cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/xm4nxzdxb2.1
title: Understanding biological carbon pump in the central Arabian Sea using phytoplankton biomarkers and diatom frustules from surface sediments.

description: The Central Arabian Sea, a tropical ocean basin, is impacted by monsoon winds that lead to high biological productivity in surface waters and form an oxygen minimum zone (OMZ) at intermediate depth. The present study aimed to understand the pattern of biological carbon pump driven by different phytoplankton groups along the central Arabians Sea, an area strongly impacted by monsoon wind forcings. The surface sediment samples from 5 locations along the central Arabian Sea were collected from 21 ° N to 11 ° N (at 2 ° intervals) along 64 ° E. These sediments accumulate materials originating from surface waters and can be used to understand the surface processes including the contributions of various phytoplankton groups in sinking materials. Bulk sediment parameters (total organic carbon, inorganic carbon, total nitrogen) were analyzed along with plankton biomarkers (sterols and alkenone) and sea surface temperature (SST) proxy using alkenone. Additionally, the frustules of diatoms that are siliceous phytoplankton shells, were also measured from the same sediments. We noticed a north-south gradient in all parameters and the biological proxies showed more organic matter preservation from larger diatoms in the north. Whereas, lower organic matter contributed by smaller phytoplankton and zooplankton were found in the south. These trends were attributed to ocean-atmospheric processes and oxygen availability in the water column.
DOI: 10.17632/fnr7vmpbz9.1
title: Tanaka et al., Immunoblotting Original Data

description: Immunoblotting original data for Tanaka, Morozumi et al. paper (2023).
DOI: 10.17632/6c2sbrfycw.1
title: SAMHD1 Attenuates Acute Inflammation by Maintaining Mitochondrial Function in Macrophages via Interaction with VDAC1

description: Abstract: Background: Over-activation of Toll-like receptor 4 (TLR4) is the key mechanism in Gram-negative bacterial infection-induced sepsis. SAM and HD domain-containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) inhibits multiple virus-es , but whether it plays a role during bacterial invasion remains unelucidated. Methods: Monocyte-macrophage specific Samhd1 knockout (Samhd1−/−) mice and Samhd1−/− macrophage cell line RAW264.7 were constructed and used as research models to evaluate the role of SAMHD1 in TLR4-activated inflammation. Results: In vivo , LPS-challenged Samhd1−/− mice showed higher serum inflammatory factors, accompanied with more severe inflammation infiltration and lower survival rate. In vitro, Samhd1−/− peritoneal macrophages had more activated TLR4 pathway upon LPS-stimulation, accompanied with mitochondrial depolarization and dysfunction and a higher tendency to be M1-polarized. These results could be rescued by overexpressing full-length wild-type SAMHD1 or its phospho-mimetic T634D mutant into Samhd1−/− RAW264.7 cells, whereas the mutants, dNTP hydrolase-function-deprived H238A and phos-pho-ablative T634A, did not exert the same effect. Lastly, co-IP and immunofluorescence assays confirmed that SAMHD1 interacted with an outer mitochondrial membrane-localized protein, voltage-dependent anion channel-1 (VDAC1). Conclusion: SAMHD1 inhibits TLR4-induced acute inflammation and M1 polarization of macrophages by interacting with VDAC1 and maintaining mitochondria function, which outlines a novel regulatory mechanism of TLR signaling upon LPS stimulation.
DOI: 10.17632/782fzwyc2d.1
title: MatP local enrichment delays segregation independently of tetramer formation and septal anchoring in Vibrio cholerae

description: Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). The choreography of segregation of the replication terminus of ChrI and ChrII, TerI and TerII, determines when and where cell division occurs. ChrI encodes for a homolog of Escherichia coli MatP. Using a combination of deep sequencing and fluorescence microscopy techniques, we show that MatP structures TerI and TerII into macrodomains, targets them to mid-cell in the course of replication and delays their segregation, demonstrating that ChrII behaves as a bona fide chromosome. We further show that the extent of the segregation delay mediated by MatP depends on the number and local density of matS sites, and is independent of its assembly into tetramers and any interaction with a cell division protein, in contrast to what has been observed in E. coli.
DOI: 10.17632/2szrhfrjjj.2
title: 1500-yr records of aquatic production, lake anoxia, and sediment Fe and P fractions in maar Lake Xiaolongwan, northeastern China

description: This Excel file contains the Data used to calculate and draw the figures for the article of Lake Xiaolongwan. https://doi.org/10.1016/j.ancene.2024.100442
DOI: 10.17632/2szrhfrjjj.1
title: 1500-yr records of aquatic production, lake anoxia, and sediment Fe and P fractions in maar Lake Xiaolongwan, northeastern China

description: This Excel file contains the Data used to calculate and draw the figures for the article of Lake Xiaolongwan. https://doi.org/10.1016/j.ancene.2024.100442
DOI: 10.17632/ps6245rd59.1
title: Raw dataset for PNAS (Itoh et al, 2024)

description: Raw dataset for the article in PNAS "Lack of evidence for direct ligand-gated ion channel activity of GluD receptors", by Masayuki Itoh, Laura Piotb, Laetitia Mony, Pierre Paoletti, and Michisuke Yuzaki.
DOI: 10.17632/5f7g6gbdbx.2
title: An ultra-sensitive optical H2S sensor based on thermal conversion combined with UV-DOAS: Dynamic detection from ppm to ppb level (Experimental data)

description: This study provides detailed experimental original data, which can be analyzed by the reader in relation to the manuscript.
DOI: 10.17632/txvdm8pbwf.1
title: LDHU3_14.1940

description: Mitochondrial pyruvate carrier protein 2 | MPC2; Leishmania donovani (HU3 strain)
DOI: 10.17632/79vsm7nxpx.1
title: LDHU3_14.1890

description: Protein kinase; Leishmania donovani (HU3 strain)
DOI: 10.17632/nstgdfbxsh.1
title: Influence of agronomic parameters and storage parameters on the frying color of French fry potatoes (solanum tuberosum L.)

description: This dataset was used to calculate the regressions presented in the publication: "Influence of agronomic parameters and storage parameters on the frying color of French fry potatoes (solanum tuberosum L.)".
Data were created during a two year field trial at two locations in Bavaria, Southern Germany. In the trials two nitrogen fertilization rates as well as three harvest dates per location were tested. The so produced material was subsequently stored at two storage temperatures (7.5°C and 6.0°C). Quality sampling in terms of frying color was done monthly with a 20 tuber sample from December to March. The baking color assessment was done with an optoelectronic method, which expresses frying color as R/G-ratio after the 3-Minute Baking test. Additionally reducing sugar content was assessed encymatically for selected samples.
DOI: 10.17632/rbnr72g4vc.1
title: LDHU3_14.1950

description: mt-LAF21 | Mitoribosomal LSU assembly factor 21; Leishmania donovani (HU3 strain)
DOI: 10.17632/ggmjwhymmf.3
title: The first complete mitochondrial genome data of the Afghan pika Ochotona rufescens (Lagomorpha, Ochotonidae), near the type locality

description: Mitogenome sequence is assembled using high throughput sequencing data for two individuals of Ochotona rufescens rufescens (FMNH102840 & FMNH102841). Genomic DNA was extracted following the modified phenol-chloroform extraction protocol (Roycroft et al. 2021; 2022). double-indexed and double-stranded library preparation; mitogenome enrichment with myBaits Custom 20-40K (Daicel Arbour Biosciences, USA); sequencing: Illumina NextSeq 550 platform; mitogenome assembled de novo in NOVOPlasty v.4.3.1 and annotated in MITOS2 web server. The circular mitogenome map was drawn using OGDRAW. Phylogenetic relationship was inferred using IQ-TREE.The mitogenome The mitogenome data are available in the GenBank under the accession number ON859136 (https://www.ncbi.nlm.nih.gov/nuccore/ON859136) & ON859137 (https://www.ncbi.nlm.nih.gov/nuccore/ON859137). Raw sequence data are available in Sequence Read Archive [BioProject: PRJNA1020817, BioSample: SAMN37529232 (individual FMNH102840) SAMN37529233 (individual FMNH102841); doi: https://www.ncbi.nlm.nih.gov/biosample/37529232; https://www.ncbi.nlm.nih.gov/biosample/37529233.]
DOI: 10.17632/sxb88y49jw.1
title: Ceruloplasmin variants might have different effects in different iron overload disorders.

description: Raw images and dataset of densitometric analysis used for the generation of the figure 1 of the paper by Pelucchi S, Ravasi G, Piperno A. Ceruloplasmin variants might have different effects in different iron overload disorders. J Hepatol. 2021, 75:1003-1004. doi: 10.1016/j.jhep.2021.05.005. 
This paper is associated to the project "Blood-cerebrospinal fluid-barrie defect as gate for targeting by liver-directed ceruloplasmin gene replacement therapy in the rare disease aceruloplasminemia" supported by Italian Ministry of Health, with the grant RF-2018-1236671 to Massimo ALESSIO as principal investigator at the IRCCS-San Raffaele Hospital, Milano, Italy.
DOI: 10.17632/b54ktpthrp.1
title: Dataset on climate distance for trade analyses

description: This folder contains datasets (in dta format) and the STATA do-file that replicate results contained in:
Bozzola, M., Lamonaca, E., & Santeramo, F. G. (2023). Impacts of climate change on global agri-food trade. Ecological Indicators, 154, 110680. https://doi.org/10.1016/j.ecolind.2023.110680
Lamonaca, E., Bozzola, M., & Santeramo, F. G. (2024). Climate distance and bilateral trade. Economics Letters, 237, 111624. https://doi.org/10.1016/j.econlet.2024.111624

The datasets contains:
(i) time-varying measures of long-run climate conditions of countries
(ii) the difference in long-run climate conditions between country-pairs, here defined as Climate Distance.
The sample includes twenty economies accounting for two-third of global agri-food exports and representatives of different prevailing climates, observed over the period 1996-2015.

Researchers, practitioners and policy makers interested in the evaluation of the economic impacts of climate changes may use climate distances for further analyses.
DOI: 10.17632/625nt7yx8c.3
title: Mangrove Ecosystem Services (MES) in Peru and Brazil

description: Dataset of scientific papers and policy papers on mangrove ecosystem services in Marine Protected Areas (MPAs) from Peru and Brazil.
Project: https://tinyurl.com/mesperubrazil
DOI: 10.17632/5n282f2kxb.2
title: Data for "Occupational exposure assessment for airborne respiratory viruses in outpatient medical clinics"

description: These files comprise the data used in the analyses reported in "Occupational exposure assessment for airborne respiratory viruses in outpatient medical clinics," submitted to the journal Aerosol Science and Technology in April 2024.
DOI: 10.17632/47tpmxhwg4.1
title: LINF_140005200

description: protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/kyf64rk6v7.1
title: LINF_130020700

description: AAA+ ATPase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/sm9t5s63rf.2
title: Dataset for "Counterintuitive Proposals for Trans-boundary Ecological Compensation Under ‘No Net Loss’ Biodiversity Policy"

description: The data is collected through a survey conducted in Denmark, Spain, and Ghana. Data is provided in both DTA and CSV format

Related Publication:
--------------------
Title: "Counterintuitive Proposals for Trans-boundary Ecological Compensation Under ‘No Net Loss’ Biodiversity Policy"
Authors: Joseph William Bull, Anna Lou Abatayo, and Niels Strange
Journal: Ecological Economics 142 (2019), pp. 185-193
 https://doi.org/10.1016/j.ecolecon.2017.06.010

Coverage:
---------
Spatial coverage:
The data was obtained from a survey in three countries: Denmark, Spain, and Ghana. Surveys in Denmark were ran at the University of Copenhagen, in Spain were ran at Pompeu Fabra University, and in Ghana at the University of Ghana. 

Temporal coverage:
The surveys were carried out in April 2016.


This dataset contains the following files:
 - A ReadMe document ("!ReadMe.txt")
 - A codebook ("~Codebook.txt")
 - One Stata DTA file ("data_wide.dta")
 - One CSV file ("data_wide.csv")
 - Four Stata Do-Files ("00 RunMe", "01 WideToLong", "02 SumStat", "03 tTest", "04Regression")

Methods, materials and software:
Stata/SE 13.2 for Apple
DOI: 10.15125/bath-01459
title: Dataset for "Low-Cost, Multi-Sensor Non-Destructive Banana Ripeness Estimation Using Machine Learning"

description: Processed datasets containing all numerical sensor data used for training and testing the ML algorithms discussed in the associated publication. Data from temperature, pressure, humidity, VOC and spectral sensors is included. The data is split into four datasets (as defined in Table V of the associated publication), each containing a different combination of sensor data and each subdivided into data ("x") and labels ("y") for both testing and training data. 30% of the cleaned data is randomly taken to form the testing data, while the remaining 70% forms the training data. Each data subset is balanced, as discussed in section 3.E.3 in the associated publication.
description: The data collection methodology can be found in the associated publication.
description: The data preparation & processing methodology can be found in the associated publication.
description: The datasets were created with Python 3.10.13, with libraries Numpy 1.26.0 and Pandas 2.1.2. The data is saved in CSV format and does not require specialist software to read.
description: Data organisation and encoding is described in the associated ReadMe files.
DOI: 10.17632/sm9t5s63rf.1
title: Dataset for "Counterintuitive Proposals for Trans-boundary Ecological Compensation Under ‘No Net Loss’ Biodiversity Policy"

description: The data is collected through a survey conducted in Denmark, Spain, and Ghana. 

Related Publication:
--------------------
Title: "Counterintuitive Proposals for Trans-boundary Ecological Compensation Under ‘No Net Loss’ Biodiversity Policy"
Authors: Joseph William Bull, Anna Lou Abatayo, and Niels Strange
Journal: Ecological Economics 142 (2019), pp. 185-193
 https://doi.org/10.1016/j.ecolecon.2017.06.010

Coverage:
---------
Spatial coverage:
The data was obtained from a survey in three countries: Denmark, Spain, and Ghana. Surveys in Denmark were ran at the University of Copenhagen, in Spain were ran at Pompeu Fabra University, and in Ghana at the University of Ghana. 

Temporal coverage:
The surveys were carried out in April 2016.


This dataset contains the following files:
 - A ReadMe document ("!ReadMe.txt")
 - A codebook ("~Codebook.txt")
 - One Stata DTA file ("data_wide.dta")
 - Four Stata Do-Files ("00 RunMe", "01 WideToLong", "02 SumStat", "03 tTest", "04Regression")

Methods, materials and software:
Stata/SE 13.2 for Apple
DOI: 10.17632/tkk5pdswty.2
title: Minimizing the Cost of Leveraging Influencers in Social Networks: IP and CP Approaches - Complementary Data

description: This dataset contains complementary data to the paper "Minimizing the Cost of Leveraging Influencers in Social Networks: IP and CP Approaches" [1], which studies integer/constraint programming formulations for the Least Cost Directed Perfect Awareness Problem, an NP-hard optimization problem that arises in the context of influence marketing. Regarding the computational experiments conducted in the paper, we make available:

- Two sets of instances;
- The best known attained solutions;
- The source code;
- An appendix with additional details about the results.

The first input set includes 300 synthetic instances composed of graphs that resemble real-world social networks [2]. The second set consists of 14 instances built from online interactions crawled from X (formerly known as Twitter) [3].

The directories "synthetic_instances" and "x_instances" contain files that describe both sets of instances. The first two lines of each file contain:




where and are the number of vertices and edges in the graph. Each of the next lines contains:

 

where identifies a vertex while and are the cost and threshold associated to that vertex. Each of the remaining lines contains:

 

where and identify an ordered pair of vertices that determines a directed edge with weight .

The directories "solutions_for_synthetic_instances" and "solutions_for_x_instances" contain files that describe the best known solutions for both sets of instances. The first line of each file contains:



where is the number of vertices in the solution. Each of the next lines contains:



where identifies a seed vertex. The last line contains:



where is the solution cost.

The directory "source_code" contains the implementations of the mathematical models studied in the paper.

Lastly, the file "appendix.pdf" presents details of the results reported in the paper [1].

This work was supported by grants from Santander Bank, Brazil, Brazilian National Council for Scientific and Technological Development (CNPq), Brazil, and São Paulo Research Foundation (FAPESP), Brazil.

Caveat: the opinions, hypotheses and conclusions or recommendations expressed in this material are the responsibility of the authors and do not necessarily reflect the views of Santander, CNPq or FAPESP.


References

[1] F. C. Pereira, P. J. de Rezende and T. Yunes. Minimizing the Cost of Leveraging Influencers in Social Networks: IP and CP Approaches. Submitted. 2023.

[2] F. C. Pereira, P. J. de Rezende. The Least Cost Directed Perfect Awareness Problem: complexity, algorithms and computations. Online Social Networks and Media, 37-38, 2023.

[3] C. Schweimer, C. Gfrerer, F. Lugstein, D. Pape, J. A. Velimsky, R. Elsässer, and B. C. Geiger. Generating simple directed social network graphs for information spreading. In Proceedings of the ACM Web Conference 2022, WWW ’22, pages 1475–1485, 2022.
DOI: 10.17632/8f8fsgszjv.1
title: Veracruz-Boca del Rio, Ver. Mexico ambient noise microtremor

description: The data contained herein are the result of different field campaigns, whose first objective was to collect environmental noise measurements (microtremors) using broadband seismometers of the GURALP brand, model 6TD, within the Veracruz-Bocal del Río conurbation, in the state of Veracruz, Mexico.
In addition, some of the dynamic characteristics of the soils could be modeled by means of one-dimensional surface stratigraphic models, such as: layer depth, P-wave velocity, S-wave velocity and density. The purpose of this was to build a soil model that could be used to convolve real earthquake records and to know the site effects of this zone.
To adapt the signal, the various tools that the GEOPSY program has for this purpose were used. Likewise, its DINVER module was used to obtain the stratigraphic profiles sought. A good adjustment was taken as the one that best reproduced the location and amplification of the theoretical fundamental frequency of the soil being modeled.
DOI: 10.17632/y79c4hpfdc.1
title: A Dataset of Mass Timber and Hybrid Mass Timber Floor Structure Designs, Including Sizing, Self-Weight, and Embodied Carbon Data

description: The design of mass timber structures affects performance outcomes such as embodied carbon (EC), floor system depth, and self-weight. To better understand the relationships between design decisions and performance outcomes, a parametric modeling approach was followed to generate a dataset for five mass timber and hybrid mass timber structural floor system types. The model consists of both a Grasshopper model interfaced with Rhino and a spreadsheet-based model, which are used to generate, size, and evaluate structural floor system designs for system depth, self-weight, and EC. The Grasshopper model is used to generate designs and perform structural sizing of the floor system elements. The spreadsheet model is used to calculate self-weight of the components of each design from the element sizing outputs. Self-weight is multiplied by each material's EC factor to estimate the total EC of the design. The modeling process and resulting dataset are part of a larger research effort to develop early-stage design guidance for practitioners. The dataset may be used by others to study trends amongst design objectives for mass timber floors, or to extract the structural element sizing data for use with customized project-specific EC data.

Two files are provided. The csv file includes only the final data values based on set assumed material EC factors. The xlsx file includes a tab which allows the user to enter custom material EC factors. The data tab automatically re-calculates the EC values for each design based on the user-entered material factors. A "Read Me" tab includes additional information and instructions for how the spreadsheet may be modified. Only blue cells in the "Material EC" tab should be edited. The xlsx file also maintains the original formulas used in post-processing additional design data following the design sizing output from the Grasshopper model. After customizing material EC factors in the xlsx file, it is recommended that a copy of the "Data" tab be saved as a csv file to reduce the file size to a more manageable size.
DOI: 10.17632/ztj2jsdyvb.1
title: Mobility and Kinematic Analysis of a 4R1H Mechanism. MATLAB Files

description: This dataset presents MATLAB scripts that perform mobility and kinematic analysis of a 1-DOF 4R1H mechanism, introduced in paper doi.org/10.5545/sv-jme.2018.5965. The corresponding paper describing the applied algorithms will be presented on the 16th IFToMM World Congress (WC2023) and published in the "Mechanism and Machine Science" series. Please check the list of works at https://orcid.org/0000-0002-3928-5440.

The dataset includes two scripts:
1. Script "mobility.m" finds a twist system of the output link of the considered mechanism.
2. Script "kinematics.m" calculates the output link motion (displacements, velocities, and accelerations) for the given input motion.
DOI: 10.17632/k6gbvbkg5z.1
title: LINF_140005800

description: DnaJ domain-containing protein | JDP76 | J76; Leishmania infantum (strain JPCM5)
DOI: 10.17632/pb688kt2x4.1
title: LINF_140007000

description: DUF4201 domain-containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/pv5294yzh2.1
title: LINF_140007500

description: Translocon-associated protein (TRAP) subunit gamma; Leishmania infantum (strain JPCM5)
DOI: 10.17632/nvrkj7cygx.1
title: Molecular Modeling Workflow for Optimizing Oxidized Graphene Quantum Dot and Epoxy Nanocomposite for Enhanced Mechanical Properties

description: Graphene quantum dots (GQDs) are the smallest carbon-based filler known to promote more intimate contact with the matrix. Their small size enables simultaneous enhancement of stiffness, strength, and toughness. Additionally, the functionalization of these materials enables other supramolecular interactions like hydrogen bonding that improve the interfacial interaction with the matrix. This dataset provides a molecular dynamics (MD) framework to model a single functionalized GQD embedded in a bisphenol-F epoxy matrix and the effective mechanical response of the nanocomposite. Ten unique chemistries were developed with different oxygen-based functional groups that capture the effect of oxidized GQD on the mechanical properties of the epoxy. Uniaxial strain simulations revealed that a maximum strength gain of 56% and stiffness gain of 18% was computed by the oxidized GQD-epoxy nanocomposite.
DOI: 10.17632/848yvpr3zj.1
title: Belkevich AE, MCB, 2023, Supplemental

description: Supplemental data for Belkevich AE, MCB, 2023 accepted manuscript "Distinct interaction modes for the eukaryotic RNA polymerase alpha-like subunits" containing uncropped protein gel and western blot images.