cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1289323.v7
title: iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach

description: Information about the interactions of drug compounds with proteins in cellular networking is very important for drug development. Unfortunately, all the existing predictors for identifying drug–protein interactions were trained by a skewed benchmark data-set where the number of non-interactive drug–protein pairs is overwhelmingly larger than that of the interactive ones. Using this kind of highly unbalanced benchmark data-set to train predictors would lead to the outcome that many interactive drug–protein pairs might be mispredicted as non-interactive. Since the minority interactive pairs often contain the most important information for drug design, it is necessary to minimize this kind of misprediction. In this study, we adopted the neighborhood cleaning rule and synthetic minority over-sampling technique to treat the skewed benchmark datasets and balance the positive and negative subsets. The new benchmark datasets thus obtained are called the optimized benchmark datasets, based on which a new predictor called iDrug-Target was developed that contains four sub-predictors: iDrug-GPCR, iDrug-Chl, iDrug-Ezy, and iDrug-NR, specialized for identifying the interactions of drug compounds with GPCRs (G-protein-coupled receptors), ion channels, enzymes, and NR (nuclear receptors), respectively. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed the existing ones for the same purpose. To maximize users’ convenience, a public accessible Web server for iDrug-Target has been established at http://www.jci-bioinfo.cn/iDrug-Target/, by which users can easily get their desired results. It has not escaped our notice that the aforementioned strategy can be widely used in many other areas as well.
DOI: 10.6084/m9.figshare.1289323.v6
title: iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach

description: Information about the interactions of drug compounds with proteins in cellular networking is very important for drug development. Unfortunately, all the existing predictors for identifying drug–protein interactions were trained by a skewed benchmark data-set where the number of non-interactive drug–protein pairs is overwhelmingly larger than that of the interactive ones. Using this kind of highly unbalanced benchmark data-set to train predictors would lead to the outcome that many interactive drug–protein pairs might be mispredicted as non-interactive. Since the minority interactive pairs often contain the most important information for drug design, it is necessary to minimize this kind of misprediction. In this study, we adopted the neighborhood cleaning rule and synthetic minority over-sampling technique to treat the skewed benchmark datasets and balance the positive and negative subsets. The new benchmark datasets thus obtained are called the optimized benchmark datasets, based on which a new predictor called iDrug-Target was developed that contains four sub-predictors: iDrug-GPCR, iDrug-Chl, iDrug-Ezy, and iDrug-NR, specialized for identifying the interactions of drug compounds with GPCRs (G-protein-coupled receptors), ion channels, enzymes, and NR (nuclear receptors), respectively. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed the existing ones for the same purpose. To maximize users’ convenience, a public accessible Web server for iDrug-Target has been established at http://www.jci-bioinfo.cn/iDrug-Target/, by which users can easily get their desired results. It has not escaped our notice that the aforementioned strategy can be widely used in many other areas as well.
DOI: 10.14459/2020mp1574595
title: Pruning Edge Research with Latency Shears

description: Cloud datacenter to user connectivity dataset collected over RIPE Atlas. The dataset accompanies research article “Pruning Edge Research with Latency Shears” accepted at ACM HotNets 2020
DOI: 10.26049/asp78-2-2020-05/1
title: Phylogeny and Systematics of Wood-Degrading Neotro­pical Bess Beetles (Coleoptera: Passalidae: Passalinae)
DOI: 10.21227/m9s7-1q10
title: Optimizing Response Time in SDN-Edge Environments for Time-Strict IoT Applications

description: The rise of the Internet of Things (IoT) has opened new research lines that focus on applying IoT applications to domains further beyond basic user-grade applications, such as Industry or Healthcare. These domains demand a very high Quality of Service (QoS), mainly a very short response time. In order to meet these demands, some works are evaluating how to modularize and deploy IoT applications in different nodes of the infrastructure (edge, fog, cloud), as well as how to place the network controllers, since these decisions affect the response time of the application. Some works in the literature have approached this problem by providing separate plans for deployment and placing of controllers. However, this approach makes sub-optimal decisions, that complicate guaranteeing the demanded response time. To guarantee an optimal response time, it is crucial to solve the problem in a single effort that considers both, the networking and computing dimensions. In this work, we analyze the influences between the response time of computing and networking in edge computing environments with SDN networks, merging both optimization efforts into a single one and proposing a solution to the joint problem. Our evaluation shows that our proposal can shorten response time by up to 28.97%.
DOI: 10.21227/hb01-tp91
title: Optimizing Response Time in SDN-Edge Environments for Time-Strict IoT Applications

description: The rise of the Internet of Things (IoT) has opened new research lines that focus on applying IoT applications to domains further beyond basic user-grade applications, such as Industry or Healthcare. These domains demand a very high Quality of Service (QoS), mainly a very short response time. In order to meet these demands, some works are evaluating how to modularize and deploy IoT applications in different nodes of the infrastructure (edge, fog, cloud), as well as how to place the network controllers, since these decisions affect the response time of the application. Some works in the literature have approached this problem by providing separate plans for deployment and placing of controllers. However, this approach makes sub-optimal decisions, that complicate guaranteeing the demanded response time. To guarantee an optimal response time, it is crucial to solve the problem in a single effort that considers both, the networking and computing dimensions. In this work, we analyze the influences between the response time of computing and networking in edge computing environments with SDN networks, merging both optimization efforts into a single one and proposing a solution to the joint problem. Our evaluation shows that our proposal can shorten response time by up to 28.97%.
DOI: 10.18112/openneuro.ds003192.v1.0.0
title: EuskalIBUR
DOI: 10.6084/m9.figshare.3126400
title: Lysine succinylation of <i>Mycobacterium tuberculosis</i> isocitrate lyase (ICL) fine-tunes the microbial resistance to antibiotics

description: Lysine succinylation (Ksucc) is a newly identified protein posttranslational modification (PTM), which may play an important role in cellular physiology. However, the role of lysine succinylation in antibiotic resistance remains elusive. Isocitrate lyase (ICL) is crucial for broad-spectrum antibiotics tolerance in <i>Mycobacterium tuberculosis</i> (Mtb). We previously found that MtbICL (Rv0467) has at least three succinylated lysine residues, namely K189, K322, and K334.To explore the effect of succinylation on the activity of MtbICL, mutants’ mimicry of the lysine succinylation were generated by site-directed mutagenesis. ICL-K189E mutant strain is more sensitive than the wild-type to rifampicin and streptomycin, but not isoniazid. For the <i>in vitro</i> activity of the purified isocitrate lyase, only K189E mutant showed significantly decreased activity. Crystal structure analysis showed that Lys189 Glu dramatically increased the pKa of Glu188 and decreased the pKa of Lys190, whereas had negligible effect on other residues within 5 Å as well as disruption of the electrostatic interaction between Lys189 and Glu182, which might prevent the closure of the active site loop and cause severe reduction of the enzyme activity. Considering the genetic, biochemical, and crystallographical evidences together, the succinylation of specific ICL residue can fine-tune the bacterial resistance to selected antibiotics. The decreased enzymatic activity resulting from the succinylation-changed electrostatic interaction might underlie this phenotype. This study provided the first insight into the link between lysine succinylation and antibiotic resistance.
DOI: 10.6084/m9.figshare.3126400.v2
title: Lysine succinylation of <i>Mycobacterium tuberculosis</i> isocitrate lyase (ICL) fine-tunes the microbial resistance to antibiotics

description: Lysine succinylation (Ksucc) is a newly identified protein posttranslational modification (PTM), which may play an important role in cellular physiology. However, the role of lysine succinylation in antibiotic resistance remains elusive. Isocitrate lyase (ICL) is crucial for broad-spectrum antibiotics tolerance in <i>Mycobacterium tuberculosis</i> (Mtb). We previously found that MtbICL (Rv0467) has at least three succinylated lysine residues, namely K189, K322, and K334.To explore the effect of succinylation on the activity of MtbICL, mutants’ mimicry of the lysine succinylation were generated by site-directed mutagenesis. ICL-K189E mutant strain is more sensitive than the wild-type to rifampicin and streptomycin, but not isoniazid. For the <i>in vitro</i> activity of the purified isocitrate lyase, only K189E mutant showed significantly decreased activity. Crystal structure analysis showed that Lys189 Glu dramatically increased the pKa of Glu188 and decreased the pKa of Lys190, whereas had negligible effect on other residues within 5 Å as well as disruption of the electrostatic interaction between Lys189 and Glu182, which might prevent the closure of the active site loop and cause severe reduction of the enzyme activity. Considering the genetic, biochemical, and crystallographical evidences together, the succinylation of specific ICL residue can fine-tune the bacterial resistance to selected antibiotics. The decreased enzymatic activity resulting from the succinylation-changed electrostatic interaction might underlie this phenotype. This study provided the first insight into the link between lysine succinylation and antibiotic resistance.
DOI: 10.34740/kaggle/dsv/1521899
title: DREAM11_IPL2020_CRICKET_LIVE
DOI: 10.14459/2020mp1544121
title: Local Yield Mapping at TUM-Weihenstephan 1990 to 2000

description: Over a 10-year period local yield measurement was undertaken in two joint research projects. Measurements covered combinable crops, silage maize, potatoes and grass.
DOI: 10.6084/m9.figshare.13013804
title: NBS_547_type.txt

description: The NBS-LRR gene list of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.13013825
title: TranscriptorFactor_list.txt

description: Predicted transcript factor genes of Miscanthus lutarioriparius
DOI: 10.6084/m9.figshare.13013804.v1
title: NBS_547_type.txt

description: The NBS-LRR gene list of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.13013819
title: Mlu_HiC_pep.fasta.gz

description: The protein sequences of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.13013507
title: Mlu_HiC_genome.fasta.gz

description: The chromosome-level genome assembly of Miscanthus lutarioriparius genome using Oxford Nanopore Technologies and Hi-C technology.
DOI: 10.6084/m9.figshare.12992984
title: Mlu_HiC_cds.fasta.gz

description: The coding sequences file of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.13014041
title: rfam_infernal.xlsx

description: miRNA genes of Miscanthus lutarioriparius
DOI: 10.6084/m9.figshare.13014041.v1
title: rfam_infernal.xlsx

description: miRNA genes of Miscanthus lutarioriparius
DOI: 10.6084/m9.figshare.12992582
title: Ml_rRNA.gff3

description: rRNA genes of Miscanthus lutarioriparius
DOI: 10.6084/m9.figshare.12992582.v1
title: Ml_rRNA.gff3

description: rRNA genes of Miscanthus lutarioriparius
DOI: 10.6084/m9.figshare.13013825.v1
title: TranscriptorFactor_list.txt

description: Predicted transcript factor genes of Miscanthus lutarioriparius
DOI: 10.6084/m9.figshare.12992585
title: KEGG_annotation.xlsx

description: KEGG annotation of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.12992906.v1
title: repeats library

description: repeat sequences file
DOI: 10.6084/m9.figshare.13013795
title: Mlu_HiC.gff3

description: The genome annotation file for the chromosome-level assembly of Miscanthus lutarioriparius.
DOI: 10.6084/m9.figshare.12992585.v1
title: KEGG_annotation.xlsx

description: KEGG annotation of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.12992588.v1
title: Mlu_chloroplast_Ref_Mjunceus_FASTA.gff3

description: Miscanthus lutarioriparius chloroplast genome sequence and genome annotation. The sequences was assembled using Miscanthus junceus as a bait sequence
DOI: 10.6084/m9.figshare.12992591
title: eggNOG.mapper.annotations.filter.txt

description: Genome annotation of Miscanthus lutarioriparius generated by eggNOG
DOI: 10.6084/m9.figshare.12992591.v1
title: eggNOG.mapper.annotations.filter.txt

description: Genome annotation of Miscanthus lutarioriparius generated by eggNOG
DOI: 10.6084/m9.figshare.12992594
title: Ml_tRNA_tRNAscanSE.gff

description: tRNA genes of Miscanthus lutarioriparius identified by tRNAscanSE
DOI: 10.6084/m9.figshare.12992600.v1
title: InterProScan_annotation.txt

description: Genome annotation of Miscanthus lutarioriparius generated by InterProScan
DOI: 10.6084/m9.figshare.12992594.v1
title: Ml_tRNA_tRNAscanSE.gff

description: tRNA genes of Miscanthus lutarioriparius identified by tRNAscanSE
DOI: 10.6084/m9.figshare.12992600
title: InterProScan_annotation.txt

description: Genome annotation of Miscanthus lutarioriparius generated by InterProScan
DOI: 10.6084/m9.figshare.12992597.v1
title: Mlu_chloroplast_genome_Ref_Sspon_FASTA.gff3

description: Miscanthus lutarioriparius chloroplast genome sequence and genome annotation. The sequences was assembled using S. spontaneum as a bait sequence
DOI: 10.6084/m9.figshare.12992984.v1
title: Miscanthus lutarioriparius CDS file

description: The coding sequences file of Miscanthus lutarioriparius genome
DOI: 10.6084/m9.figshare.12992588
title: Mlu_chloroplast_Ref_Mjunceus_FASTA.gff3

description: Miscanthus lutarioriparius chloroplast genome sequence and genome annotation. The sequences was assembled using Miscanthus junceus as a bait sequence
DOI: 10.6084/m9.figshare.12992597
title: Mlu_chloroplast_genome_Ref_Sspon_FASTA.gff3

description: Miscanthus lutarioriparius chloroplast genome sequence and genome annotation. The sequences was assembled using S. spontaneum as a bait sequence
DOI: 10.6073/pasta/7fe56916937e0c7324ab73a6b956eaa9
title: Mechanisms influencing physically sequestered soil carbon in temperate restored grasslands in South Africa and North America

description: This dataset contains a measurement of physically protected carbon (microaggregate-within-macroaggregate C) and potential drivers of physically protected C accumulation during grassland restoration. The data were collected from three independent grassland restorations from agriculture in North America and South Africa. Northeast Kansas, USA data were collected in May 2013. Northeast Free State, RSA data were collected in September–November 2005. Southeast Nebraska, USA data were collected in October 2008–May 2008. Aggregate fractionations were performed by hierarchical wet sieving (Six et al 2000). Carbon and N quantification were done by flash combustion-gas chromatography. Microbial biomass C quantification was performed with chloroform fumigation-incubation (chloroform fumigation-extraction in the case of northeast Kansas). Phospholipid fatty acid biomass analysis was conducted using the methods of Bligh and Dyer (1959).
DOI: 10.6084/m9.figshare.13014053
title: README.txt

description: README
DOI: 10.6084/m9.figshare.13013468
title: R0160_20170503a_videos

description: Rat 0160, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6073/pasta/c491086f02bc1661684eae31e337c659
title: Temperature datasets for stock tanks and natural sites at High, Medium, and Low elevations, as part of the LTREB Swordtail project in Hidalgo, Mexico, 2015 - 2025

description: The core of this project focuses on monitoring the phenotypic and genotypic evolution of experimental and natural hybrid populations of swordtails for ten generations. To get a clear understanding of how evolution shapes genome wide ancestry and the distribution of species-specific alleles at functional loci during early generations of hybridization, it's important to monitor these populations using experimental crosses. Eight replicate 2000 L mesocosm stock tanks were built at high (1514 m), intermediate (980 m), and low (186 m) elevations near the CICHAZ field site were seeded with Xiphophorus birchmanni – X. malinche F1 hybrids. The F1s were generated by crossing X. malinche females with X. birchmanni malesin stock tanks at CICHAZ, a research station in Calnali, Mexico. Tanks at higher elevations experience cooler water temperatures. Our experimental design thereby allows us to characterize how ecological selection shapes genotypic and phenotypic differences in thermal tolerance across hybrid populations exposed to different temperature regimes. The data contained in these files include recorded water temperature (in Celsius), taken every six hours from three stock tanks at low (186 m: STL), medium (980 m: STM), and high (1514 m: STH) elevations, along with three natural river sites. File Natural.csv contains the natural sites and the file Stock Tanks.csv contains the corresponding natural sites. Acuapa (ACUA) is paired with STL, Aguazarca (AGZC) is paired with STM, and Tlatemaco (TLMC) is paired with STH.
DOI: 10.25386/genetics.13010303
title: Supplemental Material for Su, Zuo, and Peterson, 2020

description: Supplemental Files to Accompany Su, Tao and Peterson "Ectopic expression of a maize gene is induced by Composite Insertions generated by Alternative Transposition" GENETICS/2020/303592R1<br>
DOI: 10.25386/genetics.13010303.v1
title: Supplemental Material for Su, Zuo, and Peterson, 2020

description: Supplemental Files to Accompany Su, Tao and Peterson "Ectopic expression of a maize gene is induced by Composite Insertions generated by Alternative Transposition" GENETICS/2020/303592R1<br>
DOI: 10.5281/zenodo.4056214
title: KNIME workflows for the evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours

description: Zebrafish (<em>Danio rerio</em>) has rapidly become a popular model species for behavioural studies that may be relevant to drug screening and safety toxicology. Zebrafish embryos show a complex behavioural repertoire already a few hours after fertilization. Particularly, early stage zebrafish show characteristic behavioural features such as spontaneous tail coiling (STC) or induced movements when exposed to a short and bright light flash (called photomotor response -PMR-). In this chapter, we provide the methods for assessing STC and PMR in zebrafish embryos and to detect changes provoked by chemicals. One of the protocols uses video analysis suitable for automated high-throughput screening. Moreover, both protocols describe the use of automated video analysis by using an open-source integration platform (KNIME analytics platform), providing a flexible workflow system that can be adapted to a diversity of video recordings. We also provide a toxicological validation of this assay and show that these protocols can be used to provide an automated, high data-content readout for zebrafish behavioural responses.
DOI: 10.5281/zenodo.3835946
title: KNIME workflows for the evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours

description: Zebrafish (<em>Danio rerio</em>) has rapidly become a popular model species for behavioural studies that may be relevant to drug screening and safety toxicology. Zebrafish embryos show a complex behavioural repertoire already a few hours after fertilization. Particularly, early stage zebrafish show characteristic behavioural features such as spontaneous tail coiling (STC) or induced movements when exposed to a short and bright light flash (called photomotor response -PMR-). In this chapter, we provide the methods for assessing STC and PMR in zebrafish embryos and to detect changes provoked by chemicals. One of the protocols uses video analysis suitable for automated high-throughput screening. Moreover, both protocols describe the use of automated video analysis by using an open-source integration platform (KNIME analytics platform), providing a flexible workflow system that can be adapted to a diversity of video recordings. We also provide a toxicological validation of this assay and show that these protocols can be used to provide an automated, high data-content readout for zebrafish behavioural responses.
DOI: 10.17604/ckxq-nh63
title:  Trajectories of drifters of different shapes released at four locations across the Atlantic Ocean

description: This data set contains trajectories of drifters of various shapes deployed at four locations across the Atlantic Ocean during the PIRATA (Prediction and Research Moored Array in the Tropical Atlantic) Northeast Extension (https://www.aoml.noaa.gov/phod/pne/index.php) cruise in 2018. The drifters were released to study how marine debris and Sargassum move under different ocean and wind conditions and assess inertial effects on their drift. These drifters were specially designed at NOAA's Atlantic Oceanographic and Meteorological Laboratory. Five types of special drifters were built. The four debris-like drifters were comprised of a main body, made of polystyrene foam, and a short-weighted tube at the bottom. Two kinds of main bodies were considered: spherical (of two sizes) and cuboidal (a cube and a square cuboid). The fifth special drifter type consisted of an artificial boxwood hedge designed to mimic a small patch of pelagic Sargassum. This data is associated with the article "How local winds and currents impact the trajectories of marine debris and Sargassum: Inertia-dependent clustering of floating material paths" published in _Geophysical Research Letters_ (forthcoming).
DOI: 10.6084/m9.figshare.13013468.v1
title: R0160_20170503a_videos

description: Rat 0160, skilled reaching data collected in Leventhal laboratory by Alexandra Bova