cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1577195.v2
title: Analysis of non-peptidic compounds as potential malarial inhibitors against <i>Plasmodial</i> cysteine proteases via integrated virtual screening workflow

description: Falcipain-2 (FP-2) and falcipain-3 (FP-3), haemoglobin-degrading enzymes in <i>Plasmodium falciparum</i>, are validated drug targets for the development of effective inhibitors against malaria. However, no commercial drug-targeting falcipains has been developed despite their central role in the life cycle of the parasites. In this work, <i>in silico</i> approaches are used to identify key structural elements that control the binding and selectivity of a diverse set of non-peptidic compounds onto FP-2, FP-3 and homologues from other <i>Plasmodium</i> species as well as human cathepsins. Hotspot residues and the underlying non-covalent interactions, important for the binding of ligands, are identified by interaction fingerprint analysis between the proteases and 2-cyanopyridine derivatives (best hits). It is observed that the size and chemical type of substituent groups within 2-cyanopyridine derivatives determine the strength of protein–ligand interactions. This research presents novel results that can further be exploited in the structure-based molecular-guided design of more potent antimalarial drugs.
DOI: 10.6084/m9.figshare.1577195.v1
title: Analysis of Non-Peptidic Compounds as Potential Malarial Inhibitors against <i>Plasmodial</i> Cysteine Proteases via Integrated Virtual Screening Workflow

description: Falcipain-2 and falcipain-3, haemoglobin degrading enzymes in <i>Plasmodium falciparum</i>, are validated drug targets for the development of effective inhibitors against malaria. However, no commercial drug targeting falcipains has been developed despite their central role in the life-cycle of the parasites. In this work, <i>in silico</i> approaches are used to identify key structural elements that control the binding and selectivity of a diverse set of non-peptidic compounds onto FP-2, FP-3 and homologs from other <i>Plasmodium</i> species as well as human cathepsins. Hotspot residues and the underlying non-covalent interactions, important for the binding of ligands, are identified by interaction fingerprint analysis between the proteases and 2-cyanopyridine derivatives (best hits). It is observed that the size and chemical type of substituent groups within 2-cyanopyridine derivatives determine the strength of protein-ligand interactions. This research presents novel results that can further be exploited in the structure-based molecular guided design of more potent antimalarial drugs.
DOI: 10.6084/m9.figshare.1576422
title: Copper oxide nanoparticles aggravate airway inflammation and mucus production in asthmatic mice via MAPK signaling

description: Copper oxide nanoparticles (CuONPs), metal oxide nanoparticles were used in multiple applications including wood preservation, antimicrobial textiles, catalysts for carbon monoxide oxidation and heat transfer fluid in machines. We investigated the effects of CuONPs on the respiratory system in Balb/c mice. In addition, to investigate the effects of CuONPs on asthma development, we used a murine model of ovalbumin (OVA)-induced asthma. CuONPs markedly increased airway hyper-responsiveness (AHR), inflammatory cell counts, proinflammatory cytokines and reactive oxygen species (ROS). CuONPs induced airway inflammation and mucus secretion with increases in phosphorylation of the MAPKs (Erk, JNK and p38). In the OVA-induced asthma model, CuONPs aggravated the increased AHR, inflammatory cell count, proinflammatory cytokines, ROS and immunoglobulin E induced by OVA exposure. In addition, CuONPs markedly increased inflammatory cell infiltration into the lung and mucus secretions, and MAPK phosphorylation was elevated compared to OVA-induced asthmatic mice. Taken together, CuONPs exhibited toxicity on the respiratory system, which was associated with the MAPK phosphorylation. In addition, CuONPs exposure aggravated the development of asthma. We conclude that CuONPs exposure has a potential toxicity in humans with respiratory disease.
DOI: 10.6084/m9.figshare.1577176.v3
title: Spatially-controlled complex molecules and their applications

description: The understanding of molecular structure and function is at the very heart of the chemical and molecular sciences. Experiments that allow for the creation of structurally pure samples and the investigation of their molecular dynamics and chemical function have developed tremendeously over the last few decades, although ‘there’s plenty of room at the bottom’ for better control as well as further applications. Here, we describe the use of inhomogeneous electric fields for the manipulation of neutral molecules in the gas-phase, i.e. for the separation of complex molecules according to size, structural isomer, and quantum state. For these complex molecules, all quantum states are strong-field seeking, requiring dynamic fields for their confinement. Current applications of these controlled samples are summarised and interesting future applications discussed.
DOI: 10.6084/m9.figshare.1576422.v1
title: Copper oxide nanoparticles aggravate airway inflammation and mucus production in asthmatic mice via MAPK signaling

description: Copper oxide nanoparticles (CuONPs), metal oxide nanoparticles were used in multiple applications including wood preservation, antimicrobial textiles, catalysts for carbon monoxide oxidation and heat transfer fluid in machines. We investigated the effects of CuONPs on the respiratory system in Balb/c mice. In addition, to investigate the effects of CuONPs on asthma development, we used a murine model of ovalbumin (OVA)-induced asthma. CuONPs markedly increased airway hyper-responsiveness (AHR), inflammatory cell counts, proinflammatory cytokines and reactive oxygen species (ROS). CuONPs induced airway inflammation and mucus secretion with increases in phosphorylation of the MAPKs (Erk, JNK and p38). In the OVA-induced asthma model, CuONPs aggravated the increased AHR, inflammatory cell count, proinflammatory cytokines, ROS and immunoglobulin E induced by OVA exposure. In addition, CuONPs markedly increased inflammatory cell infiltration into the lung and mucus secretions, and MAPK phosphorylation was elevated compared to OVA-induced asthmatic mice. Taken together, CuONPs exhibited toxicity on the respiratory system, which was associated with the MAPK phosphorylation. In addition, CuONPs exposure aggravated the development of asthma. We conclude that CuONPs exposure has a potential toxicity in humans with respiratory disease.
DOI: 10.6084/m9.figshare.1576420
title: Insect Inspired Target Tracking (IIT Dataset)

description: These image sequences are used to compare the Insect-Inspired tracker (DOI: 10.1098/rsif.2015.0083) with state-of-the-art engineering trackers.
DOI: 10.6084/m9.figshare.1576421
title: Universal stochastic multi-scale image fusion: an example application for shale rocks

description: Supplementary images for the paper by Gerke K.M., Karsanina M.V. and Mallants D.
DOI: 10.6084/m9.figshare.1576421.v1
title: Universal stochastic multi-scale image fusion: an example application for shale rocks

description: Supplementary images for the paper by Gerke K.M., Karsanina M.V. and Mallants D.
DOI: 10.6084/m9.figshare.1576420.v2
title: Insect Inspired Target Tracking (IIT Dataset)

description: These image sequences are used to compare the Insect-Inspired tracker (DOI: 10.1098/rsif.2015.0083) with state-of-the-art engineering trackers.
DOI: 10.6084/m9.figshare.1576406
title: Lactobacillus kunkeei MP2 Genome

description: Supplementary data containing tables and raw annotation files for the genome of Lactobacillus kunkeei MP2
DOI: 10.6084/m9.figshare.1576409
title: Paleohistology of Susisuchus anatoceps

description: Paleohistology of <em>Susisuchus anatoceps</em>
DOI: 10.6084/m9.figshare.1576409.v1
title: Paleohistology of Susisuchus anatoceps

description: Paleohistology of <em>Susisuchus anatoceps</em>
DOI: 10.6084/m9.figshare.1576420.v1
title: Insect Inspired Target Tracking (IIT Dataset)

description: These image sequences are used to compare the Insect-Inspired tracker (DOI: 10.1098/rsif.2015.0083) with state-of-the-art engineering trackers.
DOI: 10.6084/m9.figshare.1576389
title: Neotropical Bird Guts

description: These files were used for the paper Hird et al. (2015): Comparative gut microbiota of 59 Neotropical bird species, currently under review at Frontiers in Microbiology. Included is the sequence file (cP315.final.fasta), which is the V6 region of 16S rRNA as sequenced on an Illumina and a metadata (mapping) file that contains information about the samples. Also included is the rarefied OTU table that was used in QIIME for many of the analyses (otu_table_even3652.biom).
DOI: 10.6084/m9.figshare.1576391
title: Week 4: Dataset 1: Quadrats

description: Description The experiment was conducted on Monday September 28nd at approximately 3:45 pm until 5:00. All the data was collected in the woodlot and corresponds to dataset 1. It was cloudy, windy and humid. The temperature was around 20 degrees celcius. Materials 1) Quadrat 1m by 1m Method: 20 quadrats were used in total, 10 to be placed in the grassland and 10 to be placed in the woodlot. The selection of each quadrat in the habitat was randomized by first selecting a location and then the next one would be located 1.5 meters north to the previous location where the quadrat was placed. The quadrat was left in place for a duration of 2minutes. After the desired time elapsed 2 minutes were spent counting the insects within the quadrat. The recognizable RTUs include dragonflies, mayflies, grasshoppers,bugs,butterflies,moths beetles, flies, ants, wasps, bees and spider.
DOI: 10.6084/m9.figshare.1576406.v1
title: Lactobacillus kunkeei MP2 Genome

description: Supplementary data containing tables and raw annotation files for the genome of Lactobacillus kunkeei MP2
DOI: 10.6084/m9.figshare.1576400.v2
title: Male- and female-derived somatic and germ cell-specific toxicity of silver nanoparticles in mouse

description: Silver nanoparticles (AgNPs) are widely used as an antibiotic agent in textiles, wound dressings, medical devices, and appliances such as refrigerators and washing machines. The increasing use of AgNPs has raised concerns about their potential risks to human health. Therefore, this study was aimed to determine the impact of AgNPs in germ cell specific complications in mice. The administration of AgNPs results in toxicity in mice; however, a more detailed understanding of the effects of AgNPs on germ cells remains poorly understood. Here, we demonstrate the effects of AgNPs (20 nm in diameter) in a mouse Sertoli and granulosa cells <i>in vitro</i>, and in male and female mice <i>in vivo</i>. Soluble silver ion (Ag<sup>+</sup>)-treated cells were used as a positive control. We found that excessive AgNP-treated cells exhibited cytotoxicity, the formation of autophagosomes and autolysosomes in Sertoli cells. Furthermore, an increase in mitochondrial-mediated apoptosis by cytochrome <i>c</i> release from mitochondria due to translocation of Bax to mitochondria was observed. In <i>in vivo</i> studies, the expression of pro-inflammatory cytokines, including tumor necrosis factor α, interferon-γ, −6, −1β, and monocyte chemoattractant protein-1 were significantly increased (<i>p</i>
DOI: 10.6084/m9.figshare.1576389.v1
title: Neotropical Bird Guts

description: These files were used for the paper Hird et al. (2015): Comparative gut microbiota of 59 Neotropical bird species, currently under review at Frontiers in Microbiology. Included is the sequence file (cP315.final.fasta), which is the V6 region of 16S rRNA as sequenced on an Illumina and a metadata (mapping) file that contains information about the samples. Also included is the rarefied OTU table that was used in QIIME for many of the analyses (otu_table_even3652.biom).
DOI: 10.6084/m9.figshare.1576400
title: Male- and female-derived somatic and germ cell-specific toxicity of silver nanoparticles in mouse

description: Silver nanoparticles (AgNPs) are widely used as an antibiotic agent in textiles, wound dressings, medical devices, and appliances such as refrigerators and washing machines. The increasing use of AgNPs has raised concerns about their potential risks to human health. Therefore, this study was aimed to determine the impact of AgNPs in germ cell specific complications in mice. The administration of AgNPs results in toxicity in mice; however, a more detailed understanding of the effects of AgNPs on germ cells remains poorly understood. Here, we demonstrate the effects of AgNPs (20 nm in diameter) in a mouse Sertoli and granulosa cells <i>in vitro</i>, and in male and female mice <i>in vivo</i>. Soluble silver ion (Ag<sup>+</sup>)-treated cells were used as a positive control. We found that excessive AgNP-treated cells exhibited cytotoxicity, the formation of autophagosomes and autolysosomes in Sertoli cells. Furthermore, an increase in mitochondrial-mediated apoptosis by cytochrome <i>c</i> release from mitochondria due to translocation of Bax to mitochondria was observed. In <i>in vivo</i> studies, the expression of pro-inflammatory cytokines, including tumor necrosis factor α, interferon-γ, −6, −1β, and monocyte chemoattractant protein-1 were significantly increased (<i>p</i>
DOI: 10.6084/m9.figshare.1575837
title: Developing Sustainable Software for Science Communities Using Online Platforms, Communications and Workflows

description: White paper for CSESSP workshop Oct 2015
DOI: 10.6084/m9.figshare.1575835
title: Identifying Silence Climate in Organizations in the Framework of Contemporary Management Approaches

description: Dynamic competition conditions in present day bring about the consequence for businesses to face varied problems with each passing day. At this point, current management approaches include studies that would shed light on the new problems of businesses. Organizational Silence, a concept that has recently been being voiced in business world, has come up in such context. Organizational silence could be expressed as the employee behavior of keeping silent about certain negativities due to various reasons in an organization. Since knowledge sharing in modern organizations is of capital importance in terms of responding hastily to the changes in a competitive environment, spread of this behavior of employees to organization culture and climate presents a threat of indifference. In this study, the concept of Organizational Silence is defined and the effects of conceived silence climate on management of organizations are discussed.
DOI: 10.6084/m9.figshare.1575855
title: CSESSP Challenges Workshop - Curse of growing scales in scientific software

description: Sustainable HPC software development requires careful planning, design, and implementation from the ground up, as growing demands during the product evolution render static processes that were successful at a smaller scale untenable when scope and resource requirements expand. This white paper addresses some relevant questions to tackle the curse of growing scales in science and resources (human and computing) during various stages of scientific software evolution.
DOI: 10.6084/m9.figshare.1575837.v1
title: Developing Sustainable Software for Science Communities Using Online Platforms, Communications and Workflows

description: White paper for CSESSP workshop Oct 2015
DOI: 10.6084/m9.figshare.1575833
title: eUCP AND ELECTRONIC COMMERCE INVESTMENTS: e-SIGNATURE AND PAPERLESS FOREIGN TRADE

description: The developments in electronic documents that are seen in recent years suggest that use of paper will be completely abandoned in all business processes after some time. As an advantage of the developments in information systems, the use of electronic documents has become widespread and even compulsory in some applications. Although it is one of the areas where the benefits of electronic documents will be seen, the use of electronic documents in foreign trade has not become so popular. As the paper-based processes still prevail, it seems that there is a need for a radical and comprehensive change in this area. Although a long time has passed after the publication of eUCP, it has not produced the expected effect, which indicates the necessity of introducing new payment methods to replace letters of credit. In this article, a general evaluation was made within the framework of the latest developments and the possible effects of electronic documents on foreign trade were discussed with a proposal of a new payment method based on a single document.
DOI: 10.6084/m9.figshare.1575855.v2
title: CSESSP Challenges Workshop - Curse of growing scales in scientific software

description: Sustainable HPC software development requires careful planning, design, and implementation from the ground up, as growing demands during the product evolution render static processes that were successful at a smaller scale untenable when scope and resource requirements expand. This white paper addresses some relevant questions to tackle the curse of growing scales in science and resources (human and computing) during various stages of scientific software evolution.
DOI: 10.6084/m9.figshare.1575855.v1
title: CSESSP Challenges Workshop

description: Sustainable HPC software development requires careful planning, design, and implementation from the ground up, as growing demands during the product evolution render static processes that were successful at a smaller scale untenable when scope and resource requirements expand. This white paper addresses some relevant questions to tackle the curse of growing scales in science and resources (human and computing) during various stages of scientific software evolution.
DOI: 10.6084/m9.figshare.1575808
title: The number of responsive CN neurons by the different phases of the applied paradigm.

description: .
DOI: 10.6084/m9.figshare.1575807
title: The net discharge rates (spikes/sec) of the PANs, HFNs and TANs by the different phases of the applied paradigm.

description: Increased activities are given as net values after the subtraction of the background activity from the gross activity. Decreased activities are given as absolute values of the net changes.
DOI: 10.6084/m9.figshare.1575808.v1
title: The number of responsive CN neurons by the different phases of the applied paradigm.

description: .
DOI: 10.6084/m9.figshare.1575777
title: serico3_Trinity.fasta.gz

description: assembled transcriptome dataset of <i>Sericomyrmex</i> cf. <i>luederwaldti</i>
DOI: 10.6084/m9.figshare.1575777.v1
title: serico3_Trinity.fasta.gz

description: assembled transcriptome dataset of <i>Sericomyrmex</i> cf. <i>luederwaldti</i>
DOI: 10.6084/m9.figshare.1575778
title: serico2_Trinity.fasta.gz

description: Assembled transcriptome of <i>Sericomyrmex</i> cf. <i>parvulus</i>
DOI: 10.6084/m9.figshare.1575776
title: serico1_Trinity.fasta.gz

description: Assembled transcriptome dataset of <i>Sericomyrmex</i> cf. <i>mayri</i>
DOI: 10.6084/m9.figshare.1575775
title: aptero_Trinity.fasta.gz

description: Assembled transcriptome dataset for <i>Apterostigma</i> <i>megacephala</i>.
DOI: 10.6084/m9.figshare.1575775.v1
title: aptero_Trinity.fasta.gz

description: Assembled transcriptome dataset for <i>Apterostigma</i> <i>megacephala</i>.
DOI: 10.6084/m9.figshare.1575774
title: Broad Host-Range Phage Genomes

description: Full genomes and annotations for broad host-range phages.
DOI: 10.6084/m9.figshare.1575778.v1
title: serico2_Trinity.fasta.gz

description: Assembled transcriptome of <i>Sericomyrmex</i> cf. <i>parvulus</i>
DOI: 10.6084/m9.figshare.1575771
title: KT254130 - phiVader

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575774.v1
title: Broad Host-Range Phage Genomes

description: Full genomes and annotations for broad host-range phages.
DOI: 10.6084/m9.figshare.1575769
title: KT254132 - phiHabibi

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575770
title: KT254131 - Moody

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575771.v1
title: KT254130 - phiVader

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575768
title: KT254133 - phiFenriz

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575768.v1
title: KT254133 - phiFenriz

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575770.v1
title: KT254131 - Moody

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575765
title: Injury and illness among athletes during a multi-day elite cycling road race

description: <i>Objectives</i>: Although road bicycle races have been held for more than a century, injury and illness patterns during multi-day bicycle events have not been widely studied. The aim of this study was to determine the incidence of injury and illness among riders and describe the medical care interventions provided to participants of cycling road races. <i>Methods</i>: A prospective observational study was conducted on the Presidential Cycling Tour of Turkey, which was held between April 26 and May 3, 2015. The race lasted 8 days and covered 1258 km of road. There were 166 elite cycling athletes representing 21 teams from various countries. Data collected pertaining to incidents involving injury or illness included the following: type of injury; anatomical location of injury; details of the medical encounter; location of the intervention; treatment provided; medication administered and disposition of the rider. An <i>injury</i> was defined as a physical complaint or observable damage to the body produced by the transfer of energy of the rider. An <i>illness</i> was defined as a physical complaint or presentation not related to injury. <i>Results</i>: The overall incidence (injury and illness) was 5.83 per 1000 cycling hours. (Injury incidence was 2.82 vs illness incidence of 3.01 per 1000 hours cycling). A total of 31 incidents occurred. Of these, 15 were injuries, while 16 were complaints of a non-traumatic nature. A total of 43 interventions were made in the 15 cases of injury. The most commonly injured body regions were limbs; the majority of injuries involved the skin and soft tissue. The most common medical intervention was wound care (64% of all interventions). Two riders had to withdraw from the race, and one was hospitalized due to a traumatic pneumothorax. None of the non-traumatic cases resulted in withdrawal from the race. <i>Conclusions</i>: A broad spectrum of illness and injury occurs during elite multi-day road races, ranging from simple skin injuries to serious injuries requiring hospital admission. Most injuries and illnesses are minor; however, medical teams must be prepared to treat life-threatening trauma.
DOI: 10.6084/m9.figshare.1575769.v2
title: KT254132 - phiHabibi

description: GenBank format genome/annotation.
DOI: 10.6084/m9.figshare.1575769.v1
title: KT254132 - Habibi

description: GenBank format genome/annotation.