cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13352402
title: Sensing the interactions between carbohydrate-binding agents and <i>N</i>-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies

description: A recent surge in finding new candidate vaccines and potential antivirals to tackle atypical pneumonia triggered by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) needs new and unexplored approaches in solving this global pandemic. The homotrimeric transmembrane spike (S) glycoprotein of coronaviruses which facilitates virus entry into the host cells is covered with <i>N</i>-linked glycans having oligomannose and complex sugars. These glycans provide a unique opportunity for their targeting via carbohydrate-binding agents (CBAs) which have shown their antiviral potential against coronaviruses and enveloped viruses. However, CBA–ligand interaction is not fully explored in developing novel carbohydrate-binding-based antivirals due to associated unfavorable responses with CBAs. CBAs possess unique carbohydrate-binding specificity, therefore, CBAs like mannose-specific plant lectins/lectin-like mimic Pradimicin-A (PRM-A) can be used for targeting <i>N</i>-linked glycans of S glycoproteins. Here, we report studies on the binding and stability of lectins (NPA, UDA, GRFT, CV-N and wild-type and mutant BanLec) and PRM-A with the S glycoprotein glycans via docking and MD simulation. MM/GBSA calculations were also performed for docked complexes. Interestingly, stable BanLec mutant (H84T) also showed similar docking affinity and interactions as compared to wild-type BanLec, thus, confirming that uncoupling the mitogenic activity did not alter the lectin binding activity of BanLec. The stability of the docked complexes, i.e. PRM-A and lectins with SARS-CoV-2 S glycoprotein showed favorable intermolecular hydrogen-bond formation during the 100 ns MD simulation. Taking these together, our predicted <i>in silico</i> results will be helpful in the design and development of novel CBA-based antivirals for the SARS-CoV-2 neutralization. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13352401
title: Molecular and functional characterization of buffalo nasal epithelial odorant binding proteins and their structural insights by <i>in silico</i> and biochemical approaches

description: The olfactory system is capable of detecting and distinguishing thousands of environmental odorants that play a key role in reproduction, social behaviours including pheromones influenced classical events. Membrane secretary odorant binding proteins (OBPs) are soluble lipocalins, localized in the nasal membrane of mammals. They bind and carry odorants within the nasal epithelium to putative olfactory transmembrane receptors (ORs). OBP has not yet been exploited to develop a suitable technique to detect oestrus which is being reported as a difficult task in buffalo. In the present study, using molecular biology and protein engineering approaches, we have cloned six novel OBP isoforms from buffalo nasal epithelium odorant-binding proteins (bnOBPs). Furthermore, 3 D models were developed and molecular-docking, dynamics experiments were performed by <i>in silico</i> approaches. In particular, we found four residues (Phe104, Phe134, Phe69 and Asn118) in OBP1a, which contributed to favourable interactions towards two sex pheromones, specifically oleic acid and p-cresol. We expressed this protein in <i>Escherichia coli</i> from female buffalo urine and validated through fluorescence quenching studies to show similar strong binding affinities of OBP1a to oleic acid and p-cresol. By using structural data, the binding specificity was also verified by site-directed mutagenesis of the four residues followed by <i>in vitro</i> binding assays. Our results enable us to better understand the functions of different nasal epithelium OBP isoforms in buffaloes. They also lead to improved understanding of the interaction between olfactory proteins and odorants to develop highly selective biosensing devices for non-invasive detection of oestrus in buffaloes. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13352402.v1
title: Sensing the interactions between carbohydrate-binding agents and <i>N</i>-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies

description: A recent surge in finding new candidate vaccines and potential antivirals to tackle atypical pneumonia triggered by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) needs new and unexplored approaches in solving this global pandemic. The homotrimeric transmembrane spike (S) glycoprotein of coronaviruses which facilitates virus entry into the host cells is covered with <i>N</i>-linked glycans having oligomannose and complex sugars. These glycans provide a unique opportunity for their targeting via carbohydrate-binding agents (CBAs) which have shown their antiviral potential against coronaviruses and enveloped viruses. However, CBA–ligand interaction is not fully explored in developing novel carbohydrate-binding-based antivirals due to associated unfavorable responses with CBAs. CBAs possess unique carbohydrate-binding specificity, therefore, CBAs like mannose-specific plant lectins/lectin-like mimic Pradimicin-A (PRM-A) can be used for targeting <i>N</i>-linked glycans of S glycoproteins. Here, we report studies on the binding and stability of lectins (NPA, UDA, GRFT, CV-N and wild-type and mutant BanLec) and PRM-A with the S glycoprotein glycans via docking and MD simulation. MM/GBSA calculations were also performed for docked complexes. Interestingly, stable BanLec mutant (H84T) also showed similar docking affinity and interactions as compared to wild-type BanLec, thus, confirming that uncoupling the mitogenic activity did not alter the lectin binding activity of BanLec. The stability of the docked complexes, i.e. PRM-A and lectins with SARS-CoV-2 S glycoprotein showed favorable intermolecular hydrogen-bond formation during the 100 ns MD simulation. Taking these together, our predicted <i>in silico</i> results will be helpful in the design and development of novel CBA-based antivirals for the SARS-CoV-2 neutralization. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13302412
title: Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

description: The Coronavirus Disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with elevated mortality and morbidity. There are currently no efficacious drugs targeting coronavirus disease 2019, therefore, it is an urgent requirement for the development of drugs to control this emerging disease. Owing to the importance of nucleocapsid protein, the present study focuses on targeting the N-terminal domain of nucleocapsid protein from severe acute respiratory syndrome coronavirus 2 to identify the potential compounds by computational approaches such as pharmacophore modeling, virtual screening, docking and molecular dynamics. We found three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056), which adopted a similar conformation as guanosine monophosphate (GMP) within the N-terminal domain active site and exhibiting high binding affinity (&gt;−8.0 kcalmol<sup>−1</sup>). All the identified compounds were stabilized by hydrogen bonding with Arg107, Tyr111 and Arg149 of N-terminal domain. Additionally, the aromatic ring of lead molecules formed π interactions with Tyr109 of N-terminal domain. Molecular dynamics and Molecular mechanic/Poisson–Boltzmann surface area results revealed that N-terminal domain – ligand(s) complexes are less dynamic and more stable than N-terminal domain – GMP complex. As the identified compounds share the same corresponding pharmacophore properties, therefore, the present results may serve as a potential lead for the development of inhibitors against severe acute respiratory syndrome coronavirus 2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13302412.v1
title: Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

description: The Coronavirus Disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with elevated mortality and morbidity. There are currently no efficacious drugs targeting coronavirus disease 2019, therefore, it is an urgent requirement for the development of drugs to control this emerging disease. Owing to the importance of nucleocapsid protein, the present study focuses on targeting the N-terminal domain of nucleocapsid protein from severe acute respiratory syndrome coronavirus 2 to identify the potential compounds by computational approaches such as pharmacophore modeling, virtual screening, docking and molecular dynamics. We found three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056), which adopted a similar conformation as guanosine monophosphate (GMP) within the N-terminal domain active site and exhibiting high binding affinity (&gt;−8.0 kcalmol<sup>−1</sup>). All the identified compounds were stabilized by hydrogen bonding with Arg107, Tyr111 and Arg149 of N-terminal domain. Additionally, the aromatic ring of lead molecules formed π interactions with Tyr109 of N-terminal domain. Molecular dynamics and Molecular mechanic/Poisson–Boltzmann surface area results revealed that N-terminal domain – ligand(s) complexes are less dynamic and more stable than N-terminal domain – GMP complex. As the identified compounds share the same corresponding pharmacophore properties, therefore, the present results may serve as a potential lead for the development of inhibitors against severe acute respiratory syndrome coronavirus 2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13332710.v1
title: <i>In vitro</i> and <i>in silico</i> evaluation of <i>N</i>-(alkyl/aryl)-2-chloro-4-nitro-5- [(4-nitrophenyl)sulfamoyl]benzamide derivatives for antidiabetic potential using docking and molecular dynamic simulations

description: A series of <i>N</i>-(alkyl/aryl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide derivatives were synthesized and evaluated for its <i>in vitro</i> antidiabetic potential against α-glucosidase and α-amylase enzymes and also for its antimicrobial potential. Compounds <i>N</i>-(2-methyl-4-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide and <i>N</i>-(2-methyl-5-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide were found to be the most potent α-glucosidase and α-amylase inhibitors with IC<sub>50</sub> values of 10.13 and 1.52 µM, respectively. The docking results depicted reasonable dock score −10.2 to −8.0 kcal/mol (α-glucosidase), −11.1 to −8.3 kcal/mol (α-amylase) and binding interactions of synthesized molecules with respective targets with enzymes. During molecular dynamic simulations, analysis of RMSD of ligand protein complex suggested stability of the most active compound at binding site of target proteins. Compound <i>N</i>-(2-chloro-4-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl] benzamide showed antibacterial potential against Gram positive and Gram negative bacteria and compound <i>N</i>-(2-methyl-5-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl] benzamide showed excellent antifungal potential against <i>Candida albicans</i> and <i>Aspergillus niger</i>. The computational studies were also executed to predict the drug-likeness and ADMET properties of the title compounds. The <i>N</i>-(alkyl/aryl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide derivatives showed significant antidiabetic and antimicrobial potential which is equally supported by the molecular dynamic and docking studies. This study will prove useful in revealing the molecular structure and receptor target site details which can be further utilized for the development of newer active antidiabetic and antimicrobial agents. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13332710
title: <i>In vitro</i> and <i>in silico</i> evaluation of <i>N</i>-(alkyl/aryl)-2-chloro-4-nitro-5- [(4-nitrophenyl)sulfamoyl]benzamide derivatives for antidiabetic potential using docking and molecular dynamic simulations

description: A series of <i>N</i>-(alkyl/aryl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide derivatives were synthesized and evaluated for its <i>in vitro</i> antidiabetic potential against α-glucosidase and α-amylase enzymes and also for its antimicrobial potential. Compounds <i>N</i>-(2-methyl-4-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide and <i>N</i>-(2-methyl-5-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide were found to be the most potent α-glucosidase and α-amylase inhibitors with IC<sub>50</sub> values of 10.13 and 1.52 µM, respectively. The docking results depicted reasonable dock score −10.2 to −8.0 kcal/mol (α-glucosidase), −11.1 to −8.3 kcal/mol (α-amylase) and binding interactions of synthesized molecules with respective targets with enzymes. During molecular dynamic simulations, analysis of RMSD of ligand protein complex suggested stability of the most active compound at binding site of target proteins. Compound <i>N</i>-(2-chloro-4-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl] benzamide showed antibacterial potential against Gram positive and Gram negative bacteria and compound <i>N</i>-(2-methyl-5-nitrophenyl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl] benzamide showed excellent antifungal potential against <i>Candida albicans</i> and <i>Aspergillus niger</i>. The computational studies were also executed to predict the drug-likeness and ADMET properties of the title compounds. The <i>N</i>-(alkyl/aryl)-2-chloro-4-nitro-5-[(4-nitrophenyl)sulfamoyl]benzamide derivatives showed significant antidiabetic and antimicrobial potential which is equally supported by the molecular dynamic and docking studies. This study will prove useful in revealing the molecular structure and receptor target site details which can be further utilized for the development of newer active antidiabetic and antimicrobial agents. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.6563328
title: Twindroid - System calls traces - Android apps - Extention

description: TwinDroid - a dataset of system calls traces, from both benign and infected Android apps. For other traces you can visit https://zenodo.org/record/6464808#.Yls2yVyZNH4 To trace apps, you can use our script in: https://github.com/RaphaelKhoury/automated-apk-tracing
DOI: 10.23708/hur10f
title: Results of a survey describing the utilization of termite mounds by the population in Cambodia in 2021

description: This dataset comes from a survey carried out in Chrey Back long term observatory (Cambodia). 61 persons from 13 villages located in Chrey Back watershed were interviewed in order to understand the local perception of the utilization of termite mounds. The dataset describes the questions and responses of villagers in differentiating the soil type (Arenosol vs. Acrisol) and position within the watershed (lower land (LL) vs. upper land (UL)). Survey_detail.csv describes the number of responses per village in Chrey Back catchement according to their positions in the watershed (LL: Lower land vs. UL: Upper land) and soil types (Acrisol vs. Arenosol). Questionnaire.csv describes the percentage of positive and negative answers from a total of 17 and 14 responses in the Arenosol, in LL and UL respectively, and 15 responses in both LL and UL in the Acrisol. Open_answers.csv details the comments and replies of villagers.
DOI: 10.25402/cnc.19794106.v1
title: Supplementary material: Abnormal asymmetry correlates with abnormal enlargement in a patient with chronic moderate traumatic brain injury.docx

description: Supplementary material: Abnormal asymmetry correlates with abnormal enlargement in a patient with chronic moderate traumatic brain injury
DOI: 10.25402/cnc.19794106
title: Supplementary material: Abnormal asymmetry correlates with abnormal enlargement in a patient with chronic moderate traumatic brain injury.docx

description: Supplementary material: Abnormal asymmetry correlates with abnormal enlargement in a patient with chronic moderate traumatic brain injury
DOI: 10.23708/xkh3fc
title: Dataset describing the properties of soil protective and graveyard sheeting built by termites (Macrotermes natalensis) in controlled conditions

description: Dataset describing the properties of protective and graveyard termite sheeting produced by 3 colonies of Macrotermes natalensis reared in laboratory in France (Bondy) in comparison with the reference soil. Soil properties are: pH, concentrations in organic C and C-CaCO3 (in %), total concentration in N (in %), electrical conductivity (EC in u/cm-1) and the clay, silt and sand contents (in %). This dataset also shows the concentrations in Na, Mg, Al, P, K, Ca, Ti and Fe (in ppm) in the different soil materials (both sheeting types + reference soil), termite minor workers and plant material (straw and wood) used to feed termites.
DOI: 10.6084/m9.figshare.17032088
title: Geogenic controls on the high levels of uranium in alluvial aquifers of the Ganga Basin

description: The data set presented here include hydrochemistry and trace element analysis results of shallow groundwater and surface water collected from central part of the Indo-Gangetic Basin located in the industrial region of Kanpur and adjoining rural region. The data set is used to discern the dominant spatial variability, possible sources and factors controlling the occurrence, distribution and sources of radiotoxic element uranium in the densely populated region of central IGP.
DOI: 10.6084/m9.figshare.17032088.v8
title: Geogenic controls on the high levels of uranium in alluvial aquifers of the Ganga Basin

description: The data set presented here include hydrochemistry and trace element analysis results of shallow groundwater and surface water collected from central part of the Indo-Gangetic Basin located in the industrial region of Kanpur and adjoining rural region. The data set is used to discern the dominant spatial variability, possible sources and factors controlling the occurrence, distribution and sources of radiotoxic element uranium in the densely populated region of central IGP.
DOI: 10.6084/m9.figshare.17032088.v7
title: Geogenic controls on the high levels of uranium in alluvial aquifers of the Ganga Basin

description: The data set presented here include hydrochemistry and trace element analysis results of shallow groundwater and surface water collected from central part of the Indo-Gangetic Basin located in the industrial region of Kanpur and adjoining rural region. The data set is used to discern the dominant spatial variability, possible sources and factors controlling the occurrence, distribution and sources of radiotoxic element uranium in the densely populated region of central IGP.
DOI: 10.5281/zenodo.6563395
title: COST-ARKWORK Societal Challenges Survey Dataset

description: A survey was relating to the societal role of archaeology and the impact of societal challenges on archaeological practices is based on views collected from the members of COST Action Archaeological Practices and Knowledge Work in the Digital Environment (www.arkwork.eu). The purpose of this survey is to collect views from COST-ARKWORK members on the relation of contemporary societal challenges and archaeological practices. The survey was administered online using Survey & Report tool (survey form, Fig. 1) hosted by Swedish University Computer Network (Sunet). The survey was open from May 8, 2020 until June1, 2020. The participants of the network consist of over 200 experts of archaeological practices from a broad range of disciplinary backgrounds from archaeology to information science, museum studies, computer science and business studies, including researchers and practitioners from 30 European countries. 50 members of the network participated in the survey. The views of the Action participants were collected using an online survey with two open ended questions: 1. “From your perspective, what is the role and value of archaeology in helping to solve contemporary societal problems?”; and, 2. “What societal changes and challenges are likely to affect archaeology and archaeological practices the most during the next five years?”. In addition, the respondents were asked to indicate whether they identified themselves as being an archaeologist or not. 64% (32/50) of the experts identified themselves as archaeologists while the rest described themselves as non-archaeologists. The experts shared their opinions as individuals, not as representants of specific institutions or countries.
description: This dataset is based upon work from COST Action ARKWORK, supported by COST (European Cooperation in Science and Technology).
description: {"references": ["Huvila et al. (2022) Archaeological practices and societal challenges. Open Archaeology."]}
DOI: 10.5281/zenodo.6563394
title: COST-ARKWORK Societal Challenges Survey Dataset

description: A survey was relating to the societal role of archaeology and the impact of societal challenges on archaeological practices is based on views collected from the members of COST Action Archaeological Practices and Knowledge Work in the Digital Environment (www.arkwork.eu). The purpose of this survey is to collect views from COST-ARKWORK members on the relation of contemporary societal challenges and archaeological practices. The survey was administered online using Survey & Report tool (survey form, Fig. 1) hosted by Swedish University Computer Network (Sunet). The survey was open from May 8, 2020 until June1, 2020. The participants of the network consist of over 200 experts of archaeological practices from a broad range of disciplinary backgrounds from archaeology to information science, museum studies, computer science and business studies, including researchers and practitioners from 30 European countries. 50 members of the network participated in the survey. The views of the Action participants were collected using an online survey with two open ended questions: 1. “From your perspective, what is the role and value of archaeology in helping to solve contemporary societal problems?”; and, 2. “What societal changes and challenges are likely to affect archaeology and archaeological practices the most during the next five years?”. In addition, the respondents were asked to indicate whether they identified themselves as being an archaeologist or not. 64% (32/50) of the experts identified themselves as archaeologists while the rest described themselves as non-archaeologists. The experts shared their opinions as individuals, not as representants of specific institutions or countries.
description: This dataset is based upon work from COST Action ARKWORK, supported by COST (European Cooperation in Science and Technology).
description: {"references": ["Huvila et al. (2022) Archaeological practices and societal challenges. Open Archaeology."]}
DOI: 10.23708/12hrwm
title: Soil macrofauna diversity in Nan province, Northern Thailand, 2018

description: Soil macrofauna diversity (ind. TSBF-1) in a sloping land cultivated in maize in Na Noi District, Nan province, Thailand, during SeaWeed Project (PHC, French Embassy funding). Treatments are: the position along the slope (down, middle, up, top) in presence or abscence of biochar (yes vs. no).