cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25375/uct.14176484
title: Validation of Correlates of Risk of TB Disease in High Risk Populations (CORTIS-HR) Study: Public, subject-level RISK11 signature scores and metadata

description: The <b>Validation of Correlates of Risk of TB Disease in High Risk Populations (CORTIS-HR) Study</b>, a companion study of the CORTIS-01 Trial (ClinicalTrials.gov: NCT02735590), was conducted to test the diagnostic and prognostic performance of the RISK11 biomarker for tuberculosis (TB) disease in people living with HIV (PLHIV) in an ambulant community setting.<br><br>The “CORTIS-HR pubdata.csv” is a public, subject-level dataset for the CORTIS-HR study containing key variables necessary to reconstruct the study findings. A data dictionary is provided below. The “CORTIS-HR PCR data.csv” provides subject-level TaqMan qPCR probe raw CT (cycle threshold) gene expression data from the Fluidigm microfluidic 96.96 Gene Expression Integrated Fluidic Circuits (chips) with sample quality control (“SAMPLE_QC”) results. Analyses of the qPCR probe data are ongoing; the embargo on this data ends 1 July 2021 when the data will be available on ZivaHub. “CORTIS-HR Protocol Version 1.0.pdf” and “CORTIS-HR SAP Version 1.0.pdf” are the protocol and the statistical analysis plan for the study respectively and have been included for reference.
DOI: 10.6084/m9.figshare.14332814.v1
title: Table S1

description: Table S1
DOI: 10.25505/fiz.icsd.cc27j1sm
title: CSD 2071010: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton|2021|ICSD Communication|||
DOI: 10.6084/m9.figshare.14332802
title: Effectiveness of Narrative Therapy on Adult Attachment Styles and Expressivity in Low Marital Satisfaction

description: This paper aims to investigate the effectiveness of narrative therapy on adult attachment styles and expressivity in low marital satisfaction
DOI: 10.5281/zenodo.4570348
title: Pupillary response to real, illusory, and implied motion

description: “.mat” files contain: BUF2: Recording during fixation slide (column 1: time; column 2: right pupil width; column 3: right pupil height; column 4: left pupil width; column 5: left pupil height; column 6: glint data from right eye; column 7: glint data from right eye; column 8: image number) BUF: Recording during stimulus presentation (same columns of BUF2) c: block’s specifics (eye-tracker information, trials number and duration, start and end times of eye-tracker registrations) smile: images code Response: block’s information (first column: stimulus presentation time; variable number of other columns: smile variable; last column: trials number); Folder "Photos_blocks" contains all experimental stimuli divided per blocks (in presentation order).
DOI: 10.5281/zenodo.4570347
title: Pupillary response to real, illusory, and implied motion

description: “.mat” files contain: BUF2: Recording during fixation slide (column 1: time; column 2: right pupil width; column 3: right pupil height; column 4: left pupil width; column 5: left pupil height; column 6: glint data from right eye; column 7: glint data from right eye; column 8: image number) BUF: Recording during stimulus presentation (same columns of BUF2) c: block’s specifics (eye-tracker information, trials number and duration, start and end times of eye-tracker registrations) smile: images code Response: block’s information (first column: stimulus presentation time; variable number of other columns: smile variable; last column: trials number); Folder "Photos_blocks" contains all experimental stimuli divided per blocks (in presentation order).
DOI: 10.5281/zenodo.4643470
title: NanoString dataset for study: Predicting the clinical outcome of oral potentially malignant disorders using transcriptomic-based molecular pathology

description: Normalised NanoString mRNA abundance training and test datasets used for the discovery of 11 gene multivariable prognostic classifier of oral potentially malignant disorders (OPMD).
DOI: 10.5281/zenodo.4643469
title: NanoString dataset for study: Predicting the clinical outcome of oral potentially malignant disorders using transcriptomic-based molecular pathology

description: Normalised NanoString mRNA abundance training and test datasets used for the discovery of 11 gene multivariable prognostic classifier of oral potentially malignant disorders (OPMD).
DOI: 10.5281/zenodo.4643380
title: MItosis DOmain Generalization Challenge (MICCAI-MIDOG 2021) Training Data

description: We present the training dataset of the MICCAI-MIDOG 2021 challenge. The task of the challenge is the generalization of the detection of mitotic figures to multiple microscopy whole slide image scanners. The data set consists of 200 cases of human breast cancer. Each of the images was cropped from a whole slide image. The region for cropping was selected by a pathologist according to current guidelines. All images come from the same lab (UMC Utrecht) and have thus similar staining intensity, i.e. all visible differences in representation can be attributed to a different digital representation by the acquisition device. The images 001.tiff to 050.tiff were acquired with a Hamamatsu XR scanner.<br> The images 051.tiff to 100.tiff were acquired with a Hamamatsu S360 scanner.<br> The images 101.tiff to 150.tiff were acquired with an Aperio CS2 scanner.<br> The images 151.tiff to 200.tiff were acquired with a Leica GT450 scanner. The cases of all scanners represent a similar distribution of tumor grades. The complete collection of cases represents consecutive cases from the archive that were qualified according to inclusion criteria. The file MIDOG.json represents all annotations in MS COCO format. Please note that we did include not only mitotic figure annotations but also annotations where experts disagreed or that qualify as hard examples for machine learning.<br> The challenge description can be found at http://doi.org/10.5281/zenodo.4573978.
DOI: 10.6084/m9.figshare.14184813
title: Pharmacokinetics and metabolism of brexpiprazole, a novel serotonin-dopamine activity modulator and its main metabolite in rat, monkey and human

description: The pharmacokinetics of brexpiprazole were investigated in the <i>in vitro</i> and <i>in vivo</i>. The total body clearance of brexpiprazole in rat and monkey was 2.32 and 0.326 L/h/kg, respectively, after intravenous administration, and oral availability was 13.6% and 31.0%, respectively. Dose-dependent exposures were observed at dose ranges between 1–30 mg/kg in the rat and 0.1–3 mg/kg in the monkey. Brexpiprazole distributed widely to body tissues, and V<sub>d,z</sub> were 2.81 and 1.82 L/kg in rat and monkey, respectively. The serum protein binding of brexpiprazole was 99% or more in animals and human. Uniform distribution character among the species was suggested by a traditional animal scale-up method. A common main metabolite, DM-3411 was found in animals and humans in the metabolic reactions with the liver S9 fraction. CYP3A4 and CYP2D6 were predominantly involved in the metabolism. The affinity of DM-3411 for D<sub>2</sub> receptors was lower than that of brexpiprazole, and neither DM-3411 nor any metabolites with affinity other than M3 were detected in the brain, demonstrating that brexpiprazole is only involved in the pharmacological effects. Overall, brexpiprazole has a simple pharmacokinetic profile with good metabolic stability, linear kinetics, and no remarkable species differences with regard to metabolism and tissue distribution.
DOI: 10.5281/zenodo.4643534
title: Near surface defects: Cause of deficit between internal and external open-circuit voltage in solar cells

description: Here def files of models used in SCAPS-1D for simulations and the raw measured data of Fig. 1 a and c, 2a, 3b and d presented in the manuscript "Near surface defects: Cause of deficit between internal and external open-circuit voltage in solar cells" is provided.
DOI: 10.5281/zenodo.4643533
title: Near surface defects: Cause of deficit between internal and external open-circuit voltage in solar cells

description: Here def files of models used in SCAPS-1D for simulations and the raw measured data of Fig. 1 a and c, 2a, 3b and d presented in the manuscript "Near surface defects: Cause of deficit between internal and external open-circuit voltage in solar cells" is provided.
DOI: 10.5281/zenodo.4643558
title: Cd K-edge XAS spectra of Cd reference compounds relevant to the soil/plant system

description: Here we present a library of Cd reference compounds Cd K-edge XAS spectra relevant to soil and plant samples. We reported mu (eV) .txt files for each reference as well as a .pdf file that gives details on the preparation of the references and on the acquisition of the spectra. Additional information can be found in Pons et al., 2021, Environmental Pollution. https://doi.org/10.1016/j.envpol.2021.116897
DOI: 10.5281/zenodo.4643557
title: Cd K-edge XAS spectra of Cd reference compounds relevant to the soil/plant system

description: Here we present a library of Cd reference compounds Cd K-edge XAS spectra relevant to soil and plant samples. We reported mu (eV) .txt files for each reference as well as a .pdf file that gives details on the preparation of the references and on the acquisition of the spectra. Additional information can be found in Pons et al., 2021, Environmental Pollution. https://doi.org/10.1016/j.envpol.2021.116897
DOI: 10.6084/m9.figshare.12085806
title: In silico studies of the inhibition mechanism of dengue with papain

description: Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of −352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12063639
title: Distribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules

description: DNA topology changes continuously as replication proceeds. Unwinding of the DNA duplex by helicases is favored by negative supercoiling but it causes the progressive accumulation of positive supercoiling ahead of the fork. This torsional stress must be removed for the fork to keep advancing. Elimination of this positive torsional stress may be accomplished by topoisomerases acting solely ahead of the fork or simultaneously in the un-replicated and replicated regions after diffusion of some positive torsional strain from the un-replicated to the replicated regions by swivelling of the replication forks. In any case, once replication is completed fully replicated molecules are known to be heavily catenated and this catenation derives from pre-catenanes formed during replication. Although there is still controversy as to whether fork swiveling redistributes this positive torsional stress continuously or only as termination approaches, the forces that cause fork rotation and the generation of pre-catenanes are still poorly characterized. Here we used a numerical simulation, based on the worm-like chain model and the Metropolis Monte Carlo method, to study the interchange of supercoiling and pre-catenation in a naked circular DNA molecule of 4,440 bp partially replicated <i>in vivo</i> and <i>in vitro</i>. We propose that a dynamic gradient of torsional stress between the un-replicated and replicated regions drives fork swiveling allowing the interchange of supercoiling and pre-catenation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12063639.v2
title: Distribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules

description: DNA topology changes continuously as replication proceeds. Unwinding of the DNA duplex by helicases is favored by negative supercoiling but it causes the progressive accumulation of positive supercoiling ahead of the fork. This torsional stress must be removed for the fork to keep advancing. Elimination of this positive torsional stress may be accomplished by topoisomerases acting solely ahead of the fork or simultaneously in the un-replicated and replicated regions after diffusion of some positive torsional strain from the un-replicated to the replicated regions by swivelling of the replication forks. In any case, once replication is completed fully replicated molecules are known to be heavily catenated and this catenation derives from pre-catenanes formed during replication. Although there is still controversy as to whether fork swiveling redistributes this positive torsional stress continuously or only as termination approaches, the forces that cause fork rotation and the generation of pre-catenanes are still poorly characterized. Here we used a numerical simulation, based on the worm-like chain model and the Metropolis Monte Carlo method, to study the interchange of supercoiling and pre-catenation in a naked circular DNA molecule of 4,440 bp partially replicated <i>in vivo</i> and <i>in vitro</i>. We propose that a dynamic gradient of torsional stress between the un-replicated and replicated regions drives fork swiveling allowing the interchange of supercoiling and pre-catenation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12085806.v1
title: In silico studies of the inhibition mechanism of dengue with papain

description: Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of −352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12263099
title: Pharmacophore- based virtual screening, 3D- QSAR, molecular docking approach for identification of potential dipeptidyl peptidase IV inhibitors

description: Pharmacophore modeling, molecular docking, and in silico ADME studies have been carried out to determine the binding mode and drug likeliness profile of Pyrrolidine derivatives as Dipeptidyl peptidase IV inhibitors. A five point pharmacophore model (AAADH_1) was generated using 96 compounds with IC<sub>50</sub> values ranging from 1.8 to 13000 nM. A statistically significant 3D-QSAR model was generated from the pharmacophore hypothesis. The model had a high correlation coefficient (R<sup>2</sup> - 0.92), cross validation coefficient (Q<sup>2</sup> - 0.776) and F value (F - 144) at 6 component Partial least square factor. Pearson r of 0.7124 indicated greater degree of confidence on the model. The accuracy and predictability of the generated model were checked by Enrichment factor, Receiver operating characteristic curves, area under curve, Boltzmann-enhanced discrimination of Receiver operating characteristic and the Robust initial enhancement. To identify novel and potent Dipeptidyl peptidase IV inhibitors, virtual screening was performed using the ligand and database screening. Considering the potent hit molecules on the basis of pharmacophore virtual screening, we have designed new molecules and further subjected to see the interaction with protein. The catalytic domain of Dipeptidyl peptidase IV enzyme in complex with Vildagliptin (PDB Code: 6B1E) was obtained from protein data bank with resolution 1.77 A°. Compound 75 showed the better binding (dock score -7.966) with protein than standard drug vildagliptin (Dock Score -6.554). The hits obtained on virtual screening of the database have provided new chemical starting points for design and development of novel Dipeptidyl peptidase IV inhibitory agents. Communicated by Ramaswamy H. Sarma.
DOI: 10.6084/m9.figshare.12263099.v1
title: Pharmacophore- based virtual screening, 3D- QSAR, molecular docking approach for identification of potential dipeptidyl peptidase IV inhibitors

description: Pharmacophore modeling, molecular docking, and in silico ADME studies have been carried out to determine the binding mode and drug likeliness profile of Pyrrolidine derivatives as Dipeptidyl peptidase IV inhibitors. A five point pharmacophore model (AAADH_1) was generated using 96 compounds with IC<sub>50</sub> values ranging from 1.8 to 13000 nM. A statistically significant 3D-QSAR model was generated from the pharmacophore hypothesis. The model had a high correlation coefficient (R<sup>2</sup> - 0.92), cross validation coefficient (Q<sup>2</sup> - 0.776) and F value (F - 144) at 6 component Partial least square factor. Pearson r of 0.7124 indicated greater degree of confidence on the model. The accuracy and predictability of the generated model were checked by Enrichment factor, Receiver operating characteristic curves, area under curve, Boltzmann-enhanced discrimination of Receiver operating characteristic and the Robust initial enhancement. To identify novel and potent Dipeptidyl peptidase IV inhibitors, virtual screening was performed using the ligand and database screening. Considering the potent hit molecules on the basis of pharmacophore virtual screening, we have designed new molecules and further subjected to see the interaction with protein. The catalytic domain of Dipeptidyl peptidase IV enzyme in complex with Vildagliptin (PDB Code: 6B1E) was obtained from protein data bank with resolution 1.77 A°. Compound 75 showed the better binding (dock score -7.966) with protein than standard drug vildagliptin (Dock Score -6.554). The hits obtained on virtual screening of the database have provided new chemical starting points for design and development of novel Dipeptidyl peptidase IV inhibitory agents. Communicated by Ramaswamy H. Sarma.
DOI: 10.6084/m9.figshare.12005607.v2
title: Functional study of acetaldehyde dehydrogenase 1 (ALDH1) in keratinocytes: microarray integrating bioinformatics approaches

description: The function of acetaldehyde dehydrogenase 1 (ALDH1) has been gradually elucidated in several diseases, especially in various cancers. However, the role of ALDH1 in skin-related diseases has been mostly unknown. Previously, we found that ALDH1 is involved in the pathogenesis of atopic dermatitis (AD). In this study, we used high-throughput screening (HTS) approaches to identify critical factors associated with ALDH1 in human keratinocytes to reveal its functions in skin. We overexpressed ALDH1 in human HaCaT keratinocytes and then conducted serial HTS studies, a DNA microarray and antibody array integrated with bioinformatics algorithms. Together, those tests identified several novel genes associated with the function of ALDH1 in keratinocytes, as well as AD, including CTSG and CCL11. In particular, GNB3, GHSR, TAS2R9, FFAR1, TAS2R16, CCL21, GPR32, NPFFR1, GPR15, FBXW12, CCL19, EDNRA, FFAR3, and RXFP3 proteins were consistently detected as hub proteins in the PPI maps. By integrating the datasets obtained from these HTS studies and using the strengths of each method, we obtained new insights into the functional role of ALDH1 in skin keratinocytes. The approach used here could contribute to the clinical understanding of ALDH1-associated applications for the treatment of AD. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12005607
title: Functional study of acetaldehyde dehydrogenase 1 (ALDH1) in keratinocytes: microarray integrating bioinformatics approaches

description: The function of acetaldehyde dehydrogenase 1 (ALDH1) has been gradually elucidated in several diseases, especially in various cancers. However, the role of ALDH1 in skin-related diseases has been mostly unknown. Previously, we found that ALDH1 is involved in the pathogenesis of atopic dermatitis (AD). In this study, we used high-throughput screening (HTS) approaches to identify critical factors associated with ALDH1 in human keratinocytes to reveal its functions in skin. We overexpressed ALDH1 in human HaCaT keratinocytes and then conducted serial HTS studies, a DNA microarray and antibody array integrated with bioinformatics algorithms. Together, those tests identified several novel genes associated with the function of ALDH1 in keratinocytes, as well as AD, including CTSG and CCL11. In particular, GNB3, GHSR, TAS2R9, FFAR1, TAS2R16, CCL21, GPR32, NPFFR1, GPR15, FBXW12, CCL19, EDNRA, FFAR3, and RXFP3 proteins were consistently detected as hub proteins in the PPI maps. By integrating the datasets obtained from these HTS studies and using the strengths of each method, we obtained new insights into the functional role of ALDH1 in skin keratinocytes. The approach used here could contribute to the clinical understanding of ALDH1-associated applications for the treatment of AD. Communicated by Ramaswamy H. Sarma