cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w3r2280rf
title: Hardware perceptron and ReLU measurements and results

description: Recently, in-memory analog computing through memristive crossbar arrays
 attracted a lot of attention due to its efficient power consumption,
 area, and computing throughput. Using this computing method,
 different types of neural networks can be implemented for different
 applications. In such neural networks, memristors represent the synapses.
 However, in previous work, digital processors have been used to
 implement the activation functions or neurons. Implementing neurons using
 analog-based hardware further improves the power consumption, area, and
 throughput by removing unnecessary data conversions and
 communication.   In this study, we designed a ReLU
 activation function and built a fully hardware-based two-layer fully
 connected perceptron using memristive arrays, and verified the
 operation by classifying downsampled MNIST images. We measured
 the DC and AC characteristics of our designed ReLU, forming, set, and
 reset behavior of the memristive arrays, and the
 perceptron behavior during training and inference in the
 classification task. We also studied the non-idealities related to both
 the ReLU design and memristors which is significantly critical in future
 integrated designs. Moreover, the downsampled 8*8 MNIST images that we
 generated from the original MNIST dataset are included in the
 data which can be used in future studies with the limited size of the
 network.
DOI: 10.5281/zenodo.18397822
title: SARS-CoV-2 Infektionen in Deutschland

description: Im Datensatz "SARS-CoV-2 Infektionen in Deutschland" des Robert Koch-Instituts werden die Daten basierend auf Meldungen zu SARS-CoV-2 Infektionen nach dem Infektionsschutzgesetz (IfSG) bereitgestellt. Darin enthalten sind Informationen auf Landkreisebene zu bestätigten Infektionen, Todesfällen und Genesungen, differenziert nach Altersgruppen und Geschlecht. Diese Daten dienen als Grundlage für epidemiologische Bewertungen und gesundheitspolitische Maßnahmen.
DOI: 10.5061/dryad.qfttdz0hn
title: Host preference of a tree-killing bark beetle across a geographic boundary separating host species

description: The life cycles of bark beetles are intimately linked to their host
 species. Therefore, bark beetle species are expected to show traits that
 vary among different host species and across geographic ranges. The
 taxonomic proximity of host tree species can also influence host
 selection. Abies species native to Japan are genetically classified into
 three phylogenetic groups. Their natural distributions are separated by a
 distinct biogeographic boundary in Japan (i.e. the Tsugaru Strait, also
 referred to as Blakiston's Line). Especially, A. sachalinensis is the
 only species native to Hokkaido, north of the Tsugaru Strait. I,
 therefore, investigated the host preference of Polygraphus proximus
 Blandford within four allopatrically distributed Abies species across the
 north and south of the Tsugaru Strait through field surveys and field
 choice experiments. Field observations and field host-choice bioassays
 showed that A. sachalinensis was less severely attacked by P. proximus
 than was A. veitchii on both sides of the Tsugaru Strait. The beetles also
 preferred to attack A. firma (which belongs to a genetically distinct
 group (i.e., the section Momi) from that of A. veitchii and A.
 sachalinensis (i.e., the section Balsamea)), over A. sachalinensis in both
 Hokkaido and Honshu. Although A.homolepis also belongs to the section
 Momi, A. firma and A. veitchii had more attacks than A. homolepis. The
 results provide evidence that P. proximus does not show specialization
 across the different parts of their geographic range where the host
 species are different, and there is no positive correlation between
 taxonomic proximity and host preference for P. proximus.
DOI: 10.5061/dryad.xgxd254h5
title: Rapid northwestward extension of the East Asian summer monsoon over the last deglaciation: evidence from mollusk record

description: The magnitude and rate of spatial expansion of the East Asian summer
 monsoon (EASM) rain belt as the climate warms remains unclear. Existing
 assessments still lack the ecological records that are more sensitive to
 the EASM rainfall to quantify the spatial extension during the past
 warming scenarios. Here, the spatiotemporal extension of EASM intensity
 since the last glacial maximum (LGM) is reconstructed using six well-dated
 mollusk fossil sequences from Chinese loess sections located at the
 northern part of the EASM. The abundant occurrence of typical dominant
 mollusk species indicative of EASM intensity gradually delayed from
 southeast to northwest since the last deglacial warming. The estimated
 expansion rate of EASM intensity accelerated markedly during the ~12-9 ka
 (~50 km/ka), which corresponded with the early-Holocene rapid warming
 period, shifting northwestward ~150 km compared to present. This imply
 that northern fringe of EASM in northern China will become wetter as the
 climate warms.
description: The dataset was collected at the Key Laboratory of Cenozoic
 Geology and Environment, Institute of Geology and Geophysics, Chinese
 Academy of Sciences, Beijing 100029, China. The mollusk fossils were
 picked and identified under a binocular microscope, and counted their
 abundance to produce a MS.
description: DATA-SPECIFIC INFORMATION FOR: [mollusk records]
 1. Number of variables: 22 2. Number of
 cases/rows: 141 3. Specialized formats or other
 abbreviations used:  The variable uses the abbreviation
 YX, WN, JX, JC, SZ, LX, HX called Yaoxian, Weinan, Jixian, Jingchuan,
 Shuozhou, Linxia, Huanxian sites, respectively. PER: Percentage.
DOI: 10.5061/dryad.r2280gbdh
title: Transmission electron micrographs of AMPAR containing vesicles

description: Here we present transmission electron micrographs of AMPAR containing
 vesicles. AMPAR containing vesicles were purified from whole mouse brain
 via immunoisolation, applied to a copper electron microscopy
 grid, and stained with uranyl acetate. Vesicles were imaged at a range of
 magnifications from 4,000 to 15,000. Included in these data are
 immunoelectron micrographs where we probed for synaptobrevin-2,
 synaptophysin-1, GluA2, and GluA3.
DOI: 10.5061/dryad.v6wwpzgwm
title: Dynamics of glucose metabolism after liver transplantation: Prediabetes as a window of opportunity for patient survival and long‐term kidney function

description: Posttransplantation diabetes mellitus (PTDM) is a relevant complication
 following liver transplantation with profound impact on morbidity and
 mortality. To date, little is known about the evolution and dynamics of
 glucose metabolism and the impact of prediabetes in long-term follow-up.
 To address this issue, all consecutive adult liver transplant recipients
 (n=429) from a European university hospital transplant center between 2007
 and 2017 were analyzed retrospectively. In patients without pre-existing
 diabetes (n=327), we conducted a longitudinal characterization of glucose
 metabolism. Median follow-up was 37 [9-64, IQR] months. Median prevalence
 of prediabetes was 39 [37-39]% and of PTDM 21 [17-22]%. Throughout
 follow-up, intra-individual glucose regulation of patients was highly
 variable, continuously fluctuating between different states of glucose
 metabolism (normal glucose tolerance, prediabetes, PTDM). Whereas overall
 survival and long-term kidney function of patients with PTDM were
 significantly lower than that of patients with normal glucose metabolism,
 prediabetes was not associated with adverse outcome. This study provides
 new insight into the dynamics and impact of glucose metabolism after liver
 transplantation. Unlike PTDM, prediabetes is not associated with adverse
 outcome, providing a window of opportunity for targeted intervention. The
 results underline the need for constant screening and intervention in
 post-transplant care of liver allograft recipients.
DOI: 10.5061/dryad.nzs7h44s4
title: Fly and mouse tracking models and kinematics related to Anipose toolkit paper

description: This is a series of datasets related to the Anipose paper. We provide
 these to allow others to reproduce our tracking results and build upon
 them. Anipose is an open-source toolkit for robust markerless 3D pose
 estimation. Anipose is built on the 2D tracking method DeepLabCut, so
 users can expand their existing experimental setups to obtain accurate 3D
 tracking. It consists of four components: (1) a 3D calibration module, (2)
 filters to resolve 2D tracking errors, (3) a triangulation module that
 integrates temporal and spatial regularization, and (4) a pipeline to
 structure processing of large numbers of videos. Applying 3D tracking to
 estimate joint angles of walking Drosophila, we found that flies move
 their middle legs primarily by rotating their coxa and femur, whereas the
 front and rear legs are driven primarily by femur-tibia flexion. We then
 show how Anipose can be used to quantify differences between successful
 and unsuccessful trajectories in a mouse reaching task. We share these fly
 and mouse datasets and tracking models in this dataset to allow others to
 reproduce our findings and reuse the training data and models in their
 research.
description: Please refer to the Anipose
 paper for detailed information on the methods used to collect
 the videos and to track the 3D joint positions.
description: We share the detailed fly 3D kinematics analyzed in the paper,
 consisting of all 3D joint positions and 3D joint angles. See the
 following files: flyangles-dataset.zip -
 Dataset of 3D kinematics from 39 wild-type Berlin flies
 README - Detailed documentation of this dataset (also included
 in the zip) Furthermore, we share the
 trained DeepLabCut models and original videos with tracking from Anipose.
 Please refer to the DeepLabCut and Anipose documentation for
 the structure of these files. The files are the following:
 deeplabcut-fly-model.zip - DeepLabCut  model and
 training data for fly on a ball dataset
 deeplabcut-mouse-model.zip - DeepLabCut model and training data
 for mouse dataset fly-anipose.zip - Anipose files for
 fly dataset mouse-anipose.zip - Anipose files for
 mouse dataset
DOI: 10.5061/dryad.dz08kprz4
title: Data from: Temporal turnover of the soil microbiome composition is guild-specific

description: Although spatial and temporal variation are both important components
 structuring microbial communities, the exact quantification of temporal
 turnover rates of fungi and bacteria has not been performed to date. In
 this study, we utilized repeated resampling of bacterial and fungal
 communities at specific locations across multiple years to describe their
 patterns and rates of temporal turnover. Our results show that microbial
 communities undergo temporal change at a rate of 0.010-0.025 per year (in
 units of Sorensen similarity), and the change in soil is slightly faster
 in fungi than in bacteria, with bacterial communities changing more
 rapidly in litter than soil. Importantly, temporal development differs
 across fungal guilds and bacterial phyla with different ecologies. While
 some microbial guilds show consistent responses across regional locations,
 others show site-specific development with weak general patterns. These
 results indicate that guild-level resolution is important for
 understanding microbial community assembly, dynamics and responses to
 environmental factors.
DOI: 10.5061/dryad.rxwdbrv8x
title: Environmental data from: Potential distributions of invasive vertebrates in the Iberian Peninsula under projected changes in climate extreme events

description: This dataset includes climatic variables representing extreme events
 indices defined by the World Meteorological Organization
 (https://public.wmo.int/en). The variables were calculated based on five
 Regional Climate Models or RCMs (UAHE-REM, UCAN-WRA, UCAN-WRB, UCLM-PRO
 and UMUR-MM5) for the periods 1971-2000 (‘current climate’) and 2021-2050
 (‘future climate’) under the SRES A1B Emissions Scenario. We used RCMs
 instead of global climate models (GCMs) because the latter have an overly
 coarse resolution compared to the spatial resolution of our species
 distribution data. Since RCMs downscale climate fields from GCMs, they
 provide information at fine (meso or micro) scales that are more accurate
 for studies of regional phenomena and for application to climate impact
 assessments.  Climatic variables were calculated in collaboration
 with the Numerical Modelling Group for the Environment and Climate (MOMAC,
 https://www.uclm.es/grupos/momac) of the University of Castilla-La Mancha
 (UCLM).
description: Grid cells at Universal Transverse Mercator (UTM) zone
 boundaries, which have non-standard sizes, were left out of the
 calculations and have therefore missing values.
DOI: 10.5061/dryad.2z34tmpn5
title: Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring

description: Balancing selection is one of the mechanisms which has been proposed to
 explain the maintenance of genetic diversity in species across
 generations. For species with large populations and complex life
 histories, however, heterogeneous selection pressures may create a
 scenario in which the net effects of selection are balanced across
 developmental stages. With replicated cultures and a pooled sequencing
 approach, we show that genotype-dependent mortality in larvae of the
 Pacific oyster (Crassostrea gigas) is largely temporally dynamic and
 inconsistently in favor of a single genotype or allelic variant at each
 locus. Overall, the patterns of genetic change we observe to be taking
 place are more complex than what would be expected under classical
 examples of additive or dominant genetic interactions. They are also not
 easily explained by our current understanding of the effects of genetic
 load. Collectively, temporally heterogeneous selection pressures across
 different larval developmental stages may act to maintain genetic
 diversity in oysters, while also inherently sheltering genetic load within
 populations.
description: Pooled samples of oyster larvae  (n=200-3000) were collected at
 various points during development (days 0,2,6,10,14,22).  DNA was
 extracted in bulk, converted to 2bRAD libraries (BCGI enzyme) and
 sequenced on an Illumina Hiseq (SE 50bp reads). 
description: Please see manuscript for bioinformatic approaches and associated
 github page:  GitHub -
 E-Durland/oyster-poolseq: Methods for library preparation and
 bioinformatic analysis of pooled DNA data from larval oyster
 samples Please see README file for
 description of the files.
DOI: 10.5061/dryad.zgmsbccc5
title: Supplementary material and data from: Cranial volume and palate length of cats, Felis spp., under domestication, hybridisation and in wild populations

description: Reduced brain size, compared with wild individuals, is argued to be a key
 characteristic among domestic mammal species, and is often thought to be a
 component of the “domestication syndrome”. However, brain size comparisons
 are often based on old, inaccessible literature and in some cases drew
 comparisons between domestic animals and wild species that are no longer
 thought to represent the true progenitor species of the domesticated
 variant in question. Here we set out to replicate results concerning
 cranial volumes in domestic cats that were published in the 1960s and
 1970s and compared wildcats, domestic cats and their hybrids. In light of
 new research and ideas surrounding domestication and its effects on
 domestic animals a replication of these studies is highly relevant. Apart
 from replicating these studies we also present new data on palate length
 in Felis cat skulls. Here we provide all data (both new and old digitzed
 data) upon which we based the analysis discussed in
 this manuscript.  We further provide a link to the code
 used in the analysis.
DOI: 10.5061/dryad.tdz08kq0r
title: Supplementary material from "Evolutionary dynamics of sustainability ideas in China: inferences from ecological and economic concepts usage in People’s Daily"

description: Previous cultural evolutionary analyses have exploited the use of neutral
 models, or random copying models, analogous to neutral genetic drift, as
 null models to distinguish the unbiased copying and biased transmission of
 neutral cultural traits, but the dynamics and underlying mechanism of
 non-neutral cultural traits have not yet been explored. Adopting an
 ecological perspective, we define ecological and economic concepts as
 non-neutral cultural traits constitute a complex ecosystem of meaning
 representing sustainability ideas. We analyse the frequency distribution,
 turnover and innovation rates of nearly 4000 concepts appearing in
 People’s Daily from 1946 to 2015. The results reveal that, ecological
 concepts show stronger tendency towards random copying than economic
 concepts. The popular ecological and economic concepts may experience
 conformist bias and anti-conformist bias respectively. Semantic and
 pragmatic differences of popular concepts affect the variability which
 indicate stronger cultural drift in the ontological domain. The frequency
 change in popular concepts also suggests positive selection due to
 political strategy and governmental policy.
description: The data is retrieved from BCC corpus(BCC语料库
 (blcu.edu.cn)), using a Boolean query of "生态+N",
 "N+生态", "经济+N" and "N+经济" (means
 "Ecological+Noun",
 "Noun+Ecology"，"Economic+Noun" and
 "Noun+Economy" in English). In Chinese, the character has no
 change in writing forms even they serve for different purpose, and in our
 case, as  head noun or modifier. A total list of different combination of
 concepts around "ecology" and "economy" is derived
 from the corpus. The corpus provide diachronic frequency of each concept
 which can be used in the further analysis of frequency distribution and
 turnover rate.
description: The BCC corpus public webpage doesn't include all concepts
 or phrases number of every year. In cultural evolution, a consideration of
 the population size is necessary. For that reason, this research also
 acquired a full list of yearly phrases number directly from the corpus
 building team to support the analysis. Any reuse of the data (file name
 "yearly_phrases_number.csv") should cite this, "Xun E, Rao
 G, Xiao X, Zang J. Construction of BCC corpus in the context of big data.
 Corpus Linguistics. 2016;3(1):93-109."
DOI: 10.5281/zenodo.18397168
title: Optimizing Semi-Synthetic Diet for Sustained Laboratory Rearing of Maruca vitrata and Studying Biological Performance Using Age-Stage, Two-Sex Life Table Analysis

description: This dataset contains raw input data used for age–stage, two-sex life table analysis of Maruca vitrata reared on different semi-synthetic diets under controlled laboratory conditions. The data include age–stage survival rate (Sxj), age-specific survival rate (lx), age–stage life expectancy (Exj), age–stage reproductive value (Vxj), and age-specific cumulative fecundity required for population parameter estimation. These data were used to calculate key life table parameters, including intrinsic rate of increase, net reproductive rate, finite rate of increase, and mean generation time, as reported in the associated Journal of Applied Entomology manuscript. The dataset is provided to support transparency, reproducibility, and reuse of the life table analyses.
DOI: 10.5281/zenodo.18397169
title: Optimizing Semi-Synthetic Diet for Sustained Laboratory Rearing of Maruca vitrata and Studying Biological Performance Using Age-Stage, Two-Sex Life Table Analysis

description: This dataset contains raw input data used for age–stage, two-sex life table analysis of Maruca vitrata reared on different semi-synthetic diets under controlled laboratory conditions. The data include age–stage survival rate (Sxj), age-specific survival rate (lx), age–stage life expectancy (Exj), age–stage reproductive value (Vxj), and age-specific cumulative fecundity required for population parameter estimation. These data were used to calculate key life table parameters, including intrinsic rate of increase, net reproductive rate, finite rate of increase, and mean generation time, as reported in the associated Journal of Applied Entomology manuscript. The dataset is provided to support transparency, reproducibility, and reuse of the life table analyses.
DOI: 10.5061/dryad.3r2280ggw
title: Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability

description: Background: Variability is a hallmark of animal behavior. It contributes
 to survival by endowing individuals and populations with the capacity to
 adapt to ever-changing environmental conditions. Intra-individual
 variability is thought to reflect both endogenous and exogenous
 modulations of the neural dynamics of the central nervous system. However,
 how variability is internally regulated and modulated by external cues
 remains elusive.  Here we address this question by analyzing the
 statistics of spontaneous exploration of freely swimming zebrafish larvae,
 and by probing how these locomotor patterns are impacted when changing the
 water temperatures within an ethologically relevant range. Results: We
 show that, for this simple animal model, five short-term kinematic
 parameters - interbout interval, turn amplitude, travelled distance, turn
 probability and orientational flipping rate - together control the
 long-term exploratory dynamics. We establish that the bath temperature
 consistently impacts the means of these parameters, but leave their
 pairwise covariance unchanged. These results indicate that the temperature
 merely controls the sampling statistics within a well-defined kinematic
 space delineated by this robust statistical structure. At a given
 temperature, individual animals explore the behavioral space over a
 timescale of tens of minutes, suggestive of a slow internal state
 modulation that could be externally biased through the bath temperature.
 By combining these various observations into a minimal stochastic model of
 navigation, we show that this thermal modulation of locomotor kinematics
 results in a thermophobic behavior, complementing direct gradient-sensing
 mechanisms. Conclusions: This study establishes the existence of a
 well-defined locomotor space accessible to zebrafish larvae during
 spontaneous exploration, and quantifies self-generated modulation of
 locomotor patterns. Intra-individual variability reflects a slow
 diffusive-like probing of this space by the animal. The bath temperature
 in turn restricts the sampling statistics to sub-regions, endowing the
 animal with basic thermophobicity. This study suggests that in Zebrafish,
 as well as in other ectothermic animals, ambient temperature could be used
 to efficiently manipulate internal states in a simple and ethological way.
description: Data acquisition and pre-processing is detailed in the paper
 available as preprint here : https://doi.org/10.1101/2021.03.17.435787
description: Contains pre-processed data (i.e. larval zebrafish navigation
 parameters extracted from tracking data) as a MATLAB files. Programs are
 available on Gitlab (https://gitlab.com/GuillaumeLeGoc/thermomasterlab),
 to reproduce the figures of the paper. A README file is available and
 scripts are self-documented, in a certain extent.