cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7291/d13x2m
title: Reconstructing historical and contemporary disease dynamics: A case study using the California slender salamander

description: The fungal disease chytridiomycosis, caused by the
 pathogen Batrachochytrium dendrobatidis (Bd), has been
 implicated in the extirpation and extinction of amphibian species
 throughout the world. Recent Bd epizootics (i.e.
 epidemics in wildlife) have driven hundreds of species to near-extinction.
 Several species in California have been severely affected by Bd
 epizootics, but most work has focused on aquatic species. Our
 study focused on the most abundant and widespread terrestrial amphibian
 species in California, the California slender
 salamander, Batrachoseps attenuatus. This species is known to be
 infected by Bd, but little is known of its disease dynamics. We examined
 the effect of disease history on contemporary disease dynamics by
 combining retrospective tests for Bd emergence in museum specimens with
 contemporary field-collected infection data from the same locations. We
 found that Bd rapidly emerged in B. attenuatus and
 exhibited a non-linear pattern of spread throughout Northern California,
 and that modern-day persistence was negatively correlated with time since
 first detection of infection. To understand what factors are associated
 with Bd emergence, we correlated standard environmental variables (e.g.
 temperature, precipitation) from Bd-positive sites with Bd prevalence. We
 also compared and contrasted the degree of sociality between B.
 attenuatus populations that were recently Bd-infected with those
 that had a longer history of infection. We found that Bd infection
 in B. attenuatus was positively associated with distance
 to nearest lentic aquatic habitat, suggesting that aquatic
 carriers of Bd may be important in prevalence of pathogen within
 terrestrial B. attenuatus populations. Among our 14
 field sites, we also found that recently infected populations had larger
 group sizes, after standardizing for population density, than populations
 that had been infected over multiple decades. This result suggests that
 sociality may facilitate disease spread in terrestrial hosts and that
 populations with longer exposure to this pathogen may evolve away from the
 ancestral condition of sociality.
description: Chytridiomycosis (<em>Batrchochytrium
 dendrobatidis</em>) detected via qPCR in California slender
 salamander museum specimens (<em>Batrachoseps
 attenuatus</em>) by swabbing 30 times with a MW113 dry swab (Medical
 Wire and Equipment Company) – ten times dorsally and ventrally, and five
 times on each laterum, spanning the majority of individual’s body
 length.  Data includes specimen ID number, museum
 institution code, year collected, county of collection (all specimens from
 California), collection locality (Latitude and Longitude), and Zswab
 value. The Zswab reflects the qPCR results - the qPCR genomic equivalent
 results multiplied by 80, the dilution factor in qPCR sample
 preparation. DNA extractions from positive Bd samples were re-run in
 triplicate and the Zswab scores were then averaged across the three
 runs.
DOI: 10.5061/dryad.63xsj3v2d
title: Data from: Spectroscopic approach to correction and visualisation of bright-field light transmission microscopy biological data

description: The most realistic information about the transparent sample such as a live
 cell can be obtained only using bright-field light microscopy. At
 high-intensity pulsing LED illumination, we captured a primary
 12-bit-per-channel (bpc) response from an observed sample using a
 bright-field wide-field microscope equipped with a high-resolution
 (4872x3248) image sensor. In order to suppress data distortions
 originating from the light interactions with undesirable elements in the
 optical path, poor sensor reproduction (geometrical defects of the camera
 sensor and some peculiarities of sensor sensitivity), this uncompressed
 12-bpc data underwent a kind of correction after simultaneous calibration
 of all the parts of the experimental arrangement. Moreover, the final
 intensities of the corrected images are proportional to the photon fluxes
 detected by a camera sensor. It can be visualized in 8-bpc intensity depth
 after the Least Information Loss compression [Lect. Notes Bioinform. 9656,
 527 (2016)].
description: The raw images in "SupplFigs.pdf" were obtained using a
 nanoscope (bright-field wide-field video-enhancenced photon microscope
 developed for Institute of Complex Systems in Nové Hrady). These raw
 images were calibrated by the relevant calibration files (in the
 "calib_sets" folder) obtained by the nanoscope and an optical
 fiber spectrophotometer using a VerCa software (available upon request).
 The "scripts" folder contains Matlab scripts for further image
 processing, image analysis and drawing graphs. In the
 "calib_sets" folder, you can find a README.txt with the
 description of the subfolders' contents. In the "scripts"
 folder, the Matlab scripts are divided into subfolders according to the
 figures' labels in the paper.
DOI: 10.5061/dryad.gxd2547m6
title: Hemodynamic responses link individual differences in informational masking to the vicinity of superior temporal gyrus

description: Suppressing unwanted background sound is crucial for aural communication.
 A particularly disruptive type of background sound, informational masking
 (IM), often interferes in social settings. However, IM mechanisms are
 incompletely understood. At present, IM is identified operationally: when
 a target should be audible, based on suprathreshold target/masker energy
 ratios, yet cannot be heard because target-like background sound
 interferes. We here confirm that speech identification thresholds differ
 dramatically between low- vs. high-IM background sound. However, speech
 detection thresholds are comparable across the two conditions. Moreover,
 functional near infrared spectroscopy recordings show that task-evoked
 blood oxygenation changes near the superior temporal gyrus (STG) covary
 with behavioral speech detection performance for high-IM but not low-IM
 background sound, suggesting that the STG is part of an IM-dependent
 network. Moreover, listeners who are more vulnerable to IM show increased
 hemodynamic recruitment near STG, an effect that cannot be explained based
 on differences in task difficulty across low- vs. high-IM. In contrast,
 task-evoked responses near another auditory region of cortex, the caudal
 inferior frontal sulcus (cIFS), do not predict behavioral sensitivity,
 suggesting that the cIFS belongs to an IM-independent network. Results are
 consistent with the idea that cortical gating shapes individual
 vulnerability to IM.
description: Normally hearing participants were tasked to detect the presence
 of keyword. Participants held their eyes closed and responded via button
 presses. While participants were engaged in the task, hemodynamic
 responses near the caudal inferior frontal sulcus and superior temporal
 gyrus were recorded on both sides of the head.
   For details please see
 manuscript. 
description: All data is complete and usage descriptions are provided.
DOI: 10.5061/dryad.crjdfn343
title: Lecture of physiological activity with EEG techniques in two groups of students using a BCI device

description: Currently, there is a great interest in knowing more in detail what
 happens in a student's mind in the classroom. This dataset seeks to
 help those researchers who want to perform data analytics of student
 behavior in a classroom. This dataset has the peculiarity that it has been
 built inside a classroom in an authentic learning situation wherein a
 face-to-face model a teacher teaches his class in front of a traditional
 group. The data set achieved seeks to provide support for the analysis of
 learning activities to identify the good and bad practices and the
 availability of students to appropriate new thoughts. In addition, these
 results also serve as support to generate new research through other
 learning scenarios, whether traditional or distance learning, where the
 results of the physiological activity of the brain can be used to compare
 the didactics that produce the best results in the students and the areas
 of opportunity in the teaching processes.
description: The dataset was constructed using the neuroexperimenter tool,
 which consists of software that runs on the Windows operating system. This
 software takes information from brain activity through a BCI device from
 an EEG sensor, which was the NeuroSky MindWave. Thus, the
 neuroexperimenter software already includes the necessary libraries to
 build the data sets shown in the tables. For this data
 set, an individual reading was made student by student within a classroom
 and then using the Excel tool, all the data were integrated into a single
 CSV file were through the category Student, and the group can be
 identified each of the students who provided the reading of their brain
 activity. Each student was given a reading for five
 minutes, where for each case, the amount of data obtained was different
 due to the noise present in the wireless communications between the neuro
 Sky and the computer that received the data and organized them employing
 the neuroexperimenter software.
description: The data organized in two files presented here are already free
 of reading errors with the natural values provided by the NeuroSky BCI
 device. The vectors student, ID, gender and group refer to the readings of
 each student.
DOI: 10.5061/dryad.3ffbg79hz
title: Disentangling biotic and abiotic drivers of intraspecific trait variation in woody plant seedlings at forest edges

description: In fragmented forests, edge effects can drive intraspecific variation in
 seedling performance that influences forest regeneration and plant
 composition. However, few studies have attempted to disentangle the
 relative biotic and abiotic drivers of intraspecific variation in seedling
 performance. In this study, we carried out a seedling transplant
 experiment with a factorial experimental design on three land-bridge
 islands in the Thousand Island Lake, China, using four common native woody
 plant species. At different distances from the forest edge (2, 8, 32, 128
 m), we transplanted four seedlings of each species into each of three
 cages: full-cage, for herbivore-exclusion; half-cage, that allowed
 herbivore access but controlled for caging artefacts; and no-cage control.
 In the 576 cages, we recorded branch architecture, leaf traits and
 seedling survival for each seedling before and after the experimental
 treatment. Overall, after one full growing season, edge-induced abiotic
 drivers and varied herbivory pressure led to intraspecific variation in
 seedling performance, including trade-offs in seedling architecture and
 resource-use strategies. However, responses varied across species with
 different life-history strategies and depended on the driver in question,
 such that the abiotic and biotic effects were additive across species,
 rather than interactive. Edge-induced abiotic variation modified seedling
 architecture of a shade-tolerant species, leading to more vertical rather
 than lateral growth at edges. Meanwhile, increased herbivory pressure
 resulted in a shift toward lower dry matter investment in leaves of a
 light-demanding species. Our results suggest that edge effects can drive
 rapid directional shifts in the performance and intraspecific traits of
 some woody plants from early ontogenetic stages, but most species in this
 study showed negligible phenotypic responses to edge effects. Moreover,
 species-specific responses suggest the importance of interspecific
 differences modulating the degree of trait plasticity, implying the need
 to incorporate individual-level responses when understanding the impact of
 forest fragmentation on plant communities.
DOI: 10.5061/dryad.rbnzs7hbk
title: Fecal calprotectin as a predictor of gastrointestinal immune-related adverse events (CF-19): A prospective study - Excel data and supplementary tables

description: Background: Colitis is a
 frequent immune-related toxicity, without any
 biomarker that may predict its onset.
 It
 is endoscopically similar to intestinal inflammatory diseases, where fecal calprotectin (FC) is used as a biomarker to early-detect a relapse. We found contradictory evidence about FC and immunotherapy and no prospective study was already published.  Methods: We present an analytical, observational and prospective study of one year’s duration. We analyzed FCbasal, and then prior to each cycle until the sixth, ending with quarterly follow-up. For evaluating the predictive value of FC we estimated the area under the ROC curve for basal absolute values and for each cycle, and calculated its relative percentage change with respect to basal. We also planned to estimate sensitivity, specificity and predictive values indexes for different cut-off points. Because of lack of recruitment we did a preliminary analysis at the end of the initially estimated period before suggesting its prolongation.  Results: 24 patients were included (19 male), diagnosed from lung cancer (n=15), head and neck, renal, bladder and colorectal cancer (n=2, each), melanoma (n=1). They were treated with Anti PD-1/PDL-1 mono therapy (n=18), combo with chemo (n=2), or combo with anti-CTLA4 (n=2). Three patients had G1 colitis and two, &gt;=G2, all treated with anti-PD1 and before 6th cycle, as described on literature. ROC curve presents AUC 0,559 (CI95%:0,32-0,798) and RR for colitis taking FC value is 1,001 for each 10 units (p=0,493). Conclusion: Even though we must take into account the limitations of the study we cannot conclude that FC could be used as a predictor for detecting immune-mediated colitis.
DOI: 10.5061/dryad.02v6wwq37
title: Representation of women in stroke clinical trials: a review of 281 trials involving over 500,000 participants

description: Objective: Women have been under-represented in clinical trials areas of
 cardiovascular disease but there is less certainty over the level of
 disparity specifically in stroke. We examined the participation of women
 in trials according to stroke prevalence in the population. Methods:
 Published randomized controlled trials with ≥100 participants enrolled
 between 1990 and 2020 were identified from ClinicalTrials.gov. To quantify
 sex disparites in enrolment we calculated the participation to prevalence
 ratio (PPR), defined as the percentage of women participating in a trial
 against the prevalence of women in the disease population. Results: There
 were 281 stroke trials eligible for analyses with a total of 588,887
 participants, of whom 37.4 % were women. Overall, women were represented
 at a lower proportion relative to their prevalence in the underlying
 population (mean PPR 0.84; 95% confidence interval [CI] (0.81 to 0.87)).
 The greatest differences were observed in trials of intracerebral
 hemorrhage (PPR 0.73; 95% CI 0.71 to 0.74), trials with a mean
 age of participants &lt;70 years (PPR 0.81; 95% CI (0.78 to 0.84)),
 non-acute interventions (PPR 0.80; 95% CI (0.76 to 0.84)) and
 rehabilitation trials (PPR 0.77; 95% CI 0.71 to 0.83)). These findings did
 not significantly change over the period from 1990 to 2020 (p for trend =
 0.201). Conclusion: Women are disproportionately represented in stroke
 trials relative to the burden of disease in the population. Clear guidance
 and effective implementation strategies are required to improve the
 inclusion of women and thus broader knowledge of the impact of
 interventions in clinical trials.
DOI: 10.5061/dryad.7m0cfxptr
title: Biomassess of functional groups and ecosystem parameters predicted by ecosim models of Lake Dianchi

description: Understanding the relative importance of multiple stressors is valuable to
 prioritize conservation and restoration measures. Yet, the effects of
 multiple stressors on ecosystem functioning remain largely unknown in many
 freshwaters. Here, we provided a methodology combining ecosystem modelling
 with linear regression to disentangle the effects of multiple stressors on
 matter flow, an important ecosystem function. Treating a shallow lake as
 the model ecosystem, we simulated matter flow dynamics during 1950s-2010s
 with different combinations of stressors by Ecopath with Ecosim (EwE)
 modelling, and determined the relative importance of each stressor by
 generalized linear mixed models. We found that matter flow of the lake
 food web was highly dynamic, attributing to effects of multiple
 anthropogenic stressors. Biological invasion played the strongest role in
 driving the matter flow dynamics, followed by eutrophication, while
 biomanipulation (i.e. phytoplankton control by planktivorous fish
 stocking) was of little importance. Eutrophication had a stronger role on
 primary producers, pelagic food chain and top predators, while biological
 invasion on consumers in the middle of food chains. The former was more
 important in driving the quantity of matter flow, while the latter on
 trophic transfer efficiencies. Scenario forecasting showed that reducing
 nutrients contents could largely shape the matter flow pattern, while
 biomanipulation had little effect. Our findings provided new insights into
 understanding the mechanistic links between anthropogenic stressors and
 ecosystem functioning by combining ecosystem modelling with linear
 regression.
DOI: 10.5061/dryad.x3ffbg7k4
title: Raw sequence of: A comparative analysis of spider prey spectra analyzed through the next-generation sequencing of individual and mixed DNA samples

description: As one of the most abundant predators of insects in terrestrial
 ecosystems, spiders have long received much attention from agricultural
 scientists and ecologists. Do spiders have a certain controlling effect on
 the main insect pests of concern in farmland ecosystems? Answering this
 question requires us to fully understand the prey spectrum and prey
 preferences of spiders in the farmland ecosystem of concern.
 Next-generation sequencing (NGS) has been successfully employed to analyze
 spider prey spectra by sequencing prey DNA barcode regions and matching
 the sequence results to DNA barcodes from public databases. However,
 considering the high cost of this technology, we performed a comparative
 analysis of the prey spectra of Ovia alboannulata (Araneae, Lycosidae) (a
 dominant spider species on Chinese tea plantations) using NGS with
 individual and mixed DNA samples to demonstrate which treatment was better
 for determining the spider’s prey spectrum in the field. We collected
 spider individuals from tea plantations. Two treatments were then used to
 analyze the spider’s prey spectrum: (1) the DNA was extracted from the
 spiders individually and then sequenced separately and (2) the DNA was
 extracted from the spiders individually and then mixed and sequenced.
DOI: 10.5061/dryad.h9w0vt4hz
title: Exploring substance use and risk factors among youth of Jimma town

description: Substance use refers that using psychoactive substances such as khat,
 alcohol, cigarette, and illicit drugs. Youth are more vulnerable to
 substance use than older people. Substance use has a different impact on
 the health as well as socio-economics of one country. Globally substance
 use was the major public health concern. Currently, substance use is a
 common public health concern among the youth of Ethiopia mainly in Jimma
 town. Therefore, this study aimed to explore the substance use and risk
 factors among the youth of Jimma town, 2019.
DOI: 10.5061/dryad.g1jwstqr7
title: Corydalis austroshaanxiensis sp. nov. (Papaveraceae), a neglected species from Shaanxi, China, and a revised circumscription for C. pseudoincisa C.Y. Wu, Z.Y. Su & Lidén

description: Corydalis austroshaanxiensis, a new species of Corydalis sect. Incisae
 Fedde (Papaveraceae) from Shaanxi, China, is described. It is most similar
 to C. pseudoincisa C.Y. Wu, Z.Y. Su & Lidén, but differs in the
 outer petals retuse to emarginate, with dorsal crest (vs acuminate,
 rounded to shortly mucronate, without crest), lowermost pedicels that are
 conspicuously elongating and basally recurved in fruit (vs slightly
 elongating, straight, erect-spreading), sepals that are 3–4 × ca. 3 mm (vs
 1.5–2 × ca. 1.5 mm), lower petals that usually have a linear reddish tint
 at base (vs without reddish tint), capsules that are narrowly to broadly
 elliptic to obovoid (vs linear to narrowly oblong), and by the racemes
 corymbose, forming a very dense cluster of upper fruits (vs racemes not
 corymbose-like, flower dense in anthesis, lax in fruit). The original
 materials, which were referred to C. pseudoincisa were mosaic, and the
 original descriptions and illustrations annotated as C. pseudoincisa only
 fit in part C. pseudoincisa. A revised circumscription for C. pseudoincisa
 was given in this study. We suggest the need for caution when identifying
 additional specimens as paratypes that differ from holotype in distinct
 characters.
description: After extensive field collections and the study of herbarium
 specimens<i>,</i> we confirm that these unusual plants
 represent a hitherto undescribed species.
DOI: 10.5061/dryad.4mw6m909h
title: Data for contaminant risk mapping

description: Nitrate contamination of groundwater often occurs in urban and industrial
 areas due to point and non-point sources of anthropological activities.
 Groundwater constitutes a significant portion of the water supply system
 for Bahir Dar City in Ethiopia, though the level of groundwater pollution
 is not known. This study was conducted to assess the extent of the aquifer
 and groundwater pollution (nitrate) based on contaminant vulnerability
 risk mapping using the GIS integrated modified DRASTIC model. A field
 survey was conducted to collect samples from boreholes for nitrate
 analysis and to modify the DRASTIC model. Compared to the original
 intrinsic vulnerability assessment, land use as external factors changed
 from moderate-high to high vulnerability class from 18 % to 88 %. The
 FR-APH modified model showed a good correlation (0.53) compared to the
 other methods. Based on the FR-APH modified model, about 31% of the area
 was under moderate to high and high vulnerability range, 39% was under
 moderate vulnerability range while 30% was under low and moderate to low
 vulnerability range. The integrated vulnerability map showed high risk in
 the central part of the City due to the flat slope and shallow depth to
 groundwater. Besides, the sensitivity analysis indicated that the
 contribution of aquifer media and vadose zone to contaminant risk was
 found trivial. In general, groundwater at Bahir Dar city was found
 vulnerable to nitrate contamination and needs proper management.