditions and the host plant species, as well as those co-occurrences
 that remained unexplained and thus more likely reflect interactive
 associations. Our results indicate that positive interactions play an
 important role in shaping microbial communities in arctic plant roots. In
 particular, we found that mycorrhizal fungi are especially prone to
 positively co-occur with other fungal species. Our results bring new
 understanding to the structure of arctic interaction networks by
 suggesting that interactions among root-associated fungi are predominantly
 positive.
description: These data consist of molecularly identified root-associated
 fungal communities of five plant species occurring along an arctic
 elevational gradient. The original sequence data based on the ITS region
 are published in Abarenkov et al (2019 https://doi.org/10.5061/dryad.9dr6j0c), and the data published here consist of the postprocessed and taxonomically assigned using the Protax-fungi approach. The data further contains information about the functional group of each taxonomical unit (mycorrhizal, endophytic or unclassified), and data on the environmental covariates used in the analyses. The data are accompained by the R-scripts for carrying out the analyses presented in Abrego et al (2020, Molecular Ecology) about raw vs. environmentally constrained co-occurrences using the R-package Hmsc-R.
description: The data are given in the format of R-files which can be used as
 shown in the uploaded R-scripts. You may need to add ".rdata"
 file extension to the
DOI: 10.5061/dryad.7d7wm37s6
title: Fast saccadic eye-movements in humans suggest that numerosity perception is automatic and direct.

description: Fast saccades are rapid automatic oculomotor responses to salient and
 ecologically important visual stimuli such as animals and faces.
 Discriminating the number of friends, foe or prey may also have an
 evolutionary advantage. In this study participants were asked to saccade
 rapidly towards the more numerous of two arrays. Participants could
 discriminate numerosities with high accuracy and great speed, as fast as
 190 ms. Intermediate numerosities were more likely to elicit fast saccades
 than very low or very high numerosities. Reaction-times for vocal
 responses (collected in a separate experiment) were slower, did not depend
 on numerical range, and correlated only with the slow, not the fast
 saccades, pointing to different systems.  The short
 saccadic-reaction times we observe are surprising given that
 discrimination using numerosity estimation is thought to require a
 relatively complex neural circuit, with several relays of information
 through parietal and pre-frontal cortex. Our results suggest that fast
 numerosity-driven saccades may be generated on a single feed-forward pass
 of information recruiting a primitive system that cuts through the
 cortical hierarchy and rapidly transforms the numerosity information into
 a saccade command.
DOI: 10.5061/dryad.7m0cfxpr8
title: Data from: Climate change and landscape-use patterns influence recent past distribution of giant pandas

description: Climate change is one of the most pervasive threats to biodiversity
 globally, yet the influence of climate relative to other drivers of
 species depletion and range contraction remain difficult to disentangle.
 Here, we examine climatic and non-climatic correlates of giant panda
 (Ailuropoda melanoleuca) distribution using a large-scale 30-year dataset
 to evaluate whether a changing climate has already influenced panda
 distribution. We document several climatic patterns, including increasing
 temperatures, and alterations to seasonal temperature and precipitation.
 We found that while climatic factors were the most influential predictors
 of panda distribution, their importance diminished over time, while
 landscape variables have become relatively more influential. We conclude
 that the panda’s distribution has been influenced by changing climate, but
 conservation intervention to manage habitat is working to increasingly
 offset these negative consequences.
DOI: 10.21223/p3/ugwazl
title: Dataset for: Advanced clones of group LBHT cycle 1, population B (LBHT) in Oxapampa-Peru

description: In anticipation of the effects of global warming on potato cultivation in both tropical and subtropical environments. Since 2004, efforts have turned to the development of a new group in Population B with improved adaptation to warm environments, resistance to late blight and virus, mid-season maturity (90 day growing period under short-day length conditions), adaptation to mid elevations, low glycoalkaloids content, along with economically important traits such as high tuber yield, quality for table and industry. And so group LBHT of population B was developed, denominated LBHT because of its late blight and heat tolerance. All trials were conducted in randomized complete block design (RCBD) with 2-4 replicates or in simple lattice design at Oxapampa, located at 1810 masl in Pasco in the Eastern mountain ranges facing the Amazon. The trials were established at Oxapampa due to high disease pressure of late blight, disease endemic, highly favorable for disease development and severity during the rainy periods in these areas from 2005 to 2008.
DOI: 10.5061/dryad.79cnp5hs9
title: Earlier springs enable High-Arctic wolf spiders to produce a second clutch - supplementary data

description: Spiders at southern latitudes commonly produce multiple clutches, but this
 has not been observed at high latitudes where activity seasons are much
 shorter. Yet the timing of snowmelt is advancing in the Arctic, which may
 allow some species to produce an additional clutch. To determine if this
 is already happening, we used specimens of the wolf spider Pardosa
 glacialis caught by pitfall traps from the long-term (1996-2014)
 monitoring program at Zackenberg, Northeast Greenland. We dissected
 individual egg sacs and counted the number of eggs and partially developed
 juveniles, and measured carapace width of the mothers. Upon discovery of a
 bimodal frequency distribution of clutch sizes, as is typical for wolf
 spiders at lower latitudes producing a second clutch, we assigned egg sacs
 to being a first or second clutch depending on clutch size. We tested
 whether the median capture date differed among first and second clutches,
 whether clutch size was correlated to female size, and whether the
 proportion of second clutches produced within a season was related to
 climate. We found that assigned second clutches appeared significantly
 later in the season than first clutches. In years with earlier snowmelt,
 first clutches occurred earlier and the proportion of second clutches
 produced was larger. This is likely a result of female spiders producing
 their first clutches earlier in those years and allowing them time to
 produce another clutch. Clutch size for first clutches was correlated to
 female size, while this was not the case for second clutches. Our results
 provide the first evidence for Arctic invertebrates producing additional
 clutches in response to warming. This could be a common but overlooked
 phenomenon due to the challenges associated with long-term collection of
 life history data in the Arctic. Moreover, given that wolf spiders are a
 widely distributed, important tundra predator, we may expect to see
 population and food web consequences of their increased reproductive
 rates.
description: Pitfall traps, dissection of egg sacs, measurements of carapace
 width of female adult wolf spiders.
DOI: 10.5061/dryad.4qrfj6q7m
title: Tomato Protein Phosphatase 2C (SlPP2C3) influences fruit ripening onset and fruit glossiness

description: Abscisic acid (ABA) plays a vital role in coordinating physiological
 processes during fresh fruit ripening. ABA can bind to ABA receptors which
 interacts and inhibits their co-receptors type 2C phosphatases (PP2Cs).
 However, the dissected mechanism of PP2C during fruit ripening is unclear.
 In this study, we identify the role of SlPP2C3, a tomato type 2C
 phosphatase, as a negative regulator of ABA signaling and fruit ripening.
 SlPP2C3 selectively interacted with monomeric ABA receptors and SlSnRK2.8
 kinase in both yeast and tobacco epidermal cells. Expressions of SlPP2C3
 were observed in all tissues, and it negatively correlated with the fruit
 ripening which was induced by exogenous ABA. Tomato plants with suppressed
 SlPP2C3 expression exhibited enhanced sensitivity to ABA, while SlPP2C3
 over-expressed plants were less sensitive to ABA. Meaningfully, lack of
 SlPP2C3 expression causes the acceleration of fruit ripening onset via the
 alternation of ABA signaling activity, and the fruit gloss is affected by
 the changes of outer epidermis structure. RNA-seq analysis found
 significant different expression of cuticle-related genes in pericarp
 between wild-type and SlPP2C3 suppressed lines. Taken together, our
 finding demonstrate that SlPP2C3 plays an important role in the regulation
 of fruit ripening and fruit appearance quality in tomato. 
description: <i>RNA-seq</i> Total RNA was extracted from the skin of WT and <i>SlPP2C3</i>-RNAi4 fruits at the mature green stage. RNA degradation and contamination were monitored on 1% agarose gels. RNA integrity was assessed by an RNA 6000 Pico Assay Kit and a Bioanalyzer 2100 system (Agilent Technologies). The results were shown in Fig. S3. RNA (3 μg per sample) was used for mRNA purification and library construction with a Truseq RNA Sample Prep Kit (Illumina, CA, USA) following the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq 2000 platform (Illumina). Each sample yielded more than 6 Gb of data. Raw data in fastq format were firstly processed using in-house perl scripts. Clean data was obtained by removing reads containing adapters, and poly-N and low-quality reads from raw data. Filtered RNA-seq clean reads were aligned to the reference tomato genome (release SL2.50) using TopHat v2.0.13 (Kim <i>et al.</i>, 2013). HTSeq v0.5.3 (https://htseq.readthedocs.io/en/master/) was used to count the number of reads mapped to each gene, and reads per kilobase of transcript per million mapped reads (RPKM) values were calculated based on the length of the gene and the number of reads mapped. Differential expression analysis was performed using the DEGSeq R package (1.12.0) and Cufflinks (Trapnell <i>et al.</i>, 2012). Corrected <i>p</i>-values of 0.001 and log2 (fold change) ³1 were set as the thresholds for significant differential expression.
description: Highlight: Tomato ABA
 co-receptor type 2C phosphatase (SlPP2C3), which acts as an ABA signalling
 negative regulator, affects tomato fruit ripening onset and fruit
 glossiness.