cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/jzsx489pmk.2
title: Broadly neutralizing antibodies target a hemagglutinin anchor epitope, Guthmiller et al. 2021

description: This study was designed to analyze the B cell repertoire of cH5/1 binding B cells following vaccination with the cHA platform. Human B cells (CD19+IgM-CD27+cH5/1+) were sorted at day 113 and were used for downstream sequencing. This dataset is comprised of a collection of BCR sequences of 1952 antibodies with paired heavy chain and light chain, a collection of BCR sequences of 119 anchor antibodies, and a collection of BCR sequences of 365 VH1-69&kappa. 

PROTOCOLS: 
cH5/1+ memory B cells (CD19+CD27+HA+) were bulk sorted and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) to achieve single cell resolution using the 10x Genomics Chromium Controller and according to the manufacturer’s instruction (10x Genomics). The sorted single cells were processed according to 5’ gene expression and B cell Immunoglobulin (Ig) enrichment instruction to prepare the libraries for sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at Northwestern University or an Illumina NextSeq 500 at the University of Chicago. 

Cellranger Single-Cell Software Suite (version 3.0) was used to perform sample de-multiplexing, barcode processing, and single-cell 5’ and V(D)J counting, and Cellranger mkfastq was used to de-multiplex raw base call (BCL) files into sample-specific fastq files. Subsequently, GRCh38-1.2.0 and cellranger-vdj-GRCh38-alta-ensembl-2.0.0 were used as references for the transcriptome and V(D)J assembly, respectively. Cellranger counts and Cellranger vdj package were used to identify gene expression and assemble V(D)J pairs of antibodies. BCR sequences were then processed by IgBlast and our in-house software VGenes. 

Please see readme.xlsx file for more details.
DOI: 10.17632/zpwkwwg5xz.1
title: Kellermann et al 2022_Preparation for denitrification at the cusp of anoxia

description: Supporting information to Kellermann et al, submitted to mBio January 2022; five separate files named supplemental item 1-5. 

Paper abstract:
Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O2- repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed bet-hedging, where all cells synthesize the N2O reductase (NosZ) but only a minority synthesizes nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia, but with the possibility of escape if supplied with O2 or N2O. To test this, cells were exposed to gradual O2-depletion or sudden anoxia, and subsequent spikes of O2 and N2O. The synthesis of NirS in single cells was monitored by using an mCherry-nirS fusion replacing the native nirS, and their growth was detected as dilution of green, fluorescent FITC-stain. We demonstrate anoxic entrapment due to e--acceptor deprivation and show that O2-spiking leads to bet-hedging, while N2O-spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the N2O-spike had much lower respiration rates than those rescued by the O2-spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O2. Our results bring into relief a fitness advantage of pairing restrictive nirS expression with universal NosZ synthesis in energy limited systems.

Supplemental item 1 is a description and qualification of the glucose oxidase-catalase (GOX) approach used for the removal of residual oxygen in experimental vials before inoculation.  In supplemental item 2, we display the gas- and flow cytometry data  in the O2 spiking experiment, including the data shown in Figure 2 and 3 in the paper. In supplemental item 3, we show the gas kinetics and microscopy analyses from the N2O spiking experiment, which in the paper is summarized in Fig 4. In supplemental item 4, we describe the steps taken to estimate apparent specific growth rates in single vials and cell yield per mol electron to N-oxides. In supplemental item 5, we describe a simple experiment where nitrite reducing cultures of Paracoccus denitrificans was spiked with N2O and O2 and the subsequent rate of nitrite reduction was assessed.
DOI: 10.17632/5v6b78cd9r.1
title: Pairwise comparison matrices and initial decision matrices for rough-Z-number extended MCGDM

description: This dataset provides the five pairwise comparison matrices (PCMs) and five initial decision matrices (IDMs) used in the rough-Z-number extended MCGDM.
DOI: 10.17632/f9hfcfyt93.1
title: GBM CODEX clustered single cell data 

description: We imaged in total 58 glioblastoma explants using CODEX technology with a 55-marker panel. The imaging data was segmented into single cells  based on best-focus nuclear staining using DAPI and DRAQ5 as reference. Spatial (X/Y/Z) coordinates can locate each cell within a specific slide. Cell type annotation was thereafter performed using both VORTEX clustering and manual supervision on the slides (refer to software package from the NOLAN lab, Stanford (https://github.com/nolanlab/CODEX). 
A previously established highly multiplexed tissue cytometry platform called CO-Detection by indEXing (CODEX) was re-engineered here here to create multidimensional imaging datasets of glioblastoma (GBM) bioreactor explants. In this procedure, DNA-barcoded antibodies bound to antigens present in the tissue were iteratively rendered visible by hybridizing complementary fluorescent DNA oligonucleotides. An algorithmic pipeline was used to process raw imaging data, segment and identify single cells and their localizations within tissues, and quantify their marker expression. Unsupervised clustering, followed by manual curation of clusters based on marker expression, morphology and tissue localization, was used to call out specific cell types. Expression of selected markers per cell were manually gated in CellEngine (https://cellengine.com). Cellular neighborhoods were algorithmically identified. We identified seven conserved, distinct tissue compartments (TCs) –a collection of components characteristic of the GBM iTME. This study provides a framework for interrogating how glioblastoma patients could potentially profit from local neoadjuvant immunotherapies. 

Clustering_results.csv table contains cell types annotation, expression profiles, coordinates of all segmented objected identified in the explants analyzed in this study. Further, it contains information on the biopsy location (c=center, p= periphery of the tumor), treatment info of the explants (control, anti-CD47, anti-PD1, combination), and the respective anonymized tumor internal tumor ID.
DOI: 10.17632/x3cf8d3vz8.3
title: Associations of thiazide use with skin cancers

description: Supplementary figures and tables
DOI: 10.17632/c9mmbmkwcj.2
title: Data on point cloud scanning and ground radar of composite lining in jointly constructed tunnel

description: The dataset includes the original mining surface profile data collected by the terrestrial laser scanning (TLS) and radar information on backfill quality outside the segmental lining which was obtained by the ground-penetration radar (GPR) detection, which supports the numerical analysis outlined in the article titled “Numerical evaluation of segmental tunnel lining with voids in outside backfill.”
DOI: 10.17632/pkxg7y9msz.1
title: Dataset of the double moon classification problem and the structure of the neural networks that perform the classification

description: Description: 
The attached files contain the data points of the double moon classification problem and the neural network that performs the classification. The double moon is a commonly used binary classification problem for neural networks. The size of the two semicircular arcs can be set by the parameters r and w, which give the radius and the width of the arcs, in our case r = 10 and w = 3. The parameter d defines the position of the classes relative to each other. If d is positive, then the two classes are linearly separable. If it is negative, then the two moons "intersect" and are nonlinearly separable. In this example, d = -5. Neural networks can learn nonlinear decision boundaries, so they can be used to solve this problem. We attach some neural networks that classify these data points with 100% accuracy.

2_moons.txt:
The first column contains the "x" coordinate, the second column the "y" coordinate, and the third column indicates the class of the data point.

x.csv:
The x in the file name indicates the number of hidden layers in the network and the number of hidden neurons within a hidden layer. A special format was used to save the network. The first column contains the number of neurons per layer, including input and output layers. Since we used fully connected feedforward neural networks, it is not necessary to save the endpoints of the edges. The second column contains the bias in the neurons, the bias in the input neurons is not interpreted. Finally, the third column contains the weights of the network.
DOI: 10.15131/shef.data.9449855
title: Typhoid toxin exhausts the RPA response to DNA replication stress driving senescence and Salmonella infection

description: Data relating to Nature Communications Article 'Typhoid toxin exhausts the RPA response to DNA replication stress driving senescence and Salmonella infection'<br>Ibler et al<i>Nature Communications</i>volume 10, Article number: 4040 (2019) <br><br>AbstractSalmonella Typhi activates the host DNA damage response through the typhoid toxin, facilitating typhoid symptoms and chronic infections. Here we reveal a non-canonical DNA damage response, which we call RING (response induced by a genotoxin), characterized by accumulation of phosphorylated histone H2AX (γH2AX) at the nuclear periphery. RING is the result of persistent DNAdamage mediated by toxin nuclease activity and is characterized by hyperphosphorylation of RPA, a sensor of single-stranded DNA(ssDNA) and DNA replication stress. The toxin overloads the RPA pathway with ssDNA substrate, causing RPA exhaustion and senescence. Senescence is also induced by canonical γΗ2ΑΧ foci revealing distinct mechanisms. Senescence is transmitted to non-intoxicated bystander cells by an unidentified senescence-associated secreted factor that enhances Salmonella infections. Thus, our work uncovers a mechanism by which genotoxic Salmonella exhausts the RPA response by inducing ssDNA formation, driving host cell senescence and facilitating infection.<br>Methodology: The data is from a biological study use cultured human cells, which have been used in Salmonella infection experiments. The data was collected using biochemical and cell biology techniques. A full description of the methodology is provided in the file ' Ibler et al_merged manuscript'.
DOI: 10.15131/shef.data.9449855.v1
title: Typhoid toxin exhausts the RPA response to DNA replication stress driving senescence and Salmonella infection

description: Data relating to Nature Communications Article 'Typhoid toxin exhausts the RPA response to DNA replication stress driving senescence and Salmonella infection'<br>Ibler et al<i>Nature Communications</i>volume 10, Article number: 4040 (2019) <br><br>AbstractSalmonella Typhi activates the host DNA damage response through the typhoid toxin, facilitating typhoid symptoms and chronic infections. Here we reveal a non-canonical DNA damage response, which we call RING (response induced by a genotoxin), characterized by accumulation of phosphorylated histone H2AX (γH2AX) at the nuclear periphery. RING is the result of persistent DNAdamage mediated by toxin nuclease activity and is characterized by hyperphosphorylation of RPA, a sensor of single-stranded DNA(ssDNA) and DNA replication stress. The toxin overloads the RPA pathway with ssDNA substrate, causing RPA exhaustion and senescence. Senescence is also induced by canonical γΗ2ΑΧ foci revealing distinct mechanisms. Senescence is transmitted to non-intoxicated bystander cells by an unidentified senescence-associated secreted factor that enhances Salmonella infections. Thus, our work uncovers a mechanism by which genotoxic Salmonella exhausts the RPA response by inducing ssDNA formation, driving host cell senescence and facilitating infection.<br>Methodology: The data is from a biological study use cultured human cells, which have been used in Salmonella infection experiments. The data was collected using biochemical and cell biology techniques. A full description of the methodology is provided in the file ' Ibler et al_merged manuscript'.
DOI: 10.6084/m9.figshare.17883914
title: Question 2 for TMU PhD candidate

description: Dear TMU PhD candidate, Please run principal component analysis (PCA) for dataset as below: a) Calculate Eigenvalue for PC1 and PC2. b) Draw the scatter plot. c) Which loading plots are in the opposite direction to the others? Thank You
DOI: 10.6084/m9.figshare.17884843
title: The role of engineering geology in delivering the United Nations Sustainable Development Goals

description: Mapping exercise spreadsheet
DOI: 10.6084/m9.figshare.17884843.v1
title: The role of engineering geology in delivering the United Nations Sustainable Development Goals

description: Mapping exercise spreadsheet
DOI: 10.17632/csm5gsmr5t.1
title: Data presented in a pharmaceutical-related molecules dataset for reversed-phase chromatography retention time prediction built on combining pH and gradient time conditions - System 1

description: Presented data is introduced in the article "A pharmaceutical-related molecules dataset for reversed-phase chromatography retention time prediction built on combining pH and gradient time conditions". This is a subset with data acquired on chromatographic system 1.
DOI: 10.17632/pm6ks8k59x.1
title: Investors Characteristics towards Sustainable Investment

description: The data was collected through a structured questionnaire. Twelve municipal corporations and eleven village panchayats of Tamilnadu were selected for collecting the data. The questionnaire also elicits information on the demographic profile of the respondents. The national and international existing literature on investors’ investment decision towards the sustainable investment was reviewed for developing the questionnaire.  The questionnaire was also scrutinized by a panel of subject experts and statisticians. The questions in the questionnaire are sequentially arranged and the questions are asked in a simple and understandable manner. The respondents are first educated about the purpose of the study and assurance of confidentiality of the data is given to them.
	The survey has used different scales to measure the demographic profiles and investors’ characteristics towards the sustainable investments. In the first section of the questionnaire namely demographic/socio economic profile of the investors, nominal and ordinal scales are used. The second sections of the questionnaire, the questions are asked in the format of five-point Likert scale with 5 meaning “Strongly Agree”, 4 indicating “Agree”, 3 indicating “Neither Agree nor disagree”, 2 meaning “Disagree” and 1 indicating “Strongly Disagree”.
DOI: 10.17632/cr28w6b6m9.1
title: Mendeley supplemental figure 1.

description: Relationships between serum cytokine levels and clinical courses in SJS/TEN patients treated with the systemic steroid in combination with etanercept. The correlations between IL-18 or MIP-1α level and acute stage duration (A and C) or time of skin re-epithelialization (B and D) were tested, respectively. Correlation coefficients were determined by Pearson r correlation test in Mendeley supplemental figure 1A, and by Spearman rank correlation test in Mendeley supplemental figures 1B–1D.
DOI: 10.17632/2x8z7h3cmg.1
title: The Comparison of the Therapies on Test Anxiety:

description: The aim of this study is to compare the effectiveness of cognitive behavioral therapy (CBT) and mindfulness-based acceptance (MBA) in decreasing the anxiety of students, which negatively affects academic achievement. 
The measurement tool used to collect the data was the Test Anxiety Inventory (TAI). For the analysis of the data, Kruskal Wallis H and Wilcoxon Signed Ranks test (Z) were used. According to the results of the study, it was concluded that the TAI posttest of the MBA and CBT decreased significantly compared to the control group.
DOI: 10.17632/2w64h8pvkc.1
title: Data presented in a pharmaceutical-related molecules dataset for reversed-phase chromatography retention time prediction built on combining pH and gradient time conditions - System 2

description: Presented data is introduced in the article "A pharmaceutical-related molecules dataset for reversed-phase chromatography retention time prediction built on combining pH and gradient time conditions". This is a subset with data acquired on chromatographic system 2.
DOI: 10.17632/mpn65fcnwb.1
title: Supplemental Materials for the paper: 'An investigation into the spatiotemporal patterns of the Nymphalid butterfly Vagrans egista sinha (Kollar, [1844])' 

description: Abstract of paper (of which thes data are supplementary materials of):

Vagrans egista sinha (Kollar, [1844]), the Himalayan Vagrant is a subspecies of Nymphalid (Brush-footed) butterflies spread across Asia, whose western limit is in the north-west India. Observations of this subspecies have considerably increased over the past half-a-decade, with a spike in new sightings to the west of their previously known range. This has been considered as a range extension. The current study reports new records of this species from Bilaspur District, Himachal Pradesh, India (which are the first records for the district), through systematic and opportunistic sampling. This raises the question of whether the purported range extension towards the west could instead be a range shift or vagrancy, and whether there is any shift in elevational ranges in the populations across their known range. Questions pertaining to spatial differences in elevational ranges and seasonal variation, across their range, also piqued our curiosity. Using data from academic sources (such as published literature and museum collections), supplemented by data from public participation in scientific research and personal observations, these research questions are addressed. The accuracy of results when using citizen science data is also explored using the same dataset, focused on the impact of method of extraction of coordinates, and elevation derived from it under different scenarios. It was discovered that there has not been a range shift (either longitudinal or latitudinal) and observations don’t suggest vagrancy but a case of range extension. Other results indicated that there was no climb of population to higher elevations, no spatial differences in elevational ranges in the populations, or seasonal variation in activities across their range. It was also discovered that the method of data collection by, and extraction from, citizen science databases, can influence the accuracy of the results. Some problems involved in collecting data are discussed, and remedial solutions are suggested.
DOI: 10.17632/hxby7pf2n4.1
title: Research Instrument for Dataset for dynamic capability, digital transformation and firm competitiveness

description: This is the survey instrument for Dataset for dynamic capability, digital transformation and firm competitiveness
DOI: 10.17632/wkb5rrx8hn.1
title: Oxidative stress Markers Effect In Cmm

description: The research set out to determine the effect of the prophylactic and curative spray of the synthetic defense inducers on the tomato plant infected with Clavibacter michiganensis subsp michiganensis (Cmm), done at the Department of Plant Pathology, G B Pant University of Agriculture and Technology, India. In doing so, the tomato plants were artificially inoculated with Cmm, in two sets of plants receiving the treatment of SA, INA, BTH and lysozyme at the concentration of 200µM, 500µM and 800µM along with the positive and negative control, wherein one set of plants were treated before the pathogen inoculation and other was treated after the pathogen inoculation. The effect of defense inducers on plant was assessed through the enzymatic activity of PO (Table1 and fig1), phenyl propanoid synthesis (Table 2 , Fig.2 and Table3, Fig.3), PPO ( Table4, Fig.4), β-1,3 glucanase (PR2) (Table5, Fig.5), hydrogen peroxide production in leaf tissues (Fig.6) and lignin deposition in stem section (Fig.7). In comparing all the treatments it was observed that the prophylactic treatment is more efficient than the curative treatment (Table1) in imparting resistance to the tomato plants against the invading pathogen. These Figures and Tables are present in the attached file titled "Dataset for All Life Journal.docx".
DOI: 10.17632/7v5p4gsh4z.1
title: Data presented in a pharmaceutical-related molecules dataset for reversed-phase chromatography retention time prediction built on combining pH and gradient time conditions - System 3

description: Presented data is introduced in the article "A pharmaceutical-related molecules dataset for reversed-phase chromatography retention time prediction built on combining pH and gradient time conditions". This is a subset with data acquired on chromatographic system 3.
DOI: 10.17632/vd4g9xjt4b.2
title: Financial data of banks listed in the Dhaka Stock Exchange (DSE)

description: This dataset contains the financial information of publicly traded commercial banks listed in the Dhaka Stock Exchange (DSE) of Bangladesh through 2006 to 2017. All data are compiled from the bank annual reports. The currency of this dataset is Bangladeshi Taka (BDT).
DOI: 10.17632/v26j6t76hj.2
title: Data from: Precipitation, not elephants, best explains savanna woody cover at coarse spatial scales across eastern African protected areas 

description: This supplement provides the code and data used in "Precipitation, not elephants, best explains savanna woody cover across eastern African protected areas". Some files have not been included due to size. Contact Ryan Nagelkirk (nagelki4@msu.edu) for this data. A README document is provided to aid in the use of all data and code.
DOI: 10.17632/g2p7vwxyn2.3
title: ECG and GSR Data for Emotion Recognition

description: We present the data set of Electrocardiograms (ECG) and Galvanic Skin Response (GSR) for the emotion recognition task, helpful in human-computer interaction for individuals with cognitive and physical disorders. Wearable shimmer3 ECG and GSR sensors were used to acquire data from a total of 25 participants. The dataset consists of three parts, raw data, extracted features for ECG, and self-annotation labels. Raw data consists of multimodal data and single modal data in .mat format. Multimodal data consists of ECG and GSR for 12 participants, provided with 21 stimulus videos divided into three sessions. Similarly, single modal data consists of ECG data acquired from 13 other participants. These physiological signals correlate with the six basic emotions of surprise, anger, fear, happiness, sadness, disgust, and the addition of a neutral state. Each of these seven states was further divided into five levels of intensity of felt emotion, making a total of 35 emotional states.  Self annotation was performed by participants for these emotional states as well as scores of valence, arousal, and dominance. Twenty emotion-related features were extracted from each ECG sample and also provided as supplementary material for further analysis. This data provides a valuable addition to the physiological signal-based emotion recognition for the larger set of emotions and acquired during stressed situation of Covid-19 epidemic.