Contributors: Melody Esmaeili, Shelby Blythe, Kai Zhang, John Tobias, Jing Yang, Peter Klein
... The hypothesis being tested is that loss of competence to respond to inductive signals is mediated by loss of chromatin accessibility. This dataset describes analysis of an Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-Seq) approach to evaluate genome-wide changes in chromatin accessibility in Xenopus laevis. ATAC-seq identifies ~70,000 accessible regions at early and late gastrula stage; normalized read counts from 3 biological replicates at early (stage 10) and late (stage 12) gastrula stage are presented here. Genome wide distribution of accessible peaks, list of promoters with changes in accessibility between stage 10 and stage 12, comparison with previously published p300 ChIP-seq data to identify putative cis-regulatory modules (pCRMs), comparison of promoter accessibility and gene expression, identification of transcription factor binding motifs associated with pCRMs, and functional gene annotation analyses are presented. Promoters for dorsal genes (Sia and Xnr3) that have lost competence to respond to Wnt signaling are not accessible at the early gastrula stage but competence can be maintained by inhibiting HDACs and increasing histone acetylation at these promoters. Promoters for regulators of mesoderm and neural crest induction maintain accessibility throughout gastrulation despite the loss of competence to respond to their respective inductive signals, suggesting context-dependent regulation of competence. However, 279 promoters lose accessibility at stage 12 and are associated with transcription factors that regulate early development. Accessibility at ≥ 1800 promoter-distal pCRMs is also reduced by the end the gastrula stage, and these pCRMs are frequently near promoters for transcription factors that regulate early development, including homeobox genes. Motif analysis (HOMER) shows marked enrichment for binding sites for pluripotency factors of the Sox, Oct, and KLF transcription factor families, as well as for Fox, Grainyhead-like, and Zic transcription factors.
Instances for “A Branch-and-Cut Approach for the Weighted Target Set Selection Problem on Social Networks”
Contributors: S. Raghavan, Rui Zhang
... We provide the instances used in the paper “A Branch-and-Cut Approach for the Weighted Target Set Selection Problem on Social Networks”, by S. Raghavan and Rui Zhang, published in the INFORMS Journal on Optimization (https://doi.org/10.1287/ijoo.2019.0012) . This repository contains the 260 instances used in the paper. All the instances used in the paper are provided in a compressed archive. The accompanying data is contained in the following file: --InstancesWTSS.zip Description: There are two main folders: One called "Real-World Graphs" contains 180 instances based on real-world graphs. The other one called "Simulated Graphs" contains all instances based on simulated graphs. Within the Simulated Graphs folder, 50 200-node instances are in the "200 Nodes" folder and 30 large instances are in the "Large" folder. For each text file, there are m+2 lines. The first m lines are the edges in the graphs. Nodes are labeled from 0 to n where n is the largest number in the first m lines. The (m+1)th line contains the weight (b) for each node. The (m+2)th line contains the threshold value (g) for each node. The excel file “WTSS_Results.xlsx” reports, for each instance, the upper and lower bounds obtained in the paper.
Contributors: Sergio Valadez-Godínez, Juan Humberto Sossa Azuela, Raúl Santiago-Montero
... This data contains the Supplementary material for the paper "On the Accuracy and Computational Cost of Spiking Neuron Implementation." This is divided into five folders: 1) Source code, 2) Raw data, 3) Calculations, 4) Tables, and 5) Figures. The Source code folder has the script files written in Python 3.7.3. There are two sub-folders inside this folder separating the scripts into constant and random input current tests, respectively. Each sub-folder has a separate Python script that performs a benchmark test for each Spiking Neuron (SN) model. The Raw data folder collects the data generated by executing the scripts in the Source code folder and by following the instructions in the Testing procedure section of the paper. This stores the raw data for several SNs, firing frequencies, and input currents. This folder has a sub-folder with several files recording the random input currents used in the benchmark tests. The Raw data folder also has two sub-folders with the benchmark test results, each for a specific stimulation current type. The Benchmark test sub-folders give the CPU execution time, the SCF (Spike Coincidence Factor), the VCF (Voltage Coincidence Factor), the last spike displacement, and the firing frequency for each Numerical Method (NM) and time step. Other four sub-folders are containing the spike-timing and voltage time course data. These data are separated into constant and random input currents and NM and time step. The Calculations folder gives two files in .xlsx format with several estimates used in the paper. These files collect the CPU time, SCF, VCF, last spike displacement, and firing frequency from Raw data folder and compute the CCF (Computational Cost Factor) and GPF (Global Performance Factor) for several SNs and firing frequencies. Also, these files calculate the average and increment/decrement percent in FLOPS, CPU time, CCF, SCF, VCF, last spike displacement, and GPF among several SNs and NMs. Furthermore, these files examine the balanced, lower limit, upper limit, Skocik-Long, and Izhikevich configurations mentioned in the paper. Fourth and fifth folders contain the supplementary tables and figures, respectively, referenced in the article.
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Contributors: Kazimierz Becek
... The air temperature and light intensity were recorded in tropical rainforest of Brunei Darussalam, at 20’ interval in 2017. HOBO Pendant® data loggers were attached to tree trunks approx. 2 m above ground. The data can be used to study various microclimatic and ecological characteristics of tropical rainforests in Brunei and other locations.
Contributors: Qiankun Liu, Jingang Jiang, Changwei Jing, Zhong Liu, Jiaguo Qi
... In this paper, a new, alternative, multi-scale, multi-pollution source waste load allocation (WLA) system was developed, with a goal to produce optimal, fair quota allocations at multiple scales. The new WLA system integrates multi-constrained environmental Gini coefficients (EGCs) and Delphi-analytic hierarchy process (Delphi-AHP) optimization models to achieve the stated goal. This dataset consists of the raw data and the source code of models (The multi-constrained environmental Gini coefficients and Delphi-analytic hierarchy process optimization models). The source code of the multi-constrained EGCs and Delphi-AHP models was used to run the program in MATLAB environment to allocate waste load reduction quotas at both the regional scale and the site-specific scale with multiple pollution sources. The raw data mainly consists of the following two parts: (1) The shp files of various geographic information data, which was used to depicture the administrative divisions, pollution source distribution, geographical characteristics and patterns of Xian-jiang watershed; (2) The basic data includes the statistical yearbook data of villages and towns in Ningbo city, the various indicator data using to calculate the weights at criteria level and decision-making level, the contribution coefficients, and the EGC values of the three pollutants. On the basis of these data, a new, alternative, multi-scale, multi-sector optimal WLA framework was developed. The new scheme provides decision-makers critical information (i.e., the best compromise solutions of WLA) and practical guidance as they address the related water pollution control. The results, in comparison with existing practices by the local governments, suggested that the pollution discharge quota at regional scale is much fairer than the existing WLA and, even have some environmental economic benefits at pollutant source scale after optimal WLA. Some important conclusions had been found: 1) Reductions and proportions of pollutants at regional scale are significantly associated with the region’s actual socioeconomic development modes. 2）There are certain characteristics that high-reduced pollution sources tend to share (which are listed in the article). The sources with the above features should be the top priorities in the reduction of removals. 3）Most previous studies reported primarily on the WLA of removals among point sources pollution. Conversely, we found that the industrial pollution source should be the last option for reduction from an environmental-economic benefit perspective. Instead, the often overlooked types, such as agricultural non-point source and domestic sources, deserve more attention, especially in extensive rural areas.
Dataset for "Future risks of tsunami-induced seawater intrusion into unconfined coastal aquifers: insights from numerical simulations at Niijima Island, Japan"
Contributors: Jiaqi Liu
... This dataset includes: Geological map information of Niijima Island Information of Nankai earthquake and tsunami scenarios; Simulation parameters; Rainfall recharge setting;
Contributors: Ryan Watkins
... Version 1.0, September 9, 2019 Purpose: Created as part of a project funded by NASA’S Lunar Data Analysis Program (LDAP), the purpose of this dataset is to provide locations and diameters of boulders around small, young impact craters on the Moon. These boulder counts were conducted as part of a study aimed at determining regolith production rates and assessing landing site hazards, as discussed in the associated publications. Researchers are encouraged to read the publications and data description document to understand how the data was acquired and used. This database contains boulder distributions around small (< 1 km), young (< 200 Ma) lunar impact craters located near spacecraft landing sites. The most up-to-date database contains boulder diameters and coordinates for counts around Surveyor (Apollo 12), Cone (Apollo 14), North Ray (Apollo 16), South Ray (Apollo 16), Camelot (Apollo 17), and Zi Wei (Chang’e-3) craters. Boulders were manually identified and measured on Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images (Robinson et al., 2010) at scales of ~0.5-2 m/pixel. LROC NAC images allow for boulders ~1-2m in size and larger to be identified and measured. The tools for measuring boulders were CraterTools (Kneissl et al., 2011) and Crater Helper Tools (Nava, 2011), both developed for the ArcMap GIS platform. These boulder distributions are being used to understand boulder degradation rates on the lunar surface, and to assess landing site hazards for future surface missions to the Moon. This dataset is being archived in Mendeley Data and at the Planetary Data System (PDS) Cartography and Imaging Node for use in future boulder distribution and landing hazard studies. Future boulder counts and any refinements to existing measurements will be uploaded into subsequent versions of this dataset here and at the PDS IMG Annex: https://astrogeology.usgs.gov/search/map/Moon/Research/Regolith/lunar_boulder_data_bundle
The dataset for validation of factors affecting pre-service teachers’ use of ICT during teaching practices: Indonesian context
Contributors: akhmad habibi, Farrah Dina Yusop, Rafiza Razak
... This dataset describes two variables, technological pedagogical and content knowledge (TPACK) and theory of planned of behavior (TPB), that may affect pre-service teachers’ use of ICT (UICT) during teaching practices. Primary data is retrieved from 287 Indonesian pre-service teachers. The examination of the data was mainly conducted through the procedures of content validity index (CVI) and exploratory factor analysis (EFA).
Contributors: Louise Logsdon
... Estes arquivos compõem o "Instrumental de apoio ao projeto de moradias sociais" que alimentam o modelo de processo de projeto proposto pela autora em sua tese de doutorado: LOGSDON, Louise. Instrumental de apoio ao projeto de moradias sociais. 2019. Tese (Doutorado) - Arquitetura, Urbanismo e Tecnologia, Instituto de Arquitetura e Urbanismo, Universidade de São Paulo, São Carlos, 2019.
Extending the Ability of Near-Infrared Images to Monitor Small River Discharge on the Northeastern Tibetan Plateau (2018WR023808)
Contributors: li haojie, Hongyi Li
... Data accessing (2018WR023808) Note: All data used in this study are provided in this repository, including daily gauge discharge data, drawing data and calculations code. Please refer to this paper for details on how to use the data. 1. The all figures of this paper are provided. The vector data used in Figure 1 and Figure 4 are uploaded to separate folders (shp). 2. The data for drawing in this study are shared in data attachment file (excel). 3. Gauged discharge data The daily gauge discharge data used in this study are shared in the data attachment file (excel). 4. Landsat images and code The Landsat image sets and calculation code used in this study are available on the Google Earth Engine platform. The links of image sets and sample code as below. TM https://developers.google.com/earth-engine/datasets/catalog/LANDSAT_LT05_C01_T1 ETM https://developers.google.com/earth-engine/datasets/catalog/LANDSAT_LE07_C01_T1 OLI https://developers.google.com/earth-engine/datasets/catalog/LANDSAT_LC8_L1T Calculation code https://code.earthengine.google.com/2254187574dedb2c0b2e9a7fc1832eb2