cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5522/04/9975983.v1
title: Rapid Brain Responses to Familiar vs. Unfamiliar Music – an EEG and Pupillometry study ( data compressed in .rar format)

description: This dataset constitutes the data reported in the paper “Rapid Brain Responses to Familiar vs. Unfamiliar Music – an EEG and Pupillometry study” by authors: Robert Jagiello, Ulrich Pomper, Makoto Yoneya, Sijia Zhao, Maria Chait.<br><br>Included are the (anonymized and un-identifiable) EEG and Pupillometry data. See readme files for more details.<br><br>Experimental procedures were approved by the research ethics committee of University College London and were performed in accordance with the relevant guidelines and regulations.<br><br>Paper abstract: <br>Human listeners exhibit marked sensitivity to familiar music, perhaps most readily revealed by popular “name that tune” games, in which listeners often succeed in recognizing a familiar song based on extremely brief presentation. In this work, we used electroencephalography (EEG) and pupillometry to reveal the temporal signatures of the brain processes that allow differentiation between a familiar, well liked and unfamiliar piece of music. In contrast to previous work, which has quantified gradual changes in pupil diameter (the so-called “pupil dilation response”), here we focus on the occurrence of pupil dilation events. This approach is substantially more sensitive in the temporal domain and allowed us to tap early activity with the putative salience network. Participants (N=10) passively listened to snippets (750 ms) of a familiar, personally relevant and, an acoustically matched, unfamiliar song, presented in random order. A group of control participants (N=12), who were unfamiliar with all of the songs, was also tested. We reveal a rapid differentiation between snippets from familiar and unfamiliar songs: Pupil responses showed greater dilation rate to familiar music from 100-300 ms post-stimulus-onset, consistent with a faster activation of the autonomic salience network. Brain responses measured with EEG showed a later differentiation between familiar and unfamiliar music from 350 ms post onset. Remarkably, the cluster pattern identified in the EEG response is very similar to that commonly found in the classic old/new memory retrieval paradigms, suggesting that the recognition of brief, randomly presented, music snippets, draws on similar processes. <br><br>
DOI: 10.6084/m9.figshare.9975980
title: overview.zip

description: Output Folder of TOBIAS (https://github.com/loosolab/TOBIAS/) software on global findings, what TFs are driving individual conditions<br>
DOI: 10.6084/m9.figshare.9975965
title: Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation

description: Snake venom of <i>Naja naja</i> comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA<sub>2</sub>), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA<sub>2</sub>. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA<sub>2</sub> were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca<sup>2+</sup>, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca<sup>2+</sup> as well as the inflammatory functions of PLA<sub>2</sub>. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9975974
title: motifs.zip

description: Motifs as used for exemplary data analysis of Hendrikson et al 2017 via TOBIAS software (https://github.com/loosolab/TOBIAS/)<br>
DOI: 10.6084/m9.figshare.9975986.v1
title: Cesium uptake of field-grown <i>Amaranthus</i> species in Fukushima focusing on Cs concentration in xylem exudate and root distribution

description: Radiocesium (RCs) discharged by the Fukushima Daiichi Nuclear Power Plant (Tokyo Electric Power Co., Inc.) accident has extensively contaminated agricultural land in Fukushima Prefecture and its neighboring areas. Many studies have demonstrated that Cs (RCs and <sup>133</sup>Cs) uptake of plants is affected by the exchangeable K (Ex-K) concentration in soil. However, the precise plant–soil interaction in relation to Cs uptake is still unclear. The aim of this study was to investigate Cs uptake of plant in field by focusing on xylem exudate and roots because nutrients in xylem exudate reflect medium (soil) conditions and affect nutrient accumulation in shoots. Two varieties of amaranth, K4 (<i>Amaranthus caudatus</i> L.) and Mexico type (<i>A. hypochondriacus</i> L.), which have different Cs uptake abilities, were grown in four fields and in pots (750 to 3440 Bq kg<sup>−1</sup> of RCs) in Fukushima Prefecture. Cs concentrations in xylem exudate, shoot, and soil; Ex-K concentration in soil; and root distribution in soil were determined. RCs concentration in xylem exudate varied from 0.04 to 164 Bq kg<sup>−1</sup> and <sup>133</sup>Cs concentration in xylem exudate ranged from 0.01 to 33.7 μg kg<sup>−1</sup>. The Cs concentrations were decreased by the high Ex-K concentration and the large amount of 2:1 type clay minerals in soil. The average of the ratios of Cs concentration in shoot to Cs concentration in xylem exudate for all samples was 127 ± 112 (mean ± standard deviation), although no clear correlation was found between them. The correlations betwee\n RCs and <sup>133</sup>Cs concentrations in xylem exudate and shoot were strong in pot and in the field with low Ex-K concentration. Eighty-five percent of the total root length was distributed in the topsoil (0–20 cm soil layer). The positions where roots take up Cs were estimated from the differences in the vertical distribution of RCs and <sup>133</sup>Cs concentrations in soil. The estimated Cs uptake ratios of topsoil to total soil layer ranged from 7% to 91% and varied with the concentration and the vertical distribution of Ex-K in soil.
DOI: 10.6084/m9.figshare.9975965.v2
title: Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation

description: Snake venom of <i>Naja naja</i> comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA<sub>2</sub>), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA<sub>2</sub>. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA<sub>2</sub> were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca<sup>2+</sup>, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca<sup>2+</sup> as well as the inflammatory functions of PLA<sub>2</sub>. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9975953
title: Yield, content, and nutrient uptake by winter wheat and spring barley in response to applications of digestate, cattle slurry, and NPK mineral fertilizers

description: Supplemental material
DOI: 10.6084/m9.figshare.9975935
title: footprinting.zip

description: Output folder of TOBIAS software (https://github.com/loosolab/TOBIAS/), exemplary used to analyze Hendrikson et al. 2107 <br>
DOI: 10.6084/m9.figshare.9975941
title: flatfiles.zip

description: Annotation and genome files as used for TOBIAS analysis (https://github.com/loosolab/TOBIAS/) for exemplary dataset from Hendrikson et al 2017<br>
DOI: 10.6084/m9.figshare.9975953.v1
title: Yield, content, and nutrient uptake by winter wheat and spring barley in response to applications of digestate, cattle slurry, and NPK mineral fertilizers

description: Supplemental material
DOI: 10.17632/pwyyg8zmk5.1
title: Poribohon-BD

description: Poribohon-BD is a vehicle dataset of 15 native vehicles of Bangladesh. The vehicles are: i) Bicycle, ii) Boat, iii) Bus, iv) Car, v) CNG, vi) Easy-bike, vii) Horse-cart, viii) Launch, ix) Leguna, x) Motorbike, xi) Rickshaw, xii) Tractor, xiii) Truck, xiv) Van, xv) Wheelbarrow. The dataset contains a total of 9058 images with a high diversity of poses, angles, lighting conditions, weather conditions, backgrounds. All of the images are in JPG format. The dataset also contains 9058 image annotation files. These files state the exact positions of the objects with labels in the corresponding image. The annotation has been performed manually and the annotated values are stored in XML files. LabelImg tool by Tzuta Lin has been used to label the images. Moreover, data augmentation techniques have been applied to keep the number of images comparable to each type of vehicle. Human faces have also been blurred to maintain privacy and confidentiality. The data files are divided into 15 individual folders. Each folder contains images and annotation files of one vehicle type. The 16th folder titled ‘Multi-class Vehicles’ contains images and annotation files of more than one type of vehicle. Poribohon-BD is compatible with various CNN architectures such as YOLO, VGG-16, R-CNN, DPM.
DOI: 10.6084/m9.figshare.9975926
title: bias_correction.zip

description: Output folder of TOBIAS software (https://github.com/loosolab/TOBIAS/), applied to Hendrikson et al. 2017 dataset<br>
DOI: 10.6084/m9.figshare.9975911
title: Polychlorinated biphenyl exposure and DNA methylation in the Anniston Community Health Survey

description: Anniston, Alabama was home to a major polychlorinated biphenyl (PCB) production facility from 1929 until 1971. The Anniston Community Health Survey I and II (ACHS-I 2005–2007, ACHS-II 2013–2014) were conducted to explore the effects of PCB exposures. In this report we examined associations between PCB exposure and DNA methylation in whole blood using EPIC arrays (ACHS-I, n = 518; ACHS-II, n = 299). For both cohorts, 35 PCBs were measured in serum. We modelled methylation versus PCB wet-weight concentrations for: the sum of 35 PCBs, mono-ortho substituted PCBs, di-ortho substituted PCBs, tri/tetra-ortho substituted PCBs, oestrogenic PCBs, and antiestrogenic PCBs. Using robust multivariable linear regression, we adjusted for age, race, sex, smoking, total lipids, and six blood cell-type percentages. We carried out a two-stage analysis; discovery in ACHS-I followed by replication in ACHS-II. In ACHS-I, we identified 28 associations (17 unique CpGs) at p ≤ 6.70E-08 and 369 associations (286 unique CpGs) at FDR p ≤ 5.00E-02. A large proportion of the genes have been observed to interact with PCBs or dioxins in model studies. Among the 28 genome-wide significant CpG/PCB associations, 14 displayed replicated directional effects in ACHS-II; however, only one in ACHS-II was statistically significant at p ≤ 1.70E-04. While we identified many novel CpGs significantly associated with PCB exposures in ACHS-I, the differential methylation was modest and the effect was attenuated seven years later in ACHS-II, suggesting a lack of persistence of the associations between PCB exposures and altered DNA methylation in blood cells.
DOI: 10.6084/m9.figshare.9975911.v1
title: Polychlorinated biphenyl exposure and DNA methylation in the Anniston Community Health Survey

description: Anniston, Alabama was home to a major polychlorinated biphenyl (PCB) production facility from 1929 until 1971. The Anniston Community Health Survey I and II (ACHS-I 2005–2007, ACHS-II 2013–2014) were conducted to explore the effects of PCB exposures. In this report we examined associations between PCB exposure and DNA methylation in whole blood using EPIC arrays (ACHS-I, n = 518; ACHS-II, n = 299). For both cohorts, 35 PCBs were measured in serum. We modelled methylation versus PCB wet-weight concentrations for: the sum of 35 PCBs, mono-ortho substituted PCBs, di-ortho substituted PCBs, tri/tetra-ortho substituted PCBs, oestrogenic PCBs, and antiestrogenic PCBs. Using robust multivariable linear regression, we adjusted for age, race, sex, smoking, total lipids, and six blood cell-type percentages. We carried out a two-stage analysis; discovery in ACHS-I followed by replication in ACHS-II. In ACHS-I, we identified 28 associations (17 unique CpGs) at p ≤ 6.70E-08 and 369 associations (286 unique CpGs) at FDR p ≤ 5.00E-02. A large proportion of the genes have been observed to interact with PCBs or dioxins in model studies. Among the 28 genome-wide significant CpG/PCB associations, 14 displayed replicated directional effects in ACHS-II; however, only one in ACHS-II was statistically significant at p ≤ 1.70E-04. While we identified many novel CpGs significantly associated with PCB exposures in ACHS-I, the differential methylation was modest and the effect was attenuated seven years later in ACHS-II, suggesting a lack of persistence of the associations between PCB exposures and altered DNA methylation in blood cells.
DOI: 10.6084/m9.figshare.9975866
title: Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence

description: We studied multiple sequence alignment (MSA) consensus amino acid distributional patterns in 2844 amino acid sequences of the eight enzymes of the Kreb’s oxidative tricarboxylic acid pathway (oTCA) in Archaea, Bacteria and Eukarya and 5545 sequences of 33 bacteria as geochronologically separated enzymes with MSA consensus site modal identities. The 33 bacteria were 20 presumptive examples of early-oldest (Hadean-Archaean) (‘Epoch I’) or 13 late-newest (contemporary) (‘Epoch III’) appearing enzymes on Earth. The enzyme’s MSA consensus sites were identified by their modal identity, % Occupancy in one of nine-graded evolutionary-conservation zones (CZs) and the Euclidean distance (Å) from each of their consensus MSA Cɑs to the same atom (Anchor-atom) in their reported functional center. These MSA consensus sites are tetrad-data points called recovered-amino acids (RAA). Across Domains, the % Occupancies of the eight-dominant RAAs of the Kreb’s cycle and the 33 bacteria were found to be similarly ranked. Compared to Trifonov’s ‘putative ranked temporal order of the appearance of amino acids on Earth’ (TOAE), the greatest statistical concordance with tetrad-RAAs across Domains were those characterized as within the most-evolutionary conserved conservation zone (CZ9), typically nearest (Å) their enzyme’s catalytic/active center. The geochronologically characterized early-oldest Hadean-Archaean Bacteria ‘Epoch I’ enzymes, compared to late-newest Bacteria enzymes, had greater average numbers of amino acid residues/sequence and a statistically significant larger variability in their RAA compositional-Å<sup>3</sup>-volumes. The late-newest ‘Epoch III’ enzymes had statistically significant lower volumetric values, specifically, their native Å<sup>3</sup>-volume, void-volume and volume change on unfolding. Our enzyme data suggest a geochronological trace of ‘<i>metabolism’s progressive emergence</i>’. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9975866.v2
title: Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence

description: We studied multiple sequence alignment (MSA) consensus amino acid distributional patterns in 2844 amino acid sequences of the eight enzymes of the Kreb’s oxidative tricarboxylic acid pathway (oTCA) in Archaea, Bacteria and Eukarya and 5545 sequences of 33 bacteria as geochronologically separated enzymes with MSA consensus site modal identities. The 33 bacteria were 20 presumptive examples of early-oldest (Hadean-Archaean) (‘Epoch I’) or 13 late-newest (contemporary) (‘Epoch III’) appearing enzymes on Earth. The enzyme’s MSA consensus sites were identified by their modal identity, % Occupancy in one of nine-graded evolutionary-conservation zones (CZs) and the Euclidean distance (Å) from each of their consensus MSA Cɑs to the same atom (Anchor-atom) in their reported functional center. These MSA consensus sites are tetrad-data points called recovered-amino acids (RAA). Across Domains, the % Occupancies of the eight-dominant RAAs of the Kreb’s cycle and the 33 bacteria were found to be similarly ranked. Compared to Trifonov’s ‘putative ranked temporal order of the appearance of amino acids on Earth’ (TOAE), the greatest statistical concordance with tetrad-RAAs across Domains were those characterized as within the most-evolutionary conserved conservation zone (CZ9), typically nearest (Å) their enzyme’s catalytic/active center. The geochronologically characterized early-oldest Hadean-Archaean Bacteria ‘Epoch I’ enzymes, compared to late-newest Bacteria enzymes, had greater average numbers of amino acid residues/sequence and a statistically significant larger variability in their RAA compositional-Å<sup>3</sup>-volumes. The late-newest ‘Epoch III’ enzymes had statistically significant lower volumetric values, specifically, their native Å<sup>3</sup>-volume, void-volume and volume change on unfolding. Our enzyme data suggest a geochronological trace of ‘<i>metabolism’s progressive emergence</i>’. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9975755
title: MOESM1 of Lymphocyte homeostasis is maintained in perinatally HIV-infected patients after three decades of life

description: Additional file 1. Gender-related median values of TRECs and KRECs in perinatally HIV-infected youths (pHIVy), in non-perinatally HIV-infected youths (npHIVy) and in healthy controls (HC).
DOI: 10.6084/m9.figshare.9975755.v1
title: MOESM1 of Lymphocyte homeostasis is maintained in perinatally HIV-infected patients after three decades of life

description: Additional file 1. Gender-related median values of TRECs and KRECs in perinatally HIV-infected youths (pHIVy), in non-perinatally HIV-infected youths (npHIVy) and in healthy controls (HC).
DOI: 10.6084/m9.figshare.9975728
title: MOESM3 of Use of literature mining for early identification of emerging contaminants in freshwater resources

description: Additional file 3. Results of applying the developed methodology to recent literature, namely articles published between 2016 and 27th of August 2018. Table containing the articlesâ Electronic Identifier (EID), authors, title, publication year, journal, volume, page information, citations, Digital Object Identifier (DOI), link to the article in ScopusÂŽ, abstract, sentence matching the pattern, whether or not the article was considered to be eligible or not and why.
DOI: 10.6084/m9.figshare.9975734
title: MOESM4 of Use of literature mining for early identification of emerging contaminants in freshwater resources

description: Additional file 4. Analysis for false negatives of random selection of 1750 articles from the 23,217 articles (published between 2006 and 2012) that did not match the pattern. Table containing the articlesâ Electronic Identifier (EID), authors, title, publication year, journal, volume, page information, citations, Digital Object Identifier (DOI), link to the article in ScopusÂŽ, abstract, the sentence that matched the pattern and whether the articles is considered to be a false negative or not.
DOI: 10.6084/m9.figshare.9975734.v1
title: MOESM4 of Use of literature mining for early identification of emerging contaminants in freshwater resources

description: Additional file 4. Analysis for false negatives of random selection of 1750 articles from the 23,217 articles (published between 2006 and 2012) that did not match the pattern. Table containing the articlesâ Electronic Identifier (EID), authors, title, publication year, journal, volume, page information, citations, Digital Object Identifier (DOI), link to the article in ScopusÂŽ, abstract, the sentence that matched the pattern and whether the articles is considered to be a false negative or not.
DOI: 10.6084/m9.figshare.9975728.v1
title: MOESM3 of Use of literature mining for early identification of emerging contaminants in freshwater resources

description: Additional file 3. Results of applying the developed methodology to recent literature, namely articles published between 2016 and 27th of August 2018. Table containing the articlesâ Electronic Identifier (EID), authors, title, publication year, journal, volume, page information, citations, Digital Object Identifier (DOI), link to the article in ScopusÂŽ, abstract, sentence matching the pattern, whether or not the article was considered to be eligible or not and why.
DOI: 10.6084/m9.figshare.9975710
title: codes and data

description: The GeoLife data were derived from the following resources available in the public domain: [https://www.microsoft.com/en-us/download/details.aspx?id=52367].These codes were mainly used to compute the value of FD of trajectories and further detect the walking pattern of pedestrians. In addtion, readers can acqurie the code of pedestrian network generation based on KDE-based method from the referenced article (website: http://mapconstruction.org/). <br>