cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15383903
title: Docking of various antibiotic molecules with several proteins associated with strains of Pseudomonas aeruginosa

description: We made 3D models of a few protein sequences associated with the pathogen Pseudomonas aeruginosa  using the Swiss Model server. We picked the model with the best GMQE score, usually 0.9 or higher. 

Considering both the initial and most recent generations of antibiotics, the compounds levofloxacin (CID: 149096), ciprofloxacin (CID: 2764), norfloxacin (CID: 4539), and nalidixic acid (CID: 4421) (representing fluoroquinolones); mezlocillin (CID: 656511), and penicillin      (CID: 5904) (representing β-lactams); as well as tobramycin (CID: 36294), neomycin (CID: 8378), and streptomycin (CID: 19649) (representing aminoglycosides) were sourced from PubChem and utilized as ligands in molecular docking studies with the protein models. 

The utilization of AutoDock Vina was conducted programmatically, while the preparatory steps were executed employing AutoDock tools. The protonation of the ligands was conducted utilizing pertinent modules within Rdkit.Chem.

The results of the subsequent Molecular Dynamics simulations are presented in separate datasets as follows:



MD of DD-Transpeptidase (PBP) protein (with mutations recorded in 1999) and Penicillin: 10.5281/zenodo.15453083

MD Simulation of DD-Transpeptidase (PBP) protein of P. aeruginosa (with mutations recorded in 2018) and Penicillin: 10.5281/zenodo.15475469

MD Simulation of DD-Transpeptidase (PBP) protein of P. aeruginosa (with mutations recorded in 2018) and Mezlocilin: 10.5281/zenodo.15478360

MD Simulation of DNA gyrase subunit A (gyrA) and topoisomerase IV subunit C (parC) proteins of P. aeruginosa (with mutations recorded in 2018), each in complex with Levofloxacin: 10.5281/zenodo.15498546

MD Simulation of DNA gyrase subunit A (gyrA) protein of P. aeruginosa, with mutations recorded in 1996 and 2018, each in complex with Nalidixic Acid: 10.5281/zenodo.15511964

MD Simulation of DNA topoisomerase IV subunit C (parC) protein of P. aeruginosa, with mutations recorded in 1999 and 2018, each in complex with Nalidixic Acid: 10.5281/zenodo.15515343

MD of  Aminonucleotidyltransferase (AMINO) with Streptomycon and Tobramycin: 10.5281/zenodo.15448122
DOI: 10.7910/dvn/59qvch
title: Replication Data for: Workplace Contact and Support for Anti-Immigration Parties

description: How does an increased presence of immigrants in the workplace affect anti-immigration voting behavior? While cooperative interactions between natives and immigrants can reduce intergroup prejudice, immigrant co-workers might be regarded as a threat to native-born workers' labor market position. We combine detailed Swedish workplace data with precinct-level election outcomes for a large anti-immigration party (the Sweden Democrats) to study how the share of non-Europeans in the workplace affects opposition to immigration. We show that the share of non-Europeans in the workplace has a negative effect on support for the Sweden Democrats and that this effect is solely driven by same-skill contact in small workplaces. We interpret these results as supporting the so-called contact hypothesis: that increased interactions with minorities can reduce opposition to immigration among native-born voters, which, in turn, leads to lower support for anti-immigration parties.
DOI: 10.7910/dvn/5apd5g
title: Replication Data for: Democracy, trade and poverty in SSA

description: This study covers a sample of 24 sub-Saharan African countries over the period 2005 to 2016. The choice of sample and period is related to the availability of data on both poverty and microfinance variables. The poverty data are taken from the Poverty and Equity Database and the United Nations Development Programme (UNDP), while the microfinance data are taken from MIX-market. In addition, data on electoral democracy and institutionalized democracy are from Freedom House and Polity IV, respectively. The other variables are constructed using data from the World Development Indicators (WDI).
DOI: 10.7910/dvn/4yv8pl
title: Replication Data for: Metagenomic analysis of female Aedes aegypti mosquito RNA metaviromes reveal presence of diverse insect specific viruses

description: &lt;p&gt;This is a replication dataset for the manuscript titled: "&lt;a href=""&gt;&lt;/a&gt;" submitted to Wellcome Open Research.&lt;/p&gt;

&lt;p&gt;Coastal Kenya has experienced repeated outbreaks of DENV and CHIKV, and cases of microcephaly have also been reported. Despite the Arboviral burden, there is lack of systematic entomological surveillance. This study collected Aedes aegypti from different sites in coastal Kenya and characterized the viruses circulating in these mosquitoes. Mosquitoes were collected using BG-Sentinel traps, and pools comprised of female Aedes aegypti only generated. The resultant mosquito pools were then screened for presence of arboviruses using RT-PCR and then sequenced using a meta genomics approach to identify other viruses circulating in them. The mosquito collection dataset highlights the geographical location names and their respective geographical position coordinates (GPS) coordinates whereas the RT-PCR dataset describes arbovirus presence or absence findings. The mosquito collection dataset was key in generating a map showing sampling sites, while the RT-PCR dataset informed the mosquito pools to prioritise for sequencing. &lt;/p&gt;
description: <strong>Data Access: </strong>Open

<strong>License: </strong>Creative Commons Attribution 4.0 International
DOI: 10.7910/dvn/5mwbpx
title: Battleground Poll no. 49 - September 2012 - dataset ID 13633

description: Data associated with The Battleground Poll between the years 1993 and 2017.
description: SPSS, null
DOI: 10.7910/dvn/5nvkrf
title: Replication Data for California Politics is Local: Voting Behavior and Special Districts

description: This .zip file contains all of our research data used in the empirical chapters for California Politics is Local: Voting Behavior and Special Districts
DOI: 10.7910/dvn/52hsia
title: Replication Data for: Shoring Up Autocracy: Participatory Technologies and Regime Support in Putin's Russia

description: Replication data and Stata code
DOI: 10.7910/dvn/5cprnm
title: Replication Data for: Air Superiority and Battlefield Victory

description: Replication data for:

Saunders, R., & Souva, M. (2020). Air superiority and battlefield victory. Research & Politics, 7(4), 2053168020972816.
DOI: 10.7910/dvn/5hs3ef
title: EEG_data_part_1

description: Currently, the "EEG_data" folder is empty. You have to first download all the files in the "EEG_data_part_1" and "EEG_data_part_2" and put those MATLAB data files in this single folder, before you can run some of the MATLAB programs.

Email Dr. Gai (gaiy@slu.edu) if you have questions.
DOI: 10.15151/esrf-es-1922853784
title: Time-resolved SAXS and WAXS of low-solid shortenings under shear

description: Shortenings are fat-rich food products containing vegetable oil and a hardstock (2-30%), which can be used as an ingredient in bakery applications. In the food industry, shortenings are produced by applying high shear rates and high cooling rates to obtain the desired organoleptic properties. However, the effect of the shear rate and the cooling rate on fat crystallization at different length scales is still lacking. Until now, research focuses on the crystallization behavior without the presence of shear, which is referred to as ‘static crystallization’. Therefore, applying synchrotron SAXS and WAXS will largely contribute to better understand these effects on the nano- to mesoscale. As a result, a more in-depth knowledge on the fat crystallization process as such and the resulting product characteristics will be obtained.
DOI: 10.15468/dl.3dvvwf
title: Occurrence Download

description: A dataset containing 271 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ailuropoda melanoleuca (David, 1869)"
 ]
}

 The dataset includes 271 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001266-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/5bjooz
title: A92_5126.jpg

description: Link to OCHRE database: &lt;a href = 'http://pi.lib.uchicago.edu/1001/org/ochre/03f3d0ce-9118-12c7-7192-7f369515fb51'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/03f3d0ce-9118-12c7-7192-7f369515fb51
DOI: 10.7910/dvn/5bxl7a
title: HKS Misinfo Review _ Coronavirus Narratives

description: This dataset pertains to an article published in the Harvard Kennedy School Misinformation Review on COVID-19 narratives promoted by Chinese state media as compared to those in U.S. mainstream and U.S. government-funded media in posts by their official Facebook Pages between January 1, 2020 and March 16, 2020. 

To assess a difference in overall tone in the posts as well as a difference in how the Chinese government response was framed, we randomly selected and coded 30 posts for each outlet for both cases, resulting in 30*2*3 = 180 coded posts.

This dataset contains the text for each post and the respective coding as e.g. positive, neutral, or negative. Each sheet in the file represents an outlet type. There are six sheets - 3 types of outlets for 2 different observations (random posts from the entire subset and random posts from the subset on the CCP). The sheets are labeled accordingly.
DOI: 10.7910/dvn/56pivi
title: Replication Data for: Diversity and Violence During Conflict Migration: The Troubles in Northern Ireland

description: Diversity’s effect on violence is ambiguous. Some studies find that diverse areas
experience more violence; others find the opposite. Yet conflict displaces and
intimidates people, creating measurement challenges. We propose a novel indicator
of diversity that circumvents these problems: the location of physical structures at
disaggregated geographical levels. We introduce this solution in the context of the
Troubles in Northern Ireland. Our data reveal a curvilinear relationship between
diversity and conflict-related deaths, with the steepest increase at low diversity, driven
by an increase in violence when our proxy for the Catholic proportion of the population
rises from zero to twenty percent. These patterns are consistent with a theory of group
threat through exposure.
DOI: 10.7910/dvn/5chyja
title: A98_10333.jpg

description: Link to OCHRE database: &lt;a href = 'http://pi.lib.uchicago.edu/1001/org/ochre/0799006d-7f2e-2557-13fb-be640ed34ae7'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/0799006d-7f2e-2557-13fb-be640ed34ae7
DOI: 10.7910/dvn/5nkexv
title: Replication Data for: Environmental disasters and ecomodernist beliefs: Insights from a quasi‐natural experiment

description: Replication Data for: Environmental disasters and ecomodernist beliefs: Insights from a quasi‐natural experiment
DOI: 10.7910/dvn/58yahh
title: Bangladeshi Students And Their Potential Career Choices With Intended Degrees
title: A snapshot of Bangladeshi youth aspiration being gender specific.
title: Bangladeshi youth and their aspirations in career path

description: This dataset is collected from the clients of StudyBooth- Learn Together's ECA Mentoring Camp intending Bangladeshi students aged 14-25 about their potential career choices and the highest degree they would like to earn. This dataset can be used to rationalize the majority and minority of specific career interest. This dataset also serves the gender norms and preferred career path based on gender among Bangladeshi students. Researchers and policymakers can utilize this concise yet comprehensive resource to understand trends, fostering an environment that nurtures the unique aspirations of Bangladesh's youth.
description: csv, null
description: Data is collected by digital questionnaire from the clients of StudyBooth- Learn Together, a Bangladeshi online organization.
DOI: 10.7910/dvn/5ogixj
title: Higher scores of ambiant Temperature, Sunshine hours and UV index are associated with low Covid-19 mortality

description: ABSTRACT
Background: Following two years of the Covid-19 pandemic, thousands of deaths were registered around the world, however, death tolls differed from a country to another. A question on whether climate parameters in each country could or not affects coronavirus incidence and Covid-19 death toll is under debate. 
Objective: In the present work, it is aimed to check the numbers of deaths caused by Covid-19 in 39 countries of four continents (America, Europe, Africa and Asia), and to analyse their possible correlation with climate parameters in a given country, such as the mean of annual temperature, the annual average sunshine hours and the annual average UV index in each country. 
Methods: We have sought the deaths number caused by Covid-19 in 39 countries and have analysed its correlation degree with the mean annual temperature, the average annual sunshine hours and the average annual UV index. Correlation and determination factors were obtained by Microsoft Exell software (2016).
Results: In the present study, higher numbers of deaths related to Covid-19 were registered in many countries of Europe and America compared to other countries in Africa and Asia. On the other hand, after both the first year and the second year of the pandemic, the death numbers registered in the 39 countries of our study were very negatively correlated with the three climate factors of our study, namely, annual average temperature, sunshine hours and UV index.
Conclusion:The results of the present study prove that the above climate parameters may have some kind of influence on the coronavirus incidence through a yet unknown mechanism. Our data support the hypothesis that countries which have elevated annual temperatures and elevated sunshine hours may be less vulnerable to the coronavirus SARS-CoV-2 and to its associated Covid-19 disease. Countries with the above characteristics have also elevated levels of average annual UV rays that might play a key role against the spread of the coronavirus.Thus, geographical latitude and longitude of a given country could have been the key points for the outcome of virus incidence and Covid-19 spread around the globe during the past two years. The results prove that elevated levels of temperature, sunshine hours and UV index could play a protective effect against the coronavirus, although their mechanisms of action are still unknown.
DOI: 10.7910/dvn/5qxrj7
title: Replication Data for: Who Funds Whose Infrastructure? Country Dyadic Analysis of Global Project Finance Loans

description: Global project finance investments have become one of the primary funding mechanisms for large infrastructure projects worldwide over the past few decades. This paper examines the country-level dynamics of global project finance loans from 1981 to 2018, using data from all project finance deals reported in the DealScan database. Our analysis reveals that most international project finance loans originate from banks and financial institutions in advanced democracies, while the recipient countries vary widely in terms of regime type and economic development. Through systematic visualization and statistical analysis, we find that transnational capital flows for infrastructure projects are more likely to occur between countries with similar political systems or between those with starkly different regimes. This finding indicates significant lending and borrowing between full democracies and closed autocracies, suggesting that investments raised in liberal democracies enable some of the most closed dictatorships to finance their infrastructure development. The study suggests that closed and repressive regimes might substantially benefit from the globalized project financing system, warranting increased attention from scholars in International Political Economy on political implication of globalized project finance market.
DOI: 10.6084/m9.figshare.13302421
title: Role of cardiac drugs and flavonoids on the IRE1–JNK pathway as revealed by re-ranked molecular docking scores, MM/PBSA and umbrella sampling

description: One of the important causes of cardiac dysfunction is the triggering of apoptosis through the IRE1–JNK signaling pathway due to excessive ER stress (endoplasmic reticulum stress). Although there are various studies on beneficial or harmful side effects of cardiac drugs, knowledge about the molecular mechanism of their interactions on this pathway is very limited. In this study, we investigated interactions of statins, ace inhibitors, antiarrhythmic drugs and flavonoids in IRE1, ASK1(apoptosis signal-regulating kinase 1) and JNK1 at an atomic level in comparison with their well-known inhibitors. The rank of scores obtained from four different docking algorithms (Autodock 4, Autodock Vina, iGEMDOCK and GOLD) were combined so that they could be compared with each other and evaluated together. According to combined results, the most potent compound for each compound group was selected for molecular dynamics simulations, MM/PBSA (molecular mechanics/Poisson–Boltzmann surface area) and umbrella sampling calculations. We observed that the statin group drugs had the best affinity by interacting with ASK1 and JNK1 by having a similar effect with their inhibitors, and atorvastatin and pitavastatin came to the fore. Norizalpinine from the flavonoid group had a strong binding interaction with IRE1, and amiodarone from the antiarrhythmic drug group had high binding affinities with IRE1, ASK1 and JNK1. Our study has shown that atorvastatin, pitavastatin, norizalpinine and amiodarone may have a role in preventing cardiac dysfunctions caused by ER stress and may shed light on further <i>in vitro</i> and <i>in vivo</i> research. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13302421.v1
title: Role of cardiac drugs and flavonoids on the IRE1–JNK pathway as revealed by re-ranked molecular docking scores, MM/PBSA and umbrella sampling

description: One of the important causes of cardiac dysfunction is the triggering of apoptosis through the IRE1–JNK signaling pathway due to excessive ER stress (endoplasmic reticulum stress). Although there are various studies on beneficial or harmful side effects of cardiac drugs, knowledge about the molecular mechanism of their interactions on this pathway is very limited. In this study, we investigated interactions of statins, ace inhibitors, antiarrhythmic drugs and flavonoids in IRE1, ASK1(apoptosis signal-regulating kinase 1) and JNK1 at an atomic level in comparison with their well-known inhibitors. The rank of scores obtained from four different docking algorithms (Autodock 4, Autodock Vina, iGEMDOCK and GOLD) were combined so that they could be compared with each other and evaluated together. According to combined results, the most potent compound for each compound group was selected for molecular dynamics simulations, MM/PBSA (molecular mechanics/Poisson–Boltzmann surface area) and umbrella sampling calculations. We observed that the statin group drugs had the best affinity by interacting with ASK1 and JNK1 by having a similar effect with their inhibitors, and atorvastatin and pitavastatin came to the fore. Norizalpinine from the flavonoid group had a strong binding interaction with IRE1, and amiodarone from the antiarrhythmic drug group had high binding affinities with IRE1, ASK1 and JNK1. Our study has shown that atorvastatin, pitavastatin, norizalpinine and amiodarone may have a role in preventing cardiac dysfunctions caused by ER stress and may shed light on further <i>in vitro</i> and <i>in vivo</i> research. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13340831
title: Deciphering LncRNA–protein interactions using docking complexes

description: Deciphering RNA–protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, <i>viz.</i> including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein–RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13340831.v1
title: Deciphering LncRNA–protein interactions using docking complexes

description: Deciphering RNA–protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, <i>viz.</i> including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein–RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13246783
title: Design, synthesis and antiproliferative activity evaluation of fluorine-containing chalcone derivatives

description: A series of new chalcones containing fluoro atom at B ring have been designed, synthesized, and evaluated to be antiproliferative activity against a panel of human tumor cell lines. Some of the analogs (<b>8</b>, <b>9</b>, <b>12</b>, <b>45</b>, <b>46</b> and <b>48</b>) displayed powerful antiproliferative effects to certain human tumor cells, but all of them were devoid of any cytotoxicity towards the normal HEK 293. Acridine orange staining data supported that the cytotoxic and antiproliferative effects of the synthesized analogs on tumor cells are mediated through apoptosis. The compounds <b>12</b> and <b>46</b> manifested concentration-dependent antiproliferative activity in human hepatocellular carcinoma cell lines using an xCELLigence assay. The structures and antiproliferative activity relationship were further supported by in silico molecular docking study of the compounds against tubulin protein which suggests our compounds interference to cell division. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13246783.v2
title: Design, synthesis and antiproliferative activity evaluation of fluorine-containing chalcone derivatives

description: A series of new chalcones containing fluoro atom at B ring have been designed, synthesized, and evaluated to be antiproliferative activity against a panel of human tumor cell lines. Some of the analogs (<b>8</b>, <b>9</b>, <b>12</b>, <b>45</b>, <b>46</b> and <b>48</b>) displayed powerful antiproliferative effects to certain human tumor cells, but all of them were devoid of any cytotoxicity towards the normal HEK 293. Acridine orange staining data supported that the cytotoxic and antiproliferative effects of the synthesized analogs on tumor cells are mediated through apoptosis. The compounds <b>12</b> and <b>46</b> manifested concentration-dependent antiproliferative activity in human hepatocellular carcinoma cell lines using an xCELLigence assay. The structures and antiproliferative activity relationship were further supported by in silico molecular docking study of the compounds against tubulin protein which suggests our compounds interference to cell division. Communicated by Ramaswamy H. Sarma