cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7857791.v1
title: Mus musculus A/J CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Mus musculus A/J</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857779
title: Flow data for selected stations in the SW Amazon ("MAP" region)

description: The data in this project are associated with the so-called MAP region in the SW Amazon: the states of Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia). The methods and results are discussed in a manuscript that has been accepted for publication by Nature Scientific Data (05/11/2019).<br>Flow data for 8 hydrological stations were downloaded from the Agencia Nacional de Aguas (ANA), through its Hidroweb (http://www.snirh.gov.br/hidroweb/ or http://hidroweb.ana.gov.br/). The original data was downloaded as a .txt file.The R script "FLOW_reorder_gapfill_plot.R" extracts the relevant information and orders the data chronologically.From manual inspections and checking we concluded that the linear relationship between the stations Rio Branco and Xapuri was best (and with enough data available) to gapfill for each other - which is also done in this script.Finally, the relationship and the gapfilled data is plotted (output is 2 plots combined in one figure).The .csv files are the final data sets.<br>Code last manipulated and tested in R version 3.4.3 ("Kite-Eating Tree").
DOI: 10.6084/m9.figshare.7857785
title: Mus musculus AKR/J CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Mus musculus AKR/J</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857788.v1
title: Mus musculus 129S1/SvImJ CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Mus musculus 129S1/SvImJ</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857776
title: Source data file

description: source data files for the 5mC, 5hmC sequencing
DOI: 10.6084/m9.figshare.7857785.v1
title: Mus musculus AKR/J CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Mus musculus AKR/J</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857776.v1
title: Source data file

description: source data files for the 5mC, 5hmC sequencing
DOI: 10.6084/m9.figshare.7857758
title: Social Interaction test videos registered on day 4 in adult Japanese quail

description: Social Interaction test videos of the fourth day of testing. Japanese quail test birds were placed in a novel test environment and after an adaptation period were exposed to a photocastrated (non-aggressive) opponent. All birds were tested only once over a 5 day period. Video file names provide the ID of the animal testes. For description of test see Caliva et al. (2017) http://dx.doi.org/10.3382/ps/pex258
DOI: 10.6084/m9.figshare.7857761
title: Social Interaction test videos registered on day 5 in adult Japanese quail

description: Social Interaction test videos of the fifth day of testing. Japanese quail test birds were placed in a novel test environment and after an adaptation period were exposed to a photocastrated (non-aggressive) opponent. All birds were tested only once over a 5 day period. Video file names provide the ID of the animal testes. For description of test see Caliva et al. (2017) http://dx.doi.org/10.3382/ps/pex258
DOI: 10.6084/m9.figshare.7857758.v1
title: Social Interaction test videos registered on day 4 in adult Japanese quail

description: Social Interaction test videos of the fourth day of testing. Japanese quail test birds were placed in a novel test environment and after an adaptation period were exposed to a photocastrated (non-aggressive) opponent. All birds were tested only once over a 5 day period. Video file names provide the ID of the animal testes. For description of test see Caliva et al. (2017) http://dx.doi.org/10.3382/ps/pex258
DOI: 10.6084/m9.figshare.7857761.v1
title: Social Interaction test videos registered on day 5 in adult Japanese quail

description: Social Interaction test videos of the fifth day of testing. Japanese quail test birds were placed in a novel test environment and after an adaptation period were exposed to a photocastrated (non-aggressive) opponent. All birds were tested only once over a 5 day period. Video file names provide the ID of the animal testes. For description of test see Caliva et al. (2017) http://dx.doi.org/10.3382/ps/pex258
DOI: 10.6084/m9.figshare.7857707
title: tar.gz file

description: .gz file for download testing<br>
DOI: 10.6084/m9.figshare.7857470
title: Mus musculus CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for Mus musculus. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857488
title: Supplementary Material for: Mice Lacking Fatty Acid-Binding Protein 5 Are Resistant to <b><i>Listeria monocytogenes</i></b>

description: To investigate the role of fatty acid-binding protein 5 (FABP5) in infectious diseases, FABP5-deficient mice were challenged with <i>Listeria monocytogenes</i>, a facultative intracellular bacterial pathogen. Interestingly, FABP5-deficient animals were able to clear the infection within 3 days whereas control wild-type (WT) animals showed comparatively higher bacterial burdens in the liver and spleen. Sections of infected tissues showed an increase in inflammatory foci in WT mice compared to FABP5-deficient mice. FABP5-deficient mice had lower circulating inflammatory cytokines and increased inducible nitric oxide synthase production. FABP5-deficient mouse bone marrow-derived macrophages produced higher levels of nitrite anion than their WT counterparts in response to various stimuli. Additionally, in contrast to FABP5<sup>–/–</sup> mice, transgenic mice overexpressing FABP5 in myeloid cells (LysM-Cre driven) showed decreased survival rates and increased bacterial burden and inflammatory cytokines. Overall, these findings suggest that increased FABP5 levels correlate with a higher <i>L. monocytogenes</i> bacterial burden and elevated subsequent inflammation.
DOI: 10.6084/m9.figshare.7857464
title: Rattus norvegicus CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Rattus norvegicus</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857467
title: Homo sapiens CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Homo sapiens</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857461
title: Mammal_Ranges_1970s

description: Shapefiles (.shp) compressed as a single .zip file. The projection of the files is in Geographic coordinates (WGS84 of mammal ranges in the 1970s<br>
DOI: 10.6084/m9.figshare.7857461.v1
title: Mammal_Ranges_1970s

description: Shapefiles (.shp) compressed as a single .zip file. The projection of the files is in Geographic coordinates (WGS84 of mammal ranges in the 1970s<br>
DOI: 10.6084/m9.figshare.7857464.v1
title: Rattus norvegicus CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Rattus norvegicus</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857467.v1
title: Homo sapiens CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Homo sapiens</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7857491.v1
title: Supplementary_material (Validity of block start performance without arm forces or by kinematics-only methods).docx

description: This file involves Figure S1, S2 and S3.<br>
DOI: 10.6084/m9.figshare.7857455
title: Supplementary Material for: Urinary and Fecal Continence in 5-Year-Old Patients Who Underwent in utero Myelomeningocele Repair: A Prospective Study

description: <b><i>Introduction:</i></b> After<b><i></i></b> the successful results of in utero myelomeningocele (MMC) repair presented by the Management of Myelomeningocele Study, the concept of fetal surgery was introduced in our institution in 2011. Since then, we have been able to follow prospectively a group of patients with attention to urological care. In the present study, we were interested in estimating urinary and fecal continence in this new subset of patients. <b><i>Material and Methods:</i></b><i></i> We selected from our database patients aged 5 years or older for evaluation of urinary and fecal continence. We reviewed all charts and completed a questionnaire to study aspects of urinary and fecal continence. <b><i>Results:</i></b> We identified 14 patients, i.e., 4 (28.6%) males and 10 (71.4%) females. The mean age at MMC surgery was 25.6 gestational weeks. The uro­dynamic class was high-risk in 6 (42.9%), incontinent in 4 (28.6%), hypocontractile in 1 (7.1%), and normal in 3 (21.4%) patients. Three patients had undergone surgery (2 augmentations, i.e., 1 in association with a left colon ACE Macedo-Malone procedure and 1 mini-sling urethroplasty). Twelve patients underwent clean intermittent catheterization (CIC) (85.7%). Only 3 (21.4%) patients had no urinary leakage. Eleven patients (78.6%) used diapers. Eight patients (57.2%) underwent retrograde rectal irrigation and 11 (78.6%) complained of fecal loss. Eleven patients (78.6%) did not report an impact on their self-esteem. <b><i>Conclusion:</i></b> Despite the use of CIC in 85.7% of the cases, the continence rate in MMC patients operated on in utero was low and 78.6% of the patients used diapers. This data can be used to educate parents about future conditions of their 5-year-old children and may stimulate the debate regarding further attempts (surgical or not) to improve fecal and urinary continence.
DOI: 10.6084/m9.figshare.7857455.v1
title: Supplementary Material for: Urinary and Fecal Continence in 5-Year-Old Patients Who Underwent in utero Myelomeningocele Repair: A Prospective Study

description: <b><i>Introduction:</i></b> After<b><i></i></b> the successful results of in utero myelomeningocele (MMC) repair presented by the Management of Myelomeningocele Study, the concept of fetal surgery was introduced in our institution in 2011. Since then, we have been able to follow prospectively a group of patients with attention to urological care. In the present study, we were interested in estimating urinary and fecal continence in this new subset of patients. <b><i>Material and Methods:</i></b><i></i> We selected from our database patients aged 5 years or older for evaluation of urinary and fecal continence. We reviewed all charts and completed a questionnaire to study aspects of urinary and fecal continence. <b><i>Results:</i></b> We identified 14 patients, i.e., 4 (28.6%) males and 10 (71.4%) females. The mean age at MMC surgery was 25.6 gestational weeks. The uro­dynamic class was high-risk in 6 (42.9%), incontinent in 4 (28.6%), hypocontractile in 1 (7.1%), and normal in 3 (21.4%) patients. Three patients had undergone surgery (2 augmentations, i.e., 1 in association with a left colon ACE Macedo-Malone procedure and 1 mini-sling urethroplasty). Twelve patients underwent clean intermittent catheterization (CIC) (85.7%). Only 3 (21.4%) patients had no urinary leakage. Eleven patients (78.6%) used diapers. Eight patients (57.2%) underwent retrograde rectal irrigation and 11 (78.6%) complained of fecal loss. Eleven patients (78.6%) did not report an impact on their self-esteem. <b><i>Conclusion:</i></b> Despite the use of CIC in 85.7% of the cases, the continence rate in MMC patients operated on in utero was low and 78.6% of the patients used diapers. This data can be used to educate parents about future conditions of their 5-year-old children and may stimulate the debate regarding further attempts (surgical or not) to improve fecal and urinary continence.
DOI: 10.6084/m9.figshare.7857338
title: Supplementary Material for: A Short Cut to Mushrooms – Red Langur (<b><i>Presbytis rubicunda</i></b>) Consumption of Terrestrial Fungus

description: We report the first in-depth evidence of targeted mushroom foraging in an Asian colobine. Using direct observations (2010–2018) and camera traps (2008–2018) in the Sebangau Forest, Central Kalimantan, Indonesian Borneo, we show how adult female red langurs (<i>Presbytis rubicunda</i>) are regularly descending to the ground to consume mushrooms. We recorded 82 counts (0.36% of all focal observations, <i>n</i> = 25,502) of the focal adult langur on the ground from direct observations of habituated groups, and 80 independent images/videos of red langurs on the ground were obtained from the camera traps representing 1.12% of total images (<i>n</i> = 7,145). Mushroom consumption took place in 4 families, representing 0.04% of total focal behaviour observations and 24.3% of total time feeding on the ground. From the camera trap photos, red langurs are spending 20% of time on the ground feeding. We speculate that mushrooms could be a supplementary food for adult female langurs as there is an increase in consumption in April and November.
DOI: 10.6084/m9.figshare.7857341
title: The role of external and emergent drivers of water use change in Las Vegas

description: Over the past twenty-five years, per capita water use has declined in many US cities. Technological and policy changes partially explain this decline, but variables beyond the control of water managers also influence water use including external (e.g. drought) and emergent (e.g. public attention) changes. Importantly, these variables interact and the relationships between these variables and water use are non-stationary. However, many models assume fixed relationships between water use and its drivers, and limited interaction between variables. Here we present a flexible socio-hydrological approach to model how conservation strategies, and external and emergent changes, interact to influence per capita water use. We apply this approach to Las Vegas and find that marginal water rates, code changes coupled with population growth, and conservation response to water stress are the key drivers of the observed decline. Critically, modeling these strategies in absence of their connections to population growth and water stress cannot fully account for observed changes.
DOI: 10.6084/m9.figshare.7857338.v1
title: Supplementary Material for: A Short Cut to Mushrooms – Red Langur (<b><i>Presbytis rubicunda</i></b>) Consumption of Terrestrial Fungus

description: We report the first in-depth evidence of targeted mushroom foraging in an Asian colobine. Using direct observations (2010–2018) and camera traps (2008–2018) in the Sebangau Forest, Central Kalimantan, Indonesian Borneo, we show how adult female red langurs (<i>Presbytis rubicunda</i>) are regularly descending to the ground to consume mushrooms. We recorded 82 counts (0.36% of all focal observations, <i>n</i> = 25,502) of the focal adult langur on the ground from direct observations of habituated groups, and 80 independent images/videos of red langurs on the ground were obtained from the camera traps representing 1.12% of total images (<i>n</i> = 7,145). Mushroom consumption took place in 4 families, representing 0.04% of total focal behaviour observations and 24.3% of total time feeding on the ground. From the camera trap photos, red langurs are spending 20% of time on the ground feeding. We speculate that mushrooms could be a supplementary food for adult female langurs as there is an increase in consumption in April and November.
DOI: 10.6084/m9.figshare.7857341.v1
title: The role of external and emergent drivers of water use change in Las Vegas

description: Over the past twenty-five years, per capita water use has declined in many US cities. Technological and policy changes partially explain this decline, but variables beyond the control of water managers also influence water use including external (e.g. drought) and emergent (e.g. public attention) changes. Importantly, these variables interact and the relationships between these variables and water use are non-stationary. However, many models assume fixed relationships between water use and its drivers, and limited interaction between variables. Here we present a flexible socio-hydrological approach to model how conservation strategies, and external and emergent changes, interact to influence per capita water use. We apply this approach to Las Vegas and find that marginal water rates, code changes coupled with population growth, and conservation response to water stress are the key drivers of the observed decline. Critically, modeling these strategies in absence of their connections to population growth and water stress cannot fully account for observed changes.
DOI: 10.6084/m9.figshare.7857260
title: dataset from "The distinct phenotypic signatures of dispersal and stress in an arthropod model: from physiology to life history "

description: The dataset contains four data files:<br><br>(1)"life history.txt" : contains informations on various life history traits expressed by female mites let on leaves (bean or tomato) for 10 days after a dispersal test<br>One female founder per leaf; one leaf per row; 140 rows<br><br>(2)"metabolite.txt": contains informations on metabolite concentrations (obtained by GC-MS) of female mites let on leaves (bean or tomato) for 24h after a dispersal test<br>50 females per leaf; one leaf per row; 20 rows<br><br>(3)"dispersal rate.txt": proportion of dispersers effectively observed for 10 dispersal bridges<br><br>(4)"molecular categories.txt" : contains full names of tested metabolites, and their assignation to key molecular categories<br><br>######## FILE CONTENTS<br><br>#### Columns common to files (1) and (2)<br><br>Disp: dispersal status (binary, "Disperser" or "Resident". See manuscript for details on assignation)<br>Host: host plant after the dispersal test (binary, "Bean" or "Tomato")<br><br>#### File (1) only<br><br>Length_mm: length of the focal female, in mm (from tip of chelicerae to end of body)<br>eaten_mm2: total area of chlorotic damage observed after 24h<br>Neggs24h: number of eggs laid in the first 24h by the focal female<br>EGGS10d: number of eggs present on the leaf after 10 days<br>Nimmatures10d: number of immatures (excluding eggs) present on the leaf after 10 days<br>AFEMA10d: number of adult females present on the leaf after 10 days<br>AMALES10d: number of adult males present on the leaf after 10 days<br>N_all_mites10d = EGGS10d + Nimmatures10d + AFEMA10d + AMALES10d<br>mean_egg_vol: mean volume of eggs laid by the focal female in the first 24h (in micrometer^3)<br><br>#### File (2) only<br><br>ID: unique replicate identifier (first letter denote host plant, second letter dispersal status)<br>Fresh_mass_mg: mass of the 50 sampled mites, obtained by substracting empty tube mass to the mass of the tube + sample<br>Columns from "Lactic_acid" to "trehalose": metabolite concentrations (in nmol per mg of mite fresh mass, 37 metabolites)<br><br>### File (3) only<br><br>Bridge: replicate ID<br>Ndispersers: number of individuals (out of 100) that successfully crossed the dispersal bridge<br><br>### File (4) only<br><br>Column: legacy variable for quality controls; order of the corresponding molecule in File (2)<br>Molecule: Molecule shortened ID as in file (2)<br>Full_name: The corresponding full, unabbreviated name of the molecule<br>Category: Molecular category based on the KEGG database; see manuscript for details<br><br>
DOI: 10.6084/m9.figshare.7857269
title: Supplementary Material for: The Altered-State-of-Consciousness Aspect of a Feeling of Lightness Is Reported to Be Associated with Antidepressant Benefits by Depressed Individuals Receiving Ketamine Infusions: A Systematic Analysis of Internet Video Testimonials

description: Medicine
DOI: 10.6084/m9.figshare.7857245
title: Use of the index of ideality of correlation to improve predictive potential for biochemical endpoints

description: The CORAL software is a tool to build up quantitative structure-property/activity relationships (QSPRs/QSARs). The project of updated version of the CORAL software is discussed in terms of practical applications for building up various models. The updating is the possibility to improve the predictive potential of models using the so-called Index of Ideality of Correlation (<i>IIC</i>) as a criterion of the predictive potential for QSPR/QSAR models. Efficacy of the <i>IIC</i> is examined with three examples of building up QSARs: (i) models for anticancer activity; (ii) models for mutagenicity; and (iii) models for toxicity of psychotropic drugs. The validation of these models has been carried out with several splits into the training, invisible training, calibration, and validation sets. The ability of <i>IIC</i> to be an indicator of predictive potential of QSAR models is confirmed. The updated version of the CORAL software (CORALSEA-2017, http://www.insilico.eu/coral) is available on the Internet.