cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nk98sf7t8
title: Efficient parallelization of tensor network contractions for simulating quantum computation

description:  In this paper, we demonstrate a classical simulation framework
 for quantum computation by contracting tensor networks of sizes previously
 deemed out of reach. The main contribution of this work is a
 parallelization scheme called index slicing that breaks down an
 infeasibly large tensor network contraction task into smaller subtasks
 that can be executed fully in parallel, without interdependencies or
 intermediate communications. As a benchmarking example, we show
 that our algorithm can reduce the simulation of the Sycamore random
 circuit sampling task to less than 20 days, achieving an acceleration of
 over five orders of magnitude compared to the original proposal. We then
 showcase the capabilities of the simulation framework via investigations
 of near-term quantum algorithms and quantum error
 correction. Given the ubiquity of tensor networks in quantum
 information science, we believe that our simulation framework will be a
 valuable tool in the era of quantum information technology.
description: This dataset contains contraction schemes used in our classical
 simulation demonstration, including random quantum circuit simulation,
 quantum approximate.
description: Please see Readme file.
DOI: 10.5061/dryad.xksn02vg9
title: Prevalence and associated factors of hepatitis B and C virus in hemodialysis patients in Africa

description: Background Due to its invasive procedure patients on hemodialysis (HD) are
 at high risk of infections. Infections acquired in dialysis units can
 prolong hospitalization date and/or prolong illness in patients, and
 increase treatment cost. There are no adequate data on the prevalence of
 Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infections in HD
 patients. Therefore, this study aimed to estimate the pooled prevalence
 and associated factors of HBV and HCV infections among HD patients in
 Africa. Method The databases PubMed, Medline, EMBASE, Cochrane library,
 web of science, African Journals Online, Science Direct, and Google
 Scholar were searched to identify relevant studies. The review was
 performed based on Preferred Reporting Items for Systematic Reviews and
 Meta-Analyses (PRISMA) guidelines. Data were extracted independently by
 two authors and analyzed using STATA 11. A random-effect model was fitted
 to estimate the pooled prevalence with their 95% confidence interval. To
 detect publication bias funnel plots analysis and Egger weighted
 regression tests were done. Results The overall pooled prevalence of HBV
 and HCV infection among HD patients in Africa was 9.88% (95% CI:
 7.20-12.56) I2=97.9% and 23.04% (95% CI: 18.51-2757) I2=99.6%,
 respectively. In addition, the pooled prevalence of HBV and HCV
 co-infection was 7.18% (95% CI: 3.15-11.20) I2=99.6%. Duration of dialysis
 was found to be the contributing factor for the occurrence of HBV and HCV
 among HD patients (OR=1.44; 95% CI: 1.04, 2.01). Conclusion This study
 showed that there is high prevalence of HBV and HCV infections in HD
 patients in Africa. Therefore, strict adherence to precautions of
 infection control measures, isolation of seropositive patients,
 improvement in infrastructures, adequate screening of HBV and HCV for the
 donated blood, and decentralized HD services is needed to minimize the
 risk of HBV and HCV infections in HD facilities.
DOI: 10.5061/dryad.wstqjq2mf
title: Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi

description: The Puma lineage within the family Felidae consists of three species that
 last shared a common ancestor around 4.9 million years ago. Whole-genome
 sequences of two species from the lineage were previously reported: the
 cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The
 present report describes a whole-genome assembly of the remaining species,
 the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male
 jaguarundi with 10X Genomics linked reads and assembled the whole-genome
 sequence. The assembled genome contains a series of scaffolds that reach
 the length of chromosome arms and is similar in scaffold contiguity to the
 genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a
 scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the
 jaguarundi genome using BUSCO, aligned reads of the sequenced individual
 and another published female jaguarundi to the assembled genome, annotated
 protein-coding genes, repeats, genomic variants and their effects with
 respect to the protein-coding genes, and analyzed differences of the two
 jaguarundis from the reference mitochondrial genome. The jaguarundi genome
 assembly and its annotation were compared in quality, variants and
 features to the previously reported genome assemblies of puma and cheetah.
 Computational analyzes used in the study were implemented in transparent
 and reproducible way to allow their further reuse and modification.
description: The dataset presents aligned reads and genome annotation
 (including genomic variants) for jaguarundi (<em>Puma
 yagouaroundi</em>), aligned reads and genomic variants for cheetah
 (<em>Acinonyx jubatus</em>), and genomic variants for puma
 (<em>Puma concolor</em>). The Methods section of the related
 paper describes how the dataset was collected and processed.
description: The dataset contents are described in the ReadMe file. Please use
 the JDGA Pipelines software to reproduce results reported in the related
 paper. The link to the software is available in the Related Works
 section.
DOI: 10.5061/dryad.2547d7wqr
title: Data from: A field-friendly method of measuring faecal glucocorticoid metabolite concentration as a simple stress checker in snow leopards

description: Hormonal analysis of excrement has been employed to noninvasively assess
 the physiological conditions of domestic, experimental, zoo, and wild
 animals to. However, conventional hormone analysis techniques require
 frozen and refrigerated reagents, and laboratory equipment; therefore, it
 is almost impossible to obtain the results on-site. This study attempted
 to establish a method for the simple and rapid quantitative on-site
 analysis of faecal glucocorticoid metabolite (fGM) concentrations; this
 method involved using hand-shaking for faecal hormone extraction, and
 immunochromatography using test strips and a smartphone application. This
 study focused specifically on snow leopards and developed a new, simple
 fGM measurement method to evaluate their stress levels on-site. First, the
 effects of ultraviolet exposure and bacterial activity on fGM
 concentration, including sample age, were evaluated using faeces from a
 captive snow leopard. Second, a field-friendly hormone extraction method
 was evaluated; this method does not require storage of faeces in the field
 because the hormones are extracted by hand-shaking of faeces in ethanol at
 the time of collection. In addition, to measure hormone concentrations
 on-site, a simple immunochromatography measurement kit was used. The
 concentrations were measured by quantifying the colour reactions using a
 smartphone application. There was no consistent increase or decrease in
 fGM concentration with ultraviolet irradiation time. In addition, a high
 correlation was observed between concentrations extracted using the
 conventional method (using a vortex mixer and methanol extraction) and
 those from the field-friendly method (r = 0.812, P &lt; 0.05). Changes
 in fGM concentration measured using immunochromatography were also highly
 consistent with those measured using the conventional method
 (enzyme-immunoassay) (r = 0.825, P &lt; 0.05). The analytical
 validation of immunochromatography also showed high accuracy, i.e.
 parallelism (ANCOVA: F = 0.597, df = 1, P = 0.445) and recovery tests
 (98.2% ± 5.1% and 107.5% ± 18.7%). Further, for biological validation, the
 change in fGM concentration was examined before and after the
 transportation of the snow leopards to another zoo. This field-friendly
 hormone analysis method is expected to contribute as a simple and rapid
 stress evaluation tool to manage conservation and animal welfare by
 monitoring the stress levels.
DOI: 10.5061/dryad.s4mw6m96h
title: Pollinator visits to six plant species in an oil palm landscape

description: Pollination sustains biodiversity and food security, but pollinators are
 threatened by habitat degradation, fragmentation and loss. Here we aimed
 to assess how remaining forests influence bee visits to flowers in an oil
 palm dominated landscape in Borneo, Indonesia. To do this, we observed
 pollinator visits to six plant species: four crops (Capsicum
 frutescens L. “chili”; Citrullus lanatus (Thunb.) Matsum. & Nakai
 “watermelon”; Solanum lycopersicum L. “tomato”; and Solanum melongena L.
 “eggplant”); one native plant Melastoma malabathricum L. “melastome”; and
 the exotic Turnera subulata Smith “turnera”. We made one local grid-based
 and one landscape scale transect-based study spanning to 208 m and 2,130 m
 from forest, respectively. We recorded a total of 1,535 pollinator visits
 to 4,831 flowers in 1,046 ten-minute observation periods, with bee visits
 making up 81.4% of these visits. We observed an overall mean of
 0.23 and 0.34 bee visits per flower per ten-minute
 period for the grid-based and transect studies, respectively. C.
 lanatus had the highest observed visitation
 frequency (0.62 visits per flower per ten-minute period)
 while S. lycopersicum had no observed visits. The dataset
 includes raw data collected in the field from 22 July – 29 October 2017.
description: Please see the 'Metadata' tab within the data file for
 detail of values and variables.
DOI: 10.5061/dryad.xd2547dh0
title: Data from: Integrated population models poorly estimate the demographic contribution of immigration

description: Estimating the contribution of demographic parameters to changes in
 population growth is essential for understanding why populations
 fluctuate. Integrated Population Models (IPMs) offer a possibility to
 estimate contributions of additional demographic parameters, for which no
 data have been explicitly collected: typically immigration. Such
 parametersare often subsequently highlighted as important drivers of
 population growth. Yet, accuracy in estimating their temporal variation,
 and consequently their contribution to changes in population growth rate,
 has not been investigated. To quantify the magnitude and cause of
 potential biases when estimating the contribution of immigration using
 IPMs, we simulated data (using Northern Wheatear Oenanthe oenanthe
 population estimates) from controlled scenarios to examine potential
 biases and how they depend on IPM parameterization, formulation of priors,
 the level of temporal variation in immigration, and sample size. We also
 used empirical data on populations with known rates of immigration: Soay
 Sheep Ovis aries and Mauritius kestrel Falco punctatus with zero
 immigration and grey wolf Canis lupus in Scandinavia with near-zero
 immigration. IPMs strongly overestimated the contribution of immigration
 to changes in population growth in scenarios when immigration was
 simulated with zero temporal variation (proportion of variance attributed
 to immigration = 63% for the more constrained formulation and real sample
 size) and in the wild populations, where the true number of immigrants was
 zero or near-zero (Kestrel 19.1-98.2%, Sheep 4.2-36.1%, Wolf 84.0-99.2%).
 Although the estimation of immigration in the simulation study became more
 accurate with increasing temporal variation and sample size, it was often
 not possible to distinguish between an accurate estimation from data with
 high temporal variation versus an overestimation from data with low
 temporal variation. Unrealistically large sample sizes may be required to
 estimate the contribution of immigration well. To minimise the risk of
 overestimating the contribution of immigration (or any additional
 parameter) in IPMs, we recommend to: (i) look for evidence of variation in
 immigration before investigating its contribution to population growth,
 (ii) simulate and model data for comparison to the real data, and (iii)
 use explicit data on immigration when possible.
DOI: 10.5061/dryad.3r2280ggb
title: Lags in phenological acclimation of mountain grasslands after recent warming

description: 1. In the current biodiversity crisis, one of the crucial questions is how
 quickly plant communities can acclimate to climate warming and longer
 growing seasons to buffer the impairment of community functioning.
 Answering this question is pivotal especially for mountain grasslands that
 experience harsh conditions but provide important ecosystem services to
 people. 2. We conducted a reciprocal transplant experiment along an
 elevation gradient (1920 m vs. 2450 m) in the French Alps to test the
 ability of plant species and communities to acclimate to warming and
 cooling. For three years, we measured weekly the timing of phenological
 events (e.g. start of flowering or greening) and the length of
 phenological stages linked to demographic performance (e.g. lengths of
 flowering or greening periods). 3. We found that warming (and cooling)
 changed the timing of phenological events strongly enough to result in
 complete acclimation for graminoids, for communities in early and
 mid-season, but not at all for forbs. For example, warming resulted in
 later greening of communities and delayed all phenophases of graminoids.
 Lengths of phenological stages did not respond strongly enough to climate
 change to acclimate completely, except for graminoids. For example,
 warming led to an acclimation lag in the community’s yearly productivity
 and had a strong negative impact on flowering of forbs. Overall, when
 there was an acclimation failure, responses to cooling were mostly
 symmetric and confirmed slow acclimation in mountain grasslands. 4.
 Synthesis. Our study highlights that phenological plasticity cannot
 prevent impairment of community functioning under climate warming in the
 short-term. The failures to acclimate after three years of warming signals
 that species and communities underperform and are probably at high risk of
 being replaced by locally better-adapted plants.
description: For the dataset collection and the processing, please refer to
 the methods section of the manuscript. 
description: dataFocals_030621.RData or dataFocals_030621.csv
 Plot: Treatment groups<br>     LC:
 SubalpineControl<br>     LT: AlpineWarmed<br>     GC:
 AlpineControl<br>     GT: SubalpineCooled
 Repetition: Number of plot repetitions
 Observation_Date: Species: Focal species
 names Phenophase: Phenological phases as described in
 the main manuscript Number_of_individuals: Number of
 individuals present in the phenophase. For details, please refer to the
 main manuscript.  dataNDVI_030621.RData or
 dataNDVI_030621.csv Plot: Treatment groups     LC:
 SubalpineControl<br>     LT: AlpineWarmed<br>     GC:
 AlpineControl<br>     GT: SubalpineCooled
 Subplot: Coding for 1mx1m subplots<br>     X: Only for
 Controls<br>     A,B,C,D: Only for Treatments
 Plot_Repetition: Number of 4mx4m plot repetitions
 Measurement_Repetition: 3 times measurement repetitions
 Measurement_Date: Measurement_Sm: Gap-filled
 NDVI measurements. For the methodology, please refer to the main
 manuscript.
DOI: 10.5061/dryad.pzgmsbcm6
title: Density, parasitism, and sexual reproduction are strongly correlated in lake Daphnia populations

description: Many organisms can reproduce both asexually and sexually. For cyclical
 parthenogens, periods of asexual reproduction are punctuated by bouts of
 sexual reproduction, and the shift from asexual to sexual reproduction has
 large impacts on fitness and population dynamics. We studied populations
 of Daphnia dentifera to determine the amount of investment in sexual
 reproduction as well as the factors associated with variation in
 investment in sex. To do so, we tracked host density, infections by nine
 different parasites, and sexual reproduction in 15 lake populations of D.
 dentifera for three years. Sexual reproduction was seasonal, with male and
 ephippial female production beginning as early as late September and
 generally increasing through November. However, there was substantial
 variation in the prevalence of sexual individuals across populations, with
 some populations remaining entirely asexual throughout the study period
 and others shifting almost entirely to sexual females and males. We found
 strong relationships between density, prevalence of infection, parasite
 species richness, and sexual reproduction in these populations. However,
 strong collinearity between density, parasitism, and sexual reproduction
 means that further work will be required to disentangle the causal
 mechanisms underlying these relationships.
description: Methods are described in Gowler et al. <em>Ecology and
 Evolution</em>. Briefly, the data were collected by sampling lake
 populations in SE Michigan and then quantifying host density, reproductive
 status, and infection status. The processing included calculating area
 under the curve for density, sexual reproduction, and infection.
 Additional processing is done in the scripts associated with the
 dataset.
description: People with questions about the dataset can contact Meghan Duffy
 (duffymeg@umich.edu).
DOI: 10.5061/dryad.ns1rn8pt2
title: Alpine ibex simulation files

description: Identifying local adaptation in bottlenecked species is essential for
 conservation management. Selection detection methods have an important
 role in species management plans, assessments of adaptive capacity, and
 looking for responses to climate change. Yet, the allele frequency changes
 exploited in selection detection methods are similar to those caused by
 the strong neutral genetic drift expected during a bottleneck.
 Consequently, it is often unclear what accuracy selection detection
 methods have across bottlenecked populations. In this study, simulations
 were used to explore if signals of selection could be confidently
 distinguished from genetic drift across 23 bottlenecked and reintroduced
 populations of Alpine ibex (Capra ibex). The meticulously recorded
 demographic history of the Alpine ibex was used to generate comprehensive
 simulated SNP data. The simulated SNPs were then used to benchmark the
 confidence we could place in outliers identified in empirical Alpine ibex
 RADseq derived SNP data. Within the simulated dataset, the false positive
 rates were high for all selection detection methods (Fst outlier scans and
 Genetic-Environment Association analyses) but fell substantially when two
 or more methods were combined. True positive rates were consistently low
 and became negligible with increased stringency. Despite finding many
 outlier loci in the empirical Alpine ibex SNPs, none could be
 distinguished from genetic drift-driven false positives. Unfortunately,
 the low true positive rate also prevents the exclusion of recent local
 adaptation within the Alpine ibex. The baselines and stringent approach
 outlined here should be applied to other bottlenecked species to ensure
 the risk of false positive, or negative, signals of selection are
 accounted for in conservation management plans.
DOI: 10.5061/dryad.gtht76hmj
title: Female mate preferences do not predict male sexual signals across populations

description: New species can arise when female preferences and male sexual signals
 diverge across populations and thereby reduce mating between populations.
 Under this hypothesized mechanism for speciation, mate preferences and
 male signals should be correlated, but divergent, across populations. We
 evaluated this prediction using spadefoot toads (Spea multiplicata). We
 measured a sexually-selected male signal (call rate) for which female
 preferences are known to vary across populations in response to
 hybridization risk. Contrary to expectation, we found no correlation
 between male call rate and female preferences across populations. We
 discuss possible mechanisms of this pattern, including the effect of gene
 flow from heterospecifics on male call rate. Our results suggest that,
 even when populations vary in mating traits, the independent evolution of
 female preferences and male sexual signals might impede reproductive
 isolation between populations.
DOI: 10.5061/dryad.9cnp5hqj1
title: Topographic Relief Response to Fluvial Incision in the Central Tibetan Plateau: Evidence From Cosmogenic 10Be

description: Fluvial incision, regarded as one of the fundamental geomorphic processes,
 drives the evolution of mountainous landscapes. The transitional landscape
 from low-relief to high-relief in the central Tibetan Plateau is rapidly
 evolving as it is influenced by river dynamics, climate change and
 tectonic uplift. Combining cosmogenic 10Be depth profile dating
 and topographic analysis, this study provides new constraints on the
 formation and destruction of low-relief surfaces in the central Tibetan
 Plateau. We find that the high-relief landscape in the Suoqu area (a major
 tributary of the upper Nu River) shows a rapid fluvial incision rate of
 710 ± 70 mm kyr−1 since the
 late Pleistocene, while the low-relief topography in the adjacent Xiaqiuqu
 area presents an order of magnitude lower incision rate of
 70 ± 10 mm kyr−1. These results are
 consistent with the long-term (multi-million-year) exhumation rates
 derived from low-temperature thermochronology, suggesting that this region
 has experienced an evolving incision history. We interpret that the higher
 relief was caused by enhanced fluvial incision, and the lower relief was
 slowly developed by sedimentation and relatively steady low exhumation
 rate. The presence of a knickzone appears to mark the boundary between
 these differentially incising landscapes, which may be caused by rapid
 headward retreat and higher river discharge in the Suoqu River. The
 coincidence of fluvial terraces ages with climate-driven events, in
 addition to paleodenudation rates, indicates that the formation of fluvial
 terraces in the Xiaqiuqu and Suoqu areas might be associated with the
 quick sedimentation of weathered materials in early warming periods.
DOI: 10.5061/dryad.8w9ghx3ms
title: CCT Transit Survey Questions and Results - Data Set

description: The Colville Confederated Tribes (CCT) is a large reservation (1.4 million
 acres) the size of Connecticut with slightly under 10,000 enrolled tribal
 members in 2021. Six small towns, rural HUD subdivisions and isolated
 homes create severe problems for access to transportation, especially for
 elderly, youth, economically distressed, and physically challenged
 populations. The design and operation of tribal transit on reservations
 represents a new phase in tribal transportation since 2008. In the rush to
 create transit systems, tribal transit planning has not always fully
 involved tribal members and citizens in system design, nor have there
 always been surveys to identify transportation issues and demand, and to
 assess the potential user views toward different types of transit. This
 project represents efforts to develop and carry out citizen awareness and
 involvement in the needs, issues and opportunities of transit for the CCT,
 and developed and carried out a comprehensive survey to create data that
 will support the final design and implementation of tribal transit for the
 Colville Confederated Tribes.