cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9821228
title: Evaluating the suitability of RNA intervention mechanism exerted by some flavonoid molecules against dengue virus MTase RNA capping site: a molecular docking, molecular dynamics simulation, and binding free energy study

description: Dengue virus (DENV) is one of the most dangerous mosquito-borne human pathogens known to the mankind. Currently, no vaccines or standard therapy is avaliable to treate DENV infection. This makes the drug development against DENV more significant and challenging. The MTase domain of DENV RNA RdRp NS5 is a promising drug target, because this domain hosts the RNA capping process of DENV RNA to escape from human immune system. In the present study, we have analysed the RNA intervention mechanism exerted by flavoniod molecules against NS5 MTase RNA capping site by using molecular docking, molecular dynamics simulation and the binding free energy calculations. The results from the docking analysis confirmed that the RNA intervention mecanism is exerted by the quercetagetin (QGN) molecule with all necessary intermolecular interactions and high binding affinity. Notably, QGN forms strong hydrogen bonding interactions with Asn18, Leu20 and Ser150 residues and π⋅⋅⋅π stacking interaction with Phe25 residue. The apo and QGN bound NS5 MTase and QGN-NS5 MTase complex were used for MD simulation. The results of MD simulation reveal that the RMSD and RMSF values of QGN-MTase complex have increased on comparing the apo protein due to the effect of ligand binding. The binding free energy calulation includes prediction of total binding free energy of ligand-protein complex and per-residue free energy decomposition. The QGN binding to NS5 MTase affects it’s native motion, this result is found from Principal component analysis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9821279.v1
title: Supplementary Material for: Yes-Associated Protein Promotes the Development of Condyloma Acuminatum through EGFR Pathway Activation

description: <b><i>Objective:</i></b> Investigate the role of Yes-associated protein (YAP1) in the development of condyloma acuminatum (CA). <b><i>Methods:</i></b> We enrolled 30 male patients with CA and 20 healthy individuals as a control group, to compare the YAP1 expression in their tissue samples. Following this, we overexpressed and downregulated <i>YAP1</i> expression in HaCaT cells to examine the migratory, proliferative, and apoptotic potential of HaCaT cells expressing different levels of YAP1. <b><i>Results:</i></b> In the CA patient tissue samples, an increase in YAP1 expression can be observed. In vitro<i>,</i>the overexpression of YAP1 was shown to promote the growth and migration of HaCaT cells and to activate epidermal growth factor receptor (EGFR) pathway-associated proteins, while the downregulation of YAP1 inhibited cell growth and migration of these cells. <b><i>Conclusions:</i></b> YAP1 promotes the growth of keratinocytes in CA through the activation of the EGFR pathway, and it may mediate the development of human papilloma virus-associated diseases.
DOI: 10.6084/m9.figshare.9821213
title: Supplementary Material for: Regional Citrate Anticoagulation versus No-Anticoagulation for Continuous Venovenous Hemofiltration in Acute Severe Hypernatremia Patients with Increased Bleeding Risk: A Retrospective Cohort Study

description: <b><i>Purpose:</i></b> This study was aimed at evaluating the efficacy and safety of regional citrate anticoagulation (RCA) versus no-anticoagulation continuous venovenous hemofiltration (CVVH) in acute severe hypernatremia patients with increased bleeding risk. <b><i>Materials and Methods:</i></b> Acute severe hypernatremia patients with high bleeding risk who underwent CVVH in our center between January 2011 and October 2017 were considered as candidates. Patients who were &lt;18 years old, with hypovolemic hypernatremia, and had systemic anticoagulation were excluded. The included patients were divided into RCA and no-anticoagulation groups according to their anticoagulation strategy during CVVH and matched by age, sequential organ failure assessment scores, and vasopressor dependency. <b><i>Results:</i></b> Of the 64 included patients, no-anticoagulation and RCA were employed for CVVH in 23 and 41 patients, respectively. The serum sodium reduction rate (RRSeNa) was not significantly different between the no-anticoagulation and RCA groups (<i>p</i> = 0.729). Compared to no-anticoagulation, RCA significantly prolonged the circuit survival time (15 h [4.1–23.9] vs. 51 h [21.3–80.7], <i>p</i> = 0.001). The incidence of filter failure was 65.2% (15/23) in the no-anticoagulation group and 2.4% (1/41) in the RCA group (<i>p</i> &lt; 0.001), respectively. In the matched cohort, the RRSeNas were not different between the 2 groups (<i>p</i> = 0.569), and the filter lifespan was significantly longer in the RCA group as well (<i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> RCA might be safe and effective for acute severe hypernatremia patients who underwent CVVH treatment. Further prospective, randomized, control trials are warranted to obtain robust evidences.
DOI: 10.6084/m9.figshare.9821222.v2
title: Quantitative structure-activity relationship and molecular docking studies on human proteasome inhibitors for anticancer activity targeting NF-κB signaling pathway

description: The abnormal ubiquitin-proteasome is found as an important target in various human diseases, especially in cancer, and recently it has received prevalent attention as a challenging therapeutic target. The current work is designed to derive a predictive two-dimensional quantitative structure-activity relationship model for anticancer human proteasome target of NF-κB signaling pathway. The established 2 D-QSAR is dependent on multiple linear regression approach and validated through leave-One-Out and external test set prediction method. The robust QSAR model showed the r<sup>2</sup> of 0.83 and q<sup>2</sup> of 0.80 and pred_r<sup>2</sup> of 0.77. Three chemical properties, electronegativity count, average potential, and T_2_N_6 were identified as significant descriptors to predict the anticancer activities of the proteasome antagonists. Besides, the predicted top hit compounds were considered to check out the compliance with Rule of five and pharmacokinetic parameters for oral bioavailability in the human body. The molecular docking was accomplished to unravel the molecular mode of action of best-predicted compounds which was compatible with the standard drug. Following this approach, lastly two compounds NP and AP were recognized as the best candidates since these top compounds follow all the standard limit point of entire filters and indicated effective and decent docking score. The outcomes of the study sturdily suggested that the developed model and top hit compound’s binding conformation are rational in the exploration of unknown antagonist’s anticancer activity. The research would be of great support and is supposed to be of immense significance in the development and designing of drug-like candidates in preliminary drug discovery. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9821207
title: Supplementary Material for: Racial and Ethnic Differences in Mortality Associated with Serum Potassium in Incident Peritoneal Dialysis Patients

description: <b><i>Background:</i></b> Abnormalities in serum potassium are risk factors for sudden cardiac death and arrhythmias among dialysis patients. Although a previous study in hemodialysis patients has shown that race/ethnicity may impact the relationship between serum potassium and mortality, the relationship remains unclear among peritoneal dialysis (PD) patients where the dynamics of serum potassium is more stable. <b><i>Methods:</i></b> Among 17,664 patients who started PD between January 1, 2007 and December 31, 2011 in a large US dialysis organization, we evaluated the association of serum potassium levels with all-cause and arrhythmia-related deaths across race/ethnicity using time-dependent Cox models with adjustments for demographics. We also used restricted cubic spline functions for serum potassium levels to explore non-linear associations. <b><i>Results:</i></b> Baseline serum potassium levels were the highest among Hispanics (4.2 ± 0.7 mEq/L) and lowest among non-Hispanic blacks (4.0 ± 0.7 mEq/L). Among 2,949 deaths during the follow-up of median 2.2 (interquartile ranges 1.3–3.2) years, 683 (23%) were arrhythmia-related deaths. Overall, both hyperkalemia and hypokalemia (i.e., serum potassium levels &gt;5.0 and &lt;3.5 mEq/L, respectively) were associated with higher all-cause and arrhythmia-related mortality. In a stratified analysis according to race/ethnicity, the association of hypokalemia with all-cause and arrhythmia-related mortality was consistent with an attenuation for arrhythmia-related mortality in non-Hispanic blacks. Hyperkalemia was associated with all-cause and arrhythmia-related mortality in non-Hispanic whites and non-Hispanic blacks, but no association was observed in Hispanics. <b><i>Conclusion:</i></b> Among incident PD patients, hypokalemia was consistently associated with all-cause and arrhythmia-related deaths irrespective of race/ethnicity. However, while hyperkalemia was associated with both death outcomes in non-Hispanic blacks and whites, it was not associated with either death outcome in Hispanic patients. Further studies are needed to demonstrate whether different strategies should be followed for the management of serum potassium levels according to race/ethnicity.
DOI: 10.6084/m9.figshare.9821207.v1
title: Supplementary Material for: Racial and Ethnic Differences in Mortality Associated with Serum Potassium in Incident Peritoneal Dialysis Patients

description: <b><i>Background:</i></b> Abnormalities in serum potassium are risk factors for sudden cardiac death and arrhythmias among dialysis patients. Although a previous study in hemodialysis patients has shown that race/ethnicity may impact the relationship between serum potassium and mortality, the relationship remains unclear among peritoneal dialysis (PD) patients where the dynamics of serum potassium is more stable. <b><i>Methods:</i></b> Among 17,664 patients who started PD between January 1, 2007 and December 31, 2011 in a large US dialysis organization, we evaluated the association of serum potassium levels with all-cause and arrhythmia-related deaths across race/ethnicity using time-dependent Cox models with adjustments for demographics. We also used restricted cubic spline functions for serum potassium levels to explore non-linear associations. <b><i>Results:</i></b> Baseline serum potassium levels were the highest among Hispanics (4.2 ± 0.7 mEq/L) and lowest among non-Hispanic blacks (4.0 ± 0.7 mEq/L). Among 2,949 deaths during the follow-up of median 2.2 (interquartile ranges 1.3–3.2) years, 683 (23%) were arrhythmia-related deaths. Overall, both hyperkalemia and hypokalemia (i.e., serum potassium levels &gt;5.0 and &lt;3.5 mEq/L, respectively) were associated with higher all-cause and arrhythmia-related mortality. In a stratified analysis according to race/ethnicity, the association of hypokalemia with all-cause and arrhythmia-related mortality was consistent with an attenuation for arrhythmia-related mortality in non-Hispanic blacks. Hyperkalemia was associated with all-cause and arrhythmia-related mortality in non-Hispanic whites and non-Hispanic blacks, but no association was observed in Hispanics. <b><i>Conclusion:</i></b> Among incident PD patients, hypokalemia was consistently associated with all-cause and arrhythmia-related deaths irrespective of race/ethnicity. However, while hyperkalemia was associated with both death outcomes in non-Hispanic blacks and whites, it was not associated with either death outcome in Hispanic patients. Further studies are needed to demonstrate whether different strategies should be followed for the management of serum potassium levels according to race/ethnicity.
DOI: 10.6084/m9.figshare.9821228.v2
title: Evaluating the suitability of RNA intervention mechanism exerted by some flavonoid molecules against dengue virus MTase RNA capping site: a molecular docking, molecular dynamics simulation, and binding free energy study

description: Dengue virus (DENV) is one of the most dangerous mosquito-borne human pathogens known to the mankind. Currently, no vaccines or standard therapy is avaliable to treate DENV infection. This makes the drug development against DENV more significant and challenging. The MTase domain of DENV RNA RdRp NS5 is a promising drug target, because this domain hosts the RNA capping process of DENV RNA to escape from human immune system. In the present study, we have analysed the RNA intervention mechanism exerted by flavoniod molecules against NS5 MTase RNA capping site by using molecular docking, molecular dynamics simulation and the binding free energy calculations. The results from the docking analysis confirmed that the RNA intervention mecanism is exerted by the quercetagetin (QGN) molecule with all necessary intermolecular interactions and high binding affinity. Notably, QGN forms strong hydrogen bonding interactions with Asn18, Leu20 and Ser150 residues and π⋅⋅⋅π stacking interaction with Phe25 residue. The apo and QGN bound NS5 MTase and QGN-NS5 MTase complex were used for MD simulation. The results of MD simulation reveal that the RMSD and RMSF values of QGN-MTase complex have increased on comparing the apo protein due to the effect of ligand binding. The binding free energy calulation includes prediction of total binding free energy of ligand-protein complex and per-residue free energy decomposition. The QGN binding to NS5 MTase affects it’s native motion, this result is found from Principal component analysis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9821162
title: meta.rtf

description: 2019-09-04 <br> The repository contain 3 <b>folders</b>: <br> * Scripts (R-scripts to generate centroids based on Aboufadel and Austin method and Barmore method. Also, included is R-script to generate the area/distance plot found in the paper. <br> * AboufadelAustin (Output data from Aboufadel and Austin method) <br> * Barmore (Output data from Barmore method) <br> <br> <b>File formats</b> <br> Following files belong to ESRI vector data storage format (shape files). <br> .shp — shape format; the feature geometry itself .shx — shape index format; a positional index of the feature geometry to allow seeking forwards and backwards quickly .dbf — attribute format; columnar attributes for each shape, in dBase IV format .prj — projection description .sbn and .sbx — a spatial indexof the features .shp.xml — geospatial metadata in XML format .cpg — used to specify the code page for .dbf or identifying the character encoding to be used <br> Tabular data file format Comma separated values file (CSV) <br> In each of the .shp, .shx, and .dbf files, the shapes in each file correspond to each other in sequence (i.e., the first record in the .shp file corresponds to the first record in the .shx and .dbf files, etc.). https://en.wikipedia.org/wiki/Shapefile <br> <br> <b>Files in AboufadelAustin and Barmore folders</b> <br> The centroid datasets created were separated by algorithm (Aboufadel or Barmore), year (1992-2013), and GADM (Database of Global Administrative Areas) level (0, 1 and 2). <br> In total 132 different datasets were created each including a quality flag for each centroid point. Since each dataset is small in terms of storage they are grouped by algorithm and GADM level making the resulting data files 6 in total (3 shapefiles and 3 CSV-files). <br> Centroids that did not fall within the corresponding administrative area were flagged, as were administrative areas that did not have a corresponding centre. In each shapefile (adm0, adm1, adm2) the field OUT_FLAG is used to store the flag value. In addition, there are three corresponding CSV-files, which in tabular form report on unplaced centroids. The user can then decide how to proceed with the handling of unplaced centroids based on the specific user needs and application at hand. <br> As an example, in the aboufadel folder there are 3 shapefiles for year 1992 providing centroids for administrative levels 0, 1 and 2. In addition, there are 3 textfiles (.CSV) reporting on unplaced centroids for each administrative level. <br> <b>In the file name</b>; DMSP_xxxx corresponds to the year of nighttime lights data, e.g. DMSP_1992 _gadm28_ is the Database of Global Administrative Areas version 2.8, _admx_ is administrative level number, 0, 1 or 2. e.g, _adm0_, _name is the corresponding method, e.g. Barmore, and _gcs_that a geographic coordinate system is used. <br> <br> <br> Ola Hall, Department of Human Geography, Lund University (Ola.hall@keg.lu.se)
DOI: 10.6084/m9.figshare.9821063
title: HMM List

description: This is the list of HMM used in the study along with their description and cutoffs that were used.
DOI: 10.6084/m9.figshare.9821162.v1
title: meta.rtf

description: 2019-09-04 <br> The repository contain 3 <b>folders</b>: <br> * Scripts (R-scripts to generate centroids based on Aboufadel and Austin method and Barmore method. Also, included is R-script to generate the area/distance plot found in the paper. <br> * AboufadelAustin (Output data from Aboufadel and Austin method) <br> * Barmore (Output data from Barmore method) <br> <br> <b>File formats</b> <br> Following files belong to ESRI vector data storage format (shape files). <br> .shp — shape format; the feature geometry itself .shx — shape index format; a positional index of the feature geometry to allow seeking forwards and backwards quickly .dbf — attribute format; columnar attributes for each shape, in dBase IV format .prj — projection description .sbn and .sbx — a spatial indexof the features .shp.xml — geospatial metadata in XML format .cpg — used to specify the code page for .dbf or identifying the character encoding to be used <br> Tabular data file format Comma separated values file (CSV) <br> In each of the .shp, .shx, and .dbf files, the shapes in each file correspond to each other in sequence (i.e., the first record in the .shp file corresponds to the first record in the .shx and .dbf files, etc.). https://en.wikipedia.org/wiki/Shapefile <br> <br> <b>Files in AboufadelAustin and Barmore folders</b> <br> The centroid datasets created were separated by algorithm (Aboufadel or Barmore), year (1992-2013), and GADM (Database of Global Administrative Areas) level (0, 1 and 2). <br> In total 132 different datasets were created each including a quality flag for each centroid point. Since each dataset is small in terms of storage they are grouped by algorithm and GADM level making the resulting data files 6 in total (3 shapefiles and 3 CSV-files). <br> Centroids that did not fall within the corresponding administrative area were flagged, as were administrative areas that did not have a corresponding centre. In each shapefile (adm0, adm1, adm2) the field OUT_FLAG is used to store the flag value. In addition, there are three corresponding CSV-files, which in tabular form report on unplaced centroids. The user can then decide how to proceed with the handling of unplaced centroids based on the specific user needs and application at hand. <br> As an example, in the aboufadel folder there are 3 shapefiles for year 1992 providing centroids for administrative levels 0, 1 and 2. In addition, there are 3 textfiles (.CSV) reporting on unplaced centroids for each administrative level. <br> <b>In the file name</b>; DMSP_xxxx corresponds to the year of nighttime lights data, e.g. DMSP_1992 _gadm28_ is the Database of Global Administrative Areas version 2.8, _admx_ is administrative level number, 0, 1 or 2. e.g, _adm0_, _name is the corresponding method, e.g. Barmore, and _gcs_that a geographic coordinate system is used. <br> <br> <br> Ola Hall, Department of Human Geography, Lund University (Ola.hall@keg.lu.se)
DOI: 10.6084/m9.figshare.9821063.v1
title: HMM List

description: This is the list of HMM used in the study along with their description and cutoffs that were used.
DOI: 10.6084/m9.figshare.9820961
title: Stein et al. 2020 Dataset

description: Original research data used in the publication of Stein et al. 2020.
DOI: 10.6084/m9.figshare.9820823
title: Additional file 2: of TRPP2 dysfunction decreases ATP-evoked calcium, induces cell aggregation and stimulates proliferation in T lymphocytes

description: Table S2. â Analysis of ATP- and PAF-evoked calcium as well as PC1 and TRPP2 expression in ADPKD patientsâ . In this table are inserted the values of PC1 and TRPP2 expression, data of ATP- and PAF-evoked calcium measured in ADPKD and control subjects as well as in wild type and PKD2 silenced Jurkat cells. The type of PKD mutation (when known) is also shown. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.9820814
title: Additional file 1: of TRPP2 dysfunction decreases ATP-evoked calcium, induces cell aggregation and stimulates proliferation in T lymphocytes

description: Table S1. â ADPKD patient cohort enrolled from four Nephrology Units of Emilia Romagna Region (Italy)â . This table contains information about ADPKD patients including clinical features. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.9820823.v1
title: Additional file 2: of TRPP2 dysfunction decreases ATP-evoked calcium, induces cell aggregation and stimulates proliferation in T lymphocytes

description: Table S2. â Analysis of ATP- and PAF-evoked calcium as well as PC1 and TRPP2 expression in ADPKD patientsâ . In this table are inserted the values of PC1 and TRPP2 expression, data of ATP- and PAF-evoked calcium measured in ADPKD and control subjects as well as in wild type and PKD2 silenced Jurkat cells. The type of PKD mutation (when known) is also shown. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.9820808
title: Additional file 4: of Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

description: This VCF file contains genotypic data of 272 individuals of S. echinata at 27,887 genome-wide SNPs. (ZIP 12536â kb)
DOI: 10.6084/m9.figshare.9820814.v1
title: Additional file 1: of TRPP2 dysfunction decreases ATP-evoked calcium, induces cell aggregation and stimulates proliferation in T lymphocytes

description: Table S1. â ADPKD patient cohort enrolled from four Nephrology Units of Emilia Romagna Region (Italy)â . This table contains information about ADPKD patients including clinical features. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.9820805
title: Additional file 3: of Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

description: This file contain mitochondrial COI sequence data accession numbers for 273 individuals of S. echinata. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9820808.v1
title: Additional file 4: of Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

description: This VCF file contains genotypic data of 272 individuals of S. echinata at 27,887 genome-wide SNPs. (ZIP 12536â kb)
DOI: 10.6084/m9.figshare.9820805.v1
title: Additional file 3: of Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

description: This file contain mitochondrial COI sequence data accession numbers for 273 individuals of S. echinata. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9820766
title: Additional file 1: of Antimicrobial use policy change in pre-weaned dairy calves and its impact on antimicrobial resistance in commensal Escherichia coli: a cross sectional and ecological study

description: Table S1. Antimicrobial combination treatments given to pre-weaned calves (nâ =â 4301) on a dairy farm. Table S2. Criteria for latent class analysis model selection based on resistance to 11 antimicrobials. Table S3. Minimum inhibitory concentration (Îźg/ml) of antimicrobials used for agar dilution assay. (XLSX 14 kb)