cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12896800
title: Data from: Sexual color ornamentation, microhabitat choice, and thermal physiology in the common wall lizard (Podarcis muralis)

description: Common wall lizards (Podarcis muralis) in Italy show a striking variation in body coloration across the landscape, with highly exaggerated black and green colors in hot and dry climates and brown and white colors in cool and wet climates. Males are more intensely colored than females, and previous work has suggested that the maintenance of variation in coloration across the landscape reflects climatic effects on the strength of male–male competition, and through this sexual selection. However climatic effects on the intensity of male–male competition would need to be exceptionally strong to fully explain the geographic patterns of color variation. Thus, additional processes may contribute to the maintenance of color variation. Here we test the hypothesis that selection for green and black ornamentation in the context of male–male competition is opposed by selection against ornamentation because the genes involved in the regulation of coloration have pleiotropic effects on thermal physiology, such that ornamentation is selected against in cool climates. Field observations revealed no association between body coloration and microhabitat use or field active body temperatures. Consistent with these field data, lizards at the extreme ends of the phenotypic distribution for body coloration did not show any differences in critical minimum temperature, preferred body temperature, temperature‐dependent metabolic rate, or evaporative water loss when tested in the laboratory. Combined, these results provide no evidence that genes that underlie sexual ornamentation are selected against in cool climate because of pleiotropic effects on thermal biology.
DOI: 10.5281/zenodo.6397330
title: From Noise to Signal: Multi-layer Speckle Correlation with Applications in Visible Light Communication

description: Dataset for journal article "Enhanced Secrecy in Optical Communication using Speckle from Multiple Scattering Layers" The basic publication is:<br> Alfredo Rates, Joris Vrehen, Bert Mulder, Wilbert L. IJzerman, and Willem L. Vos, "Enhanced Secrecy in Optical Communication using Speckle from Multiple Scattering Layers", Opt. Express <strong>31</strong>, 23897-23909 (2023).<br> <br> We have uploaded to the Zenodo database all data enabling everyone to reuse our data, and to reproduce all the figures of our paper. The upload contains the file "Metadata.txt" explaining the content of the upload.
description: This work was supported by the NWO-TTW program P15-36 "Free-Form Scattering Optics" (FFSO) and the MESA+ Institute section Applied Nanophotonics (ANP).
DOI: 10.6073/pasta/809735b6ef217b7c4ab4426f7285401f
title: Storm nutrient dynamics at Andrews Experimental Forest stream gages, 2001 to 2003

description: This study examines headwater stream nutrients at stream gaging sites during selected storms in the Andrews Experimental Forest. High frequency storm sampling was conducted to examine flow path dynamics, basin characteristics, seasonal trends, and differing responses and mobility among analytes on streamwater nutrient concentrations and fluxes.
DOI: 10.6084/m9.figshare.23614104
title: dataset for dih reconstruction

description: this is dataset and experiment result for "<em>Field recovery from digital inline holographic images of Composite Propellant Combustion base on Denoising Diffusion model</em>'
DOI: 10.6084/m9.figshare.24298093
title: MOIHABFT

description: airplane, boat, butterfly, man, peppers, baboon
DOI: 10.6084/m9.figshare.24647778
title: Supplementary Material for: Impact of Bevacizumab Being Skipped due to Adverse Events of Special Interest for Bevacizumab in Patients With Unresectable Hepatocellular Carcinoma Treated With Atezolizumab Plus Bevacizumab: An Exploratory Analysis of the Phase III IMbrave150 study

description: Introduction: The Phase III IMbrave150 study established atezolizumab + bevacizumab as the global standard of care in patients with unresectable hepatocellular carcinoma (HCC). This exploratory analysis examined the impact of bevacizumab interruption due to bevacizumab adverse events of special interest (AESIs). 
Methods: Patients in IMbrave150 who were randomized to atezolizumab + bevacizumab and received treatment for ≥6 months (to reduce immortal time bias) were included in group A-1 if bevacizumab had ever been skipped due to bevacizumab AESIs or to group A-2 otherwise. Efficacy analyses included overall survival (OS) and progression-free survival (PFS) by whether bevacizumab was skipped (group A-1 vs A-2). PFS was evaluated per independent review facility (IRF)–assessed Response Evaluation Criteria in Solid Tumours (RECIST) version 1.1 and HCC-modified RECIST (IRF-HCC mRECIST). Safety was also evaluated. 
Results: Of the 210 patients who received ≥6 months of atezolizumab + bevacizumab, 69 were assigned to group A-1 and 141 to A-2. At data cutoff (August 20, 2020), hazard ratio (HR) for OS was 1.04 (95% CI: 0.64, 1.69) for group A-1 vs A-2. HR for PFS was 1.07 (95% CI: 0.74, 1.55) per IRF-assessed RECIST 1.1 and 1.10 (95% CI: 0.76, 1.59; 15.5 vs 9.7 months) per IRF-HCC mRECIST for group A-1 vs A-2. Safety profiles for atezolizumab and bevacizumab were largely similar between groups. More group A-1 patients had grade 3/4 adverse events. A separate analysis investigating the impact of immortal time bias in patients who received ≥3 months of atezolizumab + bevacizumab supported the appropriateness of the ≥6-month landmark analysis. 
Discussion/Conclusion: Efficacy was similar between patients who skipped bevacizumab due to bevacizumab AESIs and those who did not. Although this comparison was nonrandomized and exploratory, results suggest that skipping bevacizumab due to bevacizumab AESIs did not considerably impact the efficacy and safety of atezolizumab + bevacizumab.
DOI: 10.6084/m9.figshare.25304053
title: Supplementary Material for: Translation, cultural adaptation, and content validation of a pleural mesothelioma questionnaire to Portuguese context: a key tool for epidemiological surveillance

description: OBJECTIVE 
To describe the translation, cultural adaptation, and content validation process of the French National Surveillance Programme for Pleural Mesothelioma (FNSPPM) questionnaire for the Portuguese context.
METHODS
A search was conducted in the PubMed database and Web of Science, in the period from 1 January 1960 to 31 December 2022, to select the questionnaire. Forward and reverse translations, calculation of the content validity index (CVI) by a panel of experts (n=9), and cognitive interviewing with individuals with at least one exposure to asbestos (n=10) were performed. Experts rated items on a Likert scale (1-4) based on their relevance. The item-level content validity index (I-CVI), scale-level content validity index based on the average method (S-CVI/Ave), scale-level content validity index based on the universal agreement method (S-CVI/UA) were calculated.
RESULTS
The final version of the FNSPPM questionnaire for the Portuguese context resulted from a translation and content validation process. The panel of experts considered the questionnaire relevant, with an I-CVI of up to 0.78 in 68 of 69 of the questions, an S-CVI/Ave of 0.98, and an S-CVI/UA of 0.90. The participants in the cognitive interviews reported an understanding of the questionnaire.
CONCLUSION
A validated FNSPPM questionnaire for the Portuguese context is now available to study individuals with Pleura Mesothelioma (PM) and asbestos exposure.
DOI: 10.6084/m9.figshare.25470220
title: Supplementary Material for: Improvement in Echocardiographic Indexes of Systolic Heart Failure Post Kidney Transplantation – a retrospective analysis

description: Introduction: End-stage renal disease (ESRD) is a major risk factor for cardiovascular morbidity and mortality, which can be partially eliminated by kidney transplantation. Systolic heart failure might be considered as contraindication for kidney transplant although some patients demonstrate myocardial recovery post-transplant. We aim to identify and characterize the phenomenon of reverse myocardial remodelling in kidney transplanted patients.
Methods: The study is a retrospective cohort of patients undergoing kidney transplant between 2016-2019 (n=604) at Rabin Medical Center. Patients were assessed according to availability of two echocardiographic examinations: pre- and post-kidney transplant. The change in estimated ejection fraction (EF) and possible predictors of myocardial recovery were examined. 
Results: Data of 293 patients was available for the final analysis. Eighty-one (28%) patients had a LVEF improvement equal or above 5%, whereas 36 (12%) patients had a LVEF improvement 10% or more post transplantation. Twenty-five patients (8.5%) had moderate or severe systolic heart failure with LVEF reduced to 40% or less at baseline. 13 of them (52%) had a LVEF improvement of ≥5% and 10 patients (40%) had an improvement of ≥10% in their EF. Cox regression analyses identified female gender as the only independent variable associated with LVEF improvement of at least 10%. 
Conclusion
Renal transplantation might lead to improved LV systolic function in some patients.
DOI: 10.6084/m9.figshare.25828633
title: Supplementary Material for: Laser Doppler Fluximetry in Cutaneous Vasculature: Methods for Data Analyses

description: <b><i>Introduction:</i></b> Acquisition of a deeper understanding of microvascular function across physiological and pathological conditions can be complicated by poor accessibility of the vascular networks and the necessary sophistication or intrusiveness of the equipment needed to acquire meaningful data. Laser Doppler fluximetry (LDF) provides a mechanism wherein investigators can readily acquire large amounts of data with minor inconvenience for the subject. However, beyond fairly basic analyses of erythrocyte perfusion (fluximetry) data within the cutaneous microcirculation (i.e., perfusion at rest and following imposed challenges), a deeper understanding of microvascular perfusion requires a more sophisticated approach that can be challenging for many investigators. <b><i>Methods:</i></b> This manuscript provides investigators with clear guidance for data acquisition from human subjects for full analysis of fluximetry data, including levels of perfusion, single- and multiscale Lempel-Ziv complexity (LZC) and sample entropy (SampEn), and wavelet-based analyses for the major physiological components of the signal. Representative data and responses are presented from a recruited cohort of healthy volunteers, and computer codes for full data analysis (MATLAB) are provided to facilitate efforts by interested investigators. <b><i>Conclusion:</i></b> It is anticipated that these materials can reduce the challenge to investigators integrating these approaches into their research programs and facilitate translational research in cardiovascular science.
DOI: 10.6084/m9.figshare.25992037.v1
title: Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma

description: This repository contains raw sgRNA read counts from screening DAOY cells (Brunello library) and mouse SHH-MB SMB21 cell (Brie library). Furthermore, raw read counts from RNAseq of SMB21 cell treated with the DNMT1 inhibitor 5-azacytidine (2 hours and 24 hours) are provided as well.<br>Sonic hedgehog subgroup of medulloblastoma (SHH-MB) is characterized by aberrant activation of the SHH signaling pathway. An inhibition of the positive SHH regulator<i> Smoothened</i> (SMO) has demonstrated promising clinical efficacy. Yet, primary and acquired resistance to SMO inhibitors limit their efficacy. An understanding of underlying molecular mechanisms of resistance to therapy is warranted to bridge this unmet need. Here, we make use of genome-wide CRISPR-Cas9 knockout screens in SMB21 and DAOY cells, in order to unravel genetic dependencies and drug-related genetic interactors that could serve as alternative therapeutic targets for SHH-MB. Our screens reinforce SMB21 cells as a faithful model system for SHH-MB, as opposed to DAOY cells, and identify members of the epigenetic machinery including DNA methyltransferase 1 (DNMT1) as druggable targets in SHH-dependent tumors. We show that <i>Dnmt1</i> plays a crucial role in normal murine cerebellar development and is required for SHH-MB growth <i>in vivo</i>. Additionally, DNMT1 pharmacological inhibition alone and in combination with SMO inhibition effectively inhibits tumor growth in murine and human SHH-MB cell models and prolongs survival of SHH-MB mouse models by inhibiting SHH signaling output downstream of SMO. In conclusion, our data highlight the potential of inhibiting epigenetic regulators as a novel therapeutic avenue in SMO-inhibitor sensitive as well as resistant SHH-MBs.
DOI: 10.7488/ds/7497
title: An experimental study of the effect of pump pulse duration on liquid crystal laser performance

description: Much work has been done to understand the factors that impact photonic band-edge liquid crystal (LC) laser threshold and slope efficiency; two parameters often stated to quantify performance. Conventionally, LC lasers are optically pumped using Q-switched lasers with a fixed pulse duration, and thus the effect of pump pulse duration on LC laser performance has received little attention. Whilst some studies have been published at different pump pulse durations, these use different laser sources and experimental conditions, making the data incomparable. By exploiting a recent breakthrough in laser diode pumping, our experimental results prove and quantify the detrimental effect of an increase in pump pulse duration on LC laser threshold and slope efficiency. We also show that this conclusion depends upon how threshold is defined, due to an ambiguity in the definition of pulse energy in systems where peak power and pulse duration can be independently controlled. For improved comparison within the literature of LC laser performance, we thus propose an alternative convention whereby threshold can be stated in units of peak power density. This work forms the basis of the paper "An experimental study of the effect of pump pulse duration on liquid crystal laser performance" by Calum M. Brown, Ieva Pakamoryte and Philip J. W. Hands. This paper has been submitted for publication and is currently under review. The data herein pertain to Figures 2, 3, 4 and 5 in our paper.
DOI: 10.5258/soton/d3031
title: Dataset supporting the publication "Vertical Integration of KTN on SOI Wafer"

description: This dataset contains all the FIB-SEM images, experimental and simulation data used to generate the figures included in the main text of the publication "Vertical Integration of KTN on SOI Wafer" in Optics Express (2024) https://doi.org/10.1364/OE.525582

This dataset contain three main folders:
The first folder (experiment) contains all experimental data obtained from passive characterisation of the structures.
The second folder (simulation) contains simulation EME file and the final sweep results.
The third folder (images) contains the microscopic and FIB-SEM images.

The files are presented in excel files, JPG files for images and lsf, and lms files for simulations.

The data is accessible via CC BY license.
DOI: 10.6073/pasta/4fb341bdce5d020b7c186123353cc20c
title: Oxygen-18 isotope ratios, chemistry, and tracers in storm water from WS10 hillslope experiment in the HJ Andrews Experimental Forest, 2001-2003

description: Oxygen-18 ratios, expressed as Delta-18O or D18O (parts per hundred), measured in WS10 discharge and WS10 precipitation. The time series spans from January 2001 to February 2003, period during which precipitation and streamflow were sampled mostly manually and weekly. The time series also includes some periods of higher frequency automatic sampling in streamflow and precipitation in winter 2001 and winter 2002. The precipitation Delta-18O time series corresponds to the Delta-18O measured at PRIMET station located about 1 km from WS10 outlet at a similar altitude, except from 01-Sep-2002 to 04-Feb-2003, when the Delta-18O of precipitation sampled sequentially on an experimental hillslope of WS10, was used (the collector was located on the south aspect, 91 m upstream from the outlet).
DOI: 10.6084/m9.figshare.24551383
title: Supplementary Material for: A Phase 1b Study of Lenvatinib Plus Pembrolizumab in Patients With Unresectable Hepatocellular Carcinoma: Extended Analysis of Study 116

description: Background: Treatment with lenvatinib (dosing for patients who weigh ≥60 kg was 12 mg/day; for patients who weigh &lt;60 kg, the dose was 8 mg/day) plus pembrolizumab 200 mg once every 3 weeks demonstrated antitumor activity and a manageable safety profile in patients with first-line unresectable hepatocellular carcinoma (uHCC) in the open-label phase 1b Study 116/KEYNOTE-524 (primary analysis data cutoff date: October 31, 2019; median follow-up: 10.6 months). 
Objective: This analysis (updated data cutoff date: March 31, 2021) reports efficacy results from 17 months of additional follow-up time. 
Methods: 100 Patients with uHCC were included in the primary analysis (median follow-up: 27.6 months). Endpoints included overall survival (OS) and investigator-assessed progression-free survival (PFS), objective response rate (ORR), and duration of response (DOR) per modified RECIST. Landmark analyses of OS by best response at 3 and 9 months were performed. Pembrolizumab antidrug antibodies (ADAs) and concentrations were also measured (cutoff date: August 7, 2020). 
Results: ORR was 43.0% (95% CI 33.1% to 53.3%) and median DOR was 17.1 months (95% CI 6.9 to 19.3 months). Median PFS and OS were 9.3 months (95% CI 7.4 to 9.8 months) and 20.4 months (95% CI 14.4 to 25.9 months), respectively. No treatment-emergent ADAs were detected. 
Conclusion: Results show a sustained treatment effect with lenvatinib plus pembrolizumab in patients with uHCC in the first-line setting.
DOI: 10.6084/m9.figshare.5146096
title: 48-spot smFRET-PAX measurements of dsDNA oligos

description: The measurement data files in this repository have been used in the following publications:<br><i>48-spot single-molecule FRET setup with periodic acceptor excitation.</i><br>Ingargiola et al., bioRxiv (2017), doi: https://doi.org/10.1101/156182<br><i>Optical crosstalk in SPAD arrays for high-throughput single-molecule fluorescence spectroscopy.</i> Ingargiola et al., bioRxiv (2017), doi: https://doi.org/10.1101/207118<br><br><br>Copyright (C) 2017 The Regents of the University of California
DOI: 10.15468/dl.eyw64x
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((17.22430 -4.90407,46.77570 -4.90407,46.77570 6.90407,17.22430 6.90407,17.22430 -4.90407))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Euphaedra rex Stoneham, 1935"
 ]
}

 The dataset includes 51 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106067-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24339/131e6bf5-ace6-4bae-82db-bf61b30e2331
title: Novel spaces as catalysts for change; developing learner agency through transnational projects - dataset

description: This dataset comprises interview transcripts and written reflections with accompanying codes and nodes. These were gathered from seven English undergraduate students who took part in the Digital Learning Across Boundaries (DLAB) project. They centre on the students reflecting on their experiences in schools and on the transnational project culmination in Bruges, Belgium. The data was gathered whilst on the trip to Bruges, and explores the students' experiences from their perspectives.
DOI: 10.15468/dl.xmpdfq
title: Occurrence Download

description: A dataset containing 92987 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreochromis niloticus (Linnaeus, 1758)"
 ]
}

 The dataset includes 92987 records from 231 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106068-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/12999575
title: Data from: 30 years of large river restoration: how long do restored floodplain channels remain suitable for targeted rheophilic fishes in the lower river Rhine?

description: The ecological efficacy of river restoration projects may change over time, resulting in the loss of their ecological function for targeted species. The goal of this study was to evaluate the rheophilic nursery function of restored floodplain channels over time, by analysing 30 years of monitoring data from 12 restoration projects in the lower river Rhine.
DOI: 10.4121/12999575.v3
title: Data from: 30 years of large river restoration: how long do restored floodplain channels remain suitable for targeted rheophilic fishes in the lower river Rhine?

description: The ecological efficacy of river restoration projects may change over time, resulting in the loss of their ecological function for targeted species. The goal of this study was to evaluate the rheophilic nursery function of restored floodplain channels over time, by analysing 30 years of monitoring data from 12 restoration projects in the lower river Rhine.
DOI: 10.6084/m9.figshare.26084521.v1
title: <b>The Tadpole of</b><b> </b><b><i>Chiasmocleis altomontana</i></b><b> </b><b>(Anura: Microhylidae)</b>

description: <b>Background.</b> Describing the morphology of anuran larvae contributes towards filling gaps in taxonomy and natural history. This is especially relevant for explosive breeders, in which adults remain at the reproduction site for only a short period, while tadpoles may be more conspicuous. Here, we describe the larval external morphology and internal oral anatomy of the microhylid frog <i>C</i><i>hiasmocleis</i><i>altomontana</i> from near the type locality in southeastern Brazil.<b>Methods.</b> We took 13 morphometric measurements of 11 tadpoles between stages 35 and 39 from four ponds. To compare the larval external morphology of the genus, we also built a morphospace using measurements provided by the original descriptions. To impute missing data, we used a traits imputation method that considered the phylogenetic relationships of the species.<b>Results.</b> The tadpole of <i>C. altomontana</i> is the largest among the Atlantic Forest species and the second largest of the genus, after <i>C. anatipes</i>. Like all species of the genus, the larva of <i>C. altomontana</i> is exotrophic, suspension feeder, Orton type II, and occurs in lentic temporary environments. Overall, <i>C. altomontana</i> shows subtle differences in dorsal fin height, dorsal fin insertion, tip of the tail, and snout in lateral view from its congeners. <i>Chiasmocleis altomontana</i> differs greatly in terms of shape from the remaining species of the genus, especially from its sister species <i>C.</i><i>m</i><i>antiqueira</i> and others from the Atlantic Forest clade. However, the overall pattern suggests an evolutionaryconvergence in the tadpole shape, since species from distant clades were positioned at the centre of the morphospace.