cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21717245
title: Supplementary Material for: Serine Protease Networks Mediate Immune Responses in Extra-Embryonic Tissues of Eggs in the Tobacco Hornworm, <b><i>Manduca sexta</i></b>

description: The melanization and Toll pathways, regulated by a network of serine proteases and noncatalytic serine protease homologs (SPHs), have been investigated mostly in adult and larval insects. However, how these innate immune reactions are regulated in insect eggs remains unclear. Here we present evidence from transcriptome and proteome analyses that extra-embryonic tissues (yolk and serosa) of early-stage <i>Manduca sexta</i> eggs are immune competent, with expression of immune effector genes including prophenoloxidase and antimicrobial peptides. We identified gene products of the melanization and Toll pathways in <i>M. sexta</i> eggs. Through in vitro reconstitution experiments, we demonstrated that constitutive and infection-induced serine protease cascade modules that stimulate immune responses exist in the extra-embryonic tissues of <i>M. sexta</i> eggs. The constitutive module (HP14b-SP144-GP6) may promote rapid early immune signaling by forming a cascade activating the cytokine Spätzle and regulating melanization by activating prophenoloxidase (proPO). The inducible module (HP14a-HP21-HP5) may trigger enhanced activation of Spätzle and proPO at a later phase of infection. Crosstalk between the two modules may occur in transition from the constitutive to the induced response in eggs inoculated with bacteria. Examination of data from two other well-studied insect species, <i>Tribolium castaneum</i> and <i>Drosophila melanogaster</i>, supports a role for a serosa-dependent constitutive protease cascade in protecting early embryos against invading pathogens.
DOI: 10.3886/icpsr03328
title: Nationwide Personal Transportation Survey, 1969: [United States]
title: Archival Version

description: This survey is the first in the Nationwide Personal Transportation Survey (NPTS) series. NPTS was designed to collect information on all trips taken during a 24-hour period, as well as trips of 75 or more miles one-way during the preceding 14 days. Trips made by any means of transportation were recorded, including automobile, walking, bicycle, school bus, motorcycle, and various modes of public transportation. A purpose code was also assigned to each trip: earning a living, family and personal business, educational or religious, and social and recreational. Demographic information was collected on participants as well, including geographic information, age, sex, race, occupation, and employment status of household members, and whether they owned or had access to a car.
description: Datasets: 
 
 DS1: Dataset
description: Nationwide Personal Transportation Survey Series
description: It should be noted that, due to the age and incomplete documentation of this dataset, it is in less than optimal condition and is provided primarily to complement the later iterations of this series that ICPSR has acquired. A number of variables have undocumented codes and possibly invalid values and the documentation that does exist is difficult to read. In addition, only a small portion of the data that were originally collected are available in this dataset, which contains only the household information and the Travel Day Report. Questionnaire sections not included are the detailed Automobile Record, Shopping, Travel to Work, and Overnight Travel.
description: The civilian, noninstitutionalized population of the United States.
description: Multistage probability sample of housing units, drawn from every state and the District of Columbia.
DOI: 10.14458/rsu.res.2020.14
title: A Study on Design and Construction of Non-invasive Cholesterol Sensor
DOI: 10.5278/vbn.phd.med.00139
title: Spraino
title: A new concept in lateral ankle sprain injury prevention
DOI: 10.5281/zenodo.6803921
title: ARIA - Accessible Rich Internet Applications Landmarks classified dataset

description: ARIA Landmarks classified dataset. ARIA Landmarks are regions of web applications that can be accessed by specific keyboard shortcuts and are specially useful for blind users. They comprise the banner, complementary, contentinfo, form, main, navigation, region and search classes. In the dataset, samples represent DOM elements of web applications with different attributes extracted when these elements are rendered in the browser.
DOI: 10.5281/zenodo.7216126
title: Irish Drought Impacts Database v.1.0 (IDID)

description: The Irish Drought Impacts Database (IDID) presents information from drought related newspaper articles for the island of Ireland, covering the period 1733 – 2019, collected through systematic searching of the Irish Newspaper Archive. These articles were identified, assessed and categorized using a modified version of the classification scheme employed by the European Drought Impact Inventory (EDII) (Stahl et al. 2012). The IDID provides information on the documented temporal and geographical extent of drought events, their socio-economic and political contexts, their consequences and mitigation strategies employed. Temporal information includes the newspaper publication date, timing and duration of drought periods and timing of impacts. Spatial details are provided on three different levels; in addition to Nomenclature of Territorial Units for Statistics Level 2 (Nuts2) regions, county location and, if available, a more localized place name (e.g., town or city name) is also recorded. The database allows the analysis of long-term patterns in drought incidence and impacts as well as offering insights into the impacts of individual drought events over nearly three centuries of Ireland’s history. Spatially specific data provide an opportunity for further exploration of the differential vulnerability of various geographical locations, which may vary depending on biophysical conditions, economic, political and societal context. Textual excerpts offer further insight into the human experience and perception of drought and its impacts. The IDID therefore enables a better understanding of drought, vulnerability, and offers a new open access tool for multi-disciplinary investigation of drought on the island of Ireland.
description: Project: Irish Droughts: Environmental and Cultural Memories of a Neglected Hazard Project website: https://www.ucd.ie/droughtmemories/ Award/Grant title: Irish Research Council, Grant/Award Number: COALESCE/2019/43
description: {"references": ["Reference: Stahl, K. at al. (2012) A European Drought Impact Report Inventory (EDII): Design and Test for Selected Recent Droughts in Europe, DROUGHT-R&SPI Technical Report No. 3, 23 pp., available at: http://www.eu-drought.org/technicalreports/10814306/"]}
DOI: 10.5441/002/edbt.2019.05
title: Boosting SimRank with Semantics
DOI: 10.5519/0070625
title: NATRICINE

description: # Data from the NATRICINE project led by V.Deepak (veerappandeepak@gmail.com), funded by a Marie Skłodowska-Curie Action. These data have been used in several papers: 1. Deepak. V., Cooper, N., Poyarkov, N.A., Kraus, F., Burin, G., Das,A., Snarayanan, S., Streicher, J.W., Smith, S.J., & Gower, D.J. 2021. Multilocus phylogeny, natural-history traits, and classification of natricine (Serpentes: Natricinae) snakes. Zoological Journal of the Linnaean Society. 2021, zlab099. DOI: 10.1093/zlab099. 2. Deepak. V., Gower, D.J. & Cooper, N. 2022. Diet and habit explain head-shape convergences in natricine snakes. Journal of Evolutionary Biology. More details can be found at https://github.com/nhcooper123/NATRICINE-traits, https://github.com/nhcooper123/NATRICINE-ecomorph, and in the papers themselves. ## Data for paper 1 (Zoological Journal of the Linnaean Society) 1. *natricine-251tips.fas* 2. *Mol-dating-310tips.nex* 3. *Natricine-MLphylogeny250tips.tre* 4. *120tipnewick* 5. *TreePL_natricine_dated.tre* 6. *Totnat-geo-data* 7. *Tot-nat-geo-data-8areas* ## Data for paper 2 (Journal of Evolutionary Biology) ### Linear analyses (main text) 1. *new_datedtree-LM.nexus*. Dated/time-calibrated phylogeny used in LM analyses. 2. *linear-species-means-LSR.csv*. Species means for head shape variables used in analyses. 3. *metadata-data-natricine-LM.csv*. Raw specimen level measurements, along with additional data needed for analyses, including putative ecomorph. 4. *missing_taxa_data.csv*. List of missing taxa used to create pruned phylogeny for analyses. 5. *snakepca-LSR.csv*. PC (principal components) data used in analyses. ### GMM analyses (supplemental) 1. *new_datedtree-GMM.nexus*. Dated/time-calibrated phylogeny used in GMM analyses. 2. *metadata-data-natricine-GMM.csv*. Additional data needed for analyses, including putative ecomorph. 3. *natricine_landmarks.TPS*. Raw landmarks from snake heads used in GMM analyses. 4. *sliders-natricine-landmarks.csv*. Slider definitions for GMM analyses. 5. *snake-data-pca-GMM.csv*. PC (principal components) data used in analyses. 6. *GMM images.zip*. Example images for GMM analyses. We are only able to upload those taken from NHM specimens. ## Data for both papers We also include the full natural history dataset collected for this project, along with the references used to build it (`Natricine-natural-history-data.csv` and `Natricine-natural-history-data-references.csv`), used in both paper, and the time calibrated phylogeny with no species added or pruned *datedtree.nexus*. *More details and metadata are available with each resource - click on the resource to access.*
DOI: 10.5519/0082968
title: Convergent evolution in toothed whale cochleae

description: Data from the paper **Convergent evolution in toothed whale cochleae**. [link to paper](https://doi.org/10.1186/s12862-019-1525-x). &gt; Travis Park, Bastien Mennecart, Loïc Costeur, Camille Grohé & Natalie Cooper. 2019. Convergent evolution in toothed whale cochleae. BMC Evolutionary Biology, 9: 195. DOI: 10.1186/s12862-019-1525-x. Note that during revision we were asked to rename the regimes, so in the paper, regime A = purple regime; regime B = yellow regime, and regime C = green regime.
DOI: 10.18739/a2m03xz4j
title: Watercraft inspections at the Alcan Port of Entry, 2017-2021

description: This spreadsheet includes watercraft inspection data collected by the United States Fish and Wildlife Service (USFWS) under the Lacey Act from 2017-2021. The USFWS conducted a literature review and initial assessment of the risk of dreissenid mussel introduction via watercraft entering the U.S. at the Alcan Port of Entry (one of Alaska’s primary international entry points) in 2008 and 2009 and provided recommendations for subsequent prevention actions. Since 2016, the USFWS has partnered with the United States Customs and Border Protection (USCBP), with technical input from State of Alaska agency representatives, to operate a watercraft inspection and decontamination station at the Alcan Port of Entry. Inspections occurred for a short period each year from 2017 until 2020 and for the entire summer in 2021. Dreissenid mussel incrusted watercraft have been encountered during this timeframe; fortunately, no live mussels have been detected. However, the risk of entry at other entry points or pathways has not been assessed due to lack of capacity and resources across partners, thus leaving lakes and rivers in Alaska susceptible to new aquatic invasive species (AIS) introductions. The data was collected by U.S. Fish and Wildlife Service staff. The data format and selection of variables was modified from a data collection initiative by the Western Invasive Species Coordinating Effort which is a subcommittee of the Western Regional Panel on Aquatic Nuisance Species: Building Consensus in the West Workgroup. More info can be found here http://westernregionalpanel.org/wp-content/uploads/2019/11/WRP-BC-Activity-Report-FINAL.pdf
DOI: 10.3886/e120404v1
title: Data and Code for: Leadership in Social Movements. The Forty-Eighters in the Civil War

description: This paper studies the role of leaders in the social movement against slavery that culminated in the U.S. Civil War. Our analysis is organized around a natural experiment: leaders of the failed German revolution of 1848--49 were expelled to the U.S. and became anti-slavery campaigners who helped mobilize Union Army volunteers. Towns where Forty-Eighters settled show two-thirds higher Union Army enlistments. <br>Their influence worked through local newspapers and social clubs. Going beyond enlistment decisions, Forty-Eighters reduced their companies' desertion rate during the war. In the long run, Forty-Eighter towns were more likely to form a local chapter of the NAACP.<br><br>
description: N/A<br>
description: located the town of residence of about two-thirds of Union Army soldiers<br>.
DOI: 10.5281/zenodo.6815236
title: Data and R code for long-term study of fire and climate effects on water quality in Clear Lake, California

description: Long-term relationships between water quality, fire and climate for Clear Lake, California. Although the watershed has historically experienced frequent fire, the 2018 Mendocino Complex, which was the largest wildfire complex in state history, burned approximately 40% of the watershed, sparking concerns about drinking water quality and lake ecosystem health. This analysis spans approximately 1968-2021.
DOI: 10.5281/zenodo.6968925
title: abnormal CT findings among patients with abdominal pain in the radiology department of a teriary care center

description: These are Data were collected from the hospital system regarding demographic characteristics, past medical and surgical history, symptom description and physical examination findings, diagnosis (both initial and final), laboratory tests, CT findings, and results from other requested radiology modalities. All information was obtained after obtaining ethical approval.
DOI: 10.6084/m9.figshare.12393794
title: Data from: The role of corals on the abundance of a fish ectoparasite in the Great Barrier Reef

description: Data from: The role of corals on the abundance of a fish ectoparasite in the Great Barrier Reef
DOI: 10.6084/m9.figshare.20221362
title: Supplementary Material for: PKCι Is a Promising Prognosis Biomarker and Therapeutic Target for Pancreatic Cancer

description: <b><i>Background:</i></b> As the highest prevalent pancreatic cancer, pancreatic ductal adenocarcinoma (PDAC) ranks the 7th lethal malignancy worldwide. The late diagnosis, chemotherapeutic resistance, and high associated mortality make PDAC a dilemma facing the oncologists. Protein kinase C (PKC) enzymes have been shown to be important in different cancer progression. <b><i>Methods:</i></b> To understand the pattern of PKC enzymes in PDAC, we examined all PKC family member genes expression in PDAC and matched normal tissues. The critical role of PKCι was further investigated in different PDAC cells using cellular and molecular technology. <b><i>Results:</i></b> We found that PRKCI (PKCι) was the most significantly overexpressed PKCs in pancreatic cancer. However, little is known about its role and regulation of oncogenic signaling pathways in pancreatic cancer. In this study, we confirmed the overexpression of PKCι in PDAC, and this high expression was associated with poor prognosis of patients. We proved that knockdown of PKCι by small interfering RNA or shRNA significantly inhibited pancreatic cancer cell growth and migration or invasion. Conversely, PKCι overexpression promoted pancreatic cancer cell growth and migration. Moreover, bioinformatical and technical studies informed the participation of PKCι in regression of apoptosis in PDAC cells, which may be related to the regulation of both PI3K/AKT and Wnt/β-catenin pathways. <b><i>Conclusions:</i></b> Therefore, our results are adding more insight into the importance of PKCι in pancreatic cancer. PKCι induces pancreatic cancer progression through activation of PI3K/AKT and Wnt/β-catenin signaling pathways, which may provide a promising therapeutic target for pancreatic cancer.
DOI: 10.6084/m9.figshare.21286161
title: Supplementary Material for: Metformin can be safely used in patients exposed to contrast media: a systematic review and meta-analysis

description: Background: The published researches regarding the use of contrast media(CM) in patients taking metformin were very scarce.we conducted a systematic review and meta-analysis to explore the relationship between metformin and contrast-induced acute kidney injury(CI-AKI). Methods: We conducted comprehensive search for literature on associations between MAC and AF using the following databases: MEDLINE, PubMed, Embase, and the Web of Science. The pooled odds ratio (OR) or relative risk and the corresponding 95% confidence intervals (CIs) were calculated to assess the relationship between metformin and CI-AKI, as well as the incidence of lactic acidosis(LA). Results: 7 studies met our eligibility criteria on associations between metformin and CI-AKI, consisting of 2,325 individuals, including 279 cases of new CI-AKI patients during CM exposure. The pooled analysis demonstrated no statistically elevated risk of development CI-AKI in patients with uninterrupted use of metformin (Random-effects OR: 1.15, 95%CI: 0.70, 1.90; P =0.57). No cases of LA occurred during CM exposure. Conclusion: Metformin can be safely applied in patients with moderate renal impairment as low as eGFR ≥30 ml/min/1.73 m2 during the exposure of the CM.
DOI: 10.6084/m9.figshare.21716318
title: Supplementary Material for: The Efficacy and Safety of Treatment Outcomes for Refractory Benign Esophageal Strictures Using a Novel Combination of Needle-Knife Stricturoplasty, Balloon Dilation, and Steroid Injection (with Video)

description: <b><i>Background and Aims:</i></b> Benign esophageal strictures often present with dysphagia and can significantly impair a patient’s quality of life, especially when refractory to standard endoscopic techniques. When repeat dilations fail to achieve an adequate luminal diameter or resolve dysphagia, further therapy with needle-knife or steroid injections is needed. However, patients can still clinically fail. To manage such strictures, we employed a novel combination of all three techniques. <b><i>Methods:</i></b> Single-center case series of adult patients with benign strictures that were refractory to conventional endoscopic therapy and removable self-expanding metal stenting. Primary clinical success was defined as complete resolution in dysphagia. Secondary outcomes included periodic dilation index (frequency of dilations over the follow-up time), esophageal diameter changes, technical success, and complications. <b><i>Results:</i></b> Four patients (median age 49.7 years old, interquartile range [IQR] 30–59) underwent endoscopic therapy for complex, benign strictures using our triple therapy technique. Etiologies of the strictures included peptic strictures (<i>n</i> = 3) and an anastomotic stricture (<i>n</i> = 1). There was 100% technical success rate with no associated adverse events. There was a 50% clinical success rate, with 1 additional patient having partial improvement in dysphagia. The median diameter of the esophagus before and after triple therapy was 3.2 mm (IQR 3.5–5.5) and 12.8 mm (IQR 11.7–14.2), respectively. The periodic dilation index was 6.3 before and 1.5 after triple therapy. The median length of follow-up was 362.5 days. <b><i>Conclusion:</i></b> Triple combination therapy may be useful in benign strictures that are refractory to standard techniques. Larger studies are needed to validate these findings.
DOI: 10.17036/researchdata.aston.ac.uk.00000589
title: Ultra-wideband discrete Raman amplifier optimisation for single-span S-C-L-band coherent transmission systems
DOI: 10.17632/vhw6t2pdrg.1
title: Alao et al 2022 Trends in MTB Rifampicin Resistance in a tertiary Hospital in Nigeria

description: A four-year data of 4,526 presumptive TB cases diagnosed using GeneXpert. Data included MTB cases, Rifampicin Resistance  TBs and TB-HIV co-infection cases in a Nigerian Tertiary Hospital
DOI: 10.5281/zenodo.7303679
title: Focus-ISM for Sharp and Gentle Super-Resolved Microscopy

description: To date, the feasibility of super-resolution microscopy for imaging live and thick samples is still limited. Stimulated emission depletion (STED) microscopy requires high-intensity illumination to achieve sub-diffraction resolution, potentially introducing photodamage to live specimens. Moreover, the out-of-focus background may degrade the signal stemming from the focal plane. Here, we propose a new method to mitigate these limitations without drawbacks. First, we enhanced a STED microscope with a detector array, enabling image scanning microscopy (ISM). Therefore, we implemented STED-ISM, a method that exploits the working principle of ISM to reduce the depletion intensity and achieve a target resolution. Later, we developed Focus-ISM, a strategy to improve the optical sectioning and remove the background of any ISM-based imaging technique, with or without a STED beam. The proposed approach requires minimal architectural changes to a conventional microscope but provides substantial advantages for live and thick sample imaging.
DOI: 10.5281/zenodo.4603598
title: CENP-F-dependent DRP1 function regulates APC/C activity during oocyte meiosis I

description: The raw data of MALD/MS after cenp-f CO-IP
DOI: 10.15151/esrf-es-1023337436
title: Study on BSA

description: Screening of grids to find good conditions
DOI: 10.15151/esrf-es-1005347817
title: 3D strain and orientation mapping of an aluminum single crystal during in situ tensile deformation

description: Dislocations and how they self-organize with increasing deformation into 3D structures of dislocation boundaries have, under current understanding, been labeled as a multi-scale process leading to work hardening. In this experiment we will study this self-ogranizing under in situ tensile deformation.
DOI: 10.17632/9vnztvcrcp.1
title: Climate induced change in spatial distribution of bee forage species in Southwest Western Australia

description: Species distribution models (SDM) for thirty key bee forage species targetted by beekeepers in Western Australia were obtained for current and a moderate emission climate scenario using the presence-only Maxent algorithm. Species occurrences are included as a Comma Separated Value (CSV) files with species name, latitude and longitude coordinates. Maxent outputs are formatted as GeoTiff files and included in folders named as respective scenario (i.e. Baseline and Future). Maxent outputs were converted to presence absence grids using maximum training sensitivity plus specificity threshold. Change in geographic distribution distribution between baseline and future was calculated for each bee forage species using QGIS. Tablular data containing Names of the study species, sample size, Maxent results, magnitude and the direction of species range shift is included as pdf file.
DOI: 10.17632/frhjtk3jf9.1
title: Original membranes Kataura-Sedlackova et al Dev Cell

description: Immunoblotting and RT-PCR original scan.
DOI: 10.4121/20261392
title: Analysis results of the paper baseLess: Lightweight detection of sequences in raw MinION data

description: BaseLess reduces your MinION sequencing device to a simple species detector. As a trade-off, it runs on inexpensive computational hardware like single-board computers. The baseLess code base can be found here. All data and analysis results described in the paper describing baseLess are stored in this file.
DOI: 10.4121/20261392.v2
title: Analysis results of the paper baseLess: Lightweight detection of sequences in raw MinION data

description: BaseLess reduces your MinION sequencing device to a simple species detector. As a trade-off, it runs on inexpensive computational hardware like single-board computers. The baseLess code base can be found here. All data and analysis results described in the paper describing baseLess are stored in this file.