cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12922253
title: Systematic analysis of long intergenic non-coding RNAs in <i>C. elegans</i> germline uncovers roles in somatic growth

description: Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode <i>Caenorhabditis elegans</i> to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the <i>C. elegans</i> gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, <i>linc-4</i> was required for somatic growth. Slower growth was observed in <i>linc-4</i>-deletion mutants and in worms depleted of <i>linc-4</i> using RNAi, indicating that <i>linc-4</i> transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of <i>linc-4</i> in soma versus germline showed that the somatic role stems from <i>linc-4</i> expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions.
DOI: 10.6084/m9.figshare.12895029.v1
title: Circular <i>ANRIL</i> isoforms switch from repressors to activators of <i>p15/CDKN2B</i> expression during RAF1 oncogene-induced senescence

description: Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The <i>INK4</i> locus encodes the tumour suppressor proteins p15<sup>INK4b</sup>, p16<sup>INK4a</sup> and p14<sup>ARF</sup> required for cell cycle arrest and whose expression increases during senescence. <i>ANRIL</i> is a ncRNA antisense to the <i>p15</i> gene. In proliferative cells, <i>ANRIL</i> prevents senescence by repressing <i>INK4</i> genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of <i>ANRIL</i> and Polycomb proteins decreases, thus allowing <i>INK4</i> derepression. Here, we found in a model of RAF1 OIS that <i>ANRIL</i> expression rather increases, due in particular to an increased stability. This led us to search for circular <i>ANRIL</i> isoforms, as circular RNAs are rather stable species. We found that the expression of two circular <i>ANRIL</i> increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress <i>p15</i> expression, while in RAF1 OIS, they promote full induction of <i>p15, p16</i> and <i>p14<sup>ARF</sup> </i> expression. Further analysis of one of these circular <i>ANRIL</i> shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the <i>p15</i> and <i>p16</i> promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular <i>ANRIL</i> isoforms allow these isoforms to switch from repressors of <i>p15</i> gene to activators of all <i>INK4</i> genes in RAF1 OIS. Our data reveal that regulation of <i>ANRIL</i> expression depends on the senescence inducer and underline the importance of circular <i>ANRIL</i> in the regulation of <i>INK4</i> gene expression and senescence.
DOI: 10.6084/m9.figshare.12994121
title: Transposon clusters as substrates for aberrant splice-site activation

description: Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and <i>Alu</i>J and was activated by a C &gt; T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved <i>Alu</i>J stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central <i>Alu</i> hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing <i>Alu</i> exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
DOI: 10.5281/zenodo.5536016
title: Europeana Sounds genres dataset

description: Europeana Sounds was a project focused on accessing digital audio files. The current dataset aims to provide semistructured data for learning audio-representations using machine learning techniques. The motivation for this dataset is to allow experimentation with audio content and metadata. The current dataset is a subset of a dataset used in this research paper containing 24k audios belonging to different musical genres. Find more information about the Europeana Sounds project and dataset in this website, together with raw audio features. <br> The audio files can be downloaded using the original media URL. Additional data about the object may be obtained in JSON or in RDF. In JSON, by querying with the ID on the Europeana Record API. RDF can be obtained by requesting the URI with HTTP Content Negotiation for a well-known RDF serialization format. The URI also provides access to the object's page at Europeana, if HTTP Content Negotiation is not used. The objects were obtained using the Europeana Search API. More information about Europeana APIs can be found here.
DOI: 10.5281/zenodo.5536015
title: Europeana Sounds genres dataset

description: Europeana Sounds was a project focused on accessing digital audio files. The current dataset aims to provide semistructured data for learning audio-representations using machine learning techniques. The motivation for this dataset is to allow experimentation with audio content and metadata. The current dataset is a subset of a dataset used in this research paper containing 24k audios belonging to different musical genres. Find more information about the Europeana Sounds project and dataset in this website, together with raw audio features. <br> The audio files can be downloaded using the original media URL. Additional data about the object may be obtained in JSON or in RDF. In JSON, by querying with the ID on the Europeana Record API. RDF can be obtained by requesting the URI with HTTP Content Negotiation for a well-known RDF serialization format. The URI also provides access to the object's page at Europeana, if HTTP Content Negotiation is not used. The objects were obtained using the Europeana Search API. More information about Europeana APIs can be found here.
DOI: 10.5281/zenodo.5528591
title: Neural Network Radiation Emulator (KMA/NIMS), February

description: The dataset is a part of https://doi.org/10.5281/zenodo.5220712. (February)
DOI: 10.5281/zenodo.5528590
title: Neural Network Radiation Emulator (KMA/NIMS), February

description: The dataset is a part of https://doi.org/10.5281/zenodo.5220712. (February)
DOI: 10.5066/p9bxcn7e
title: Imagery, soil temperature and humidity profiles, and meteorological data from December 2020 to April 2021, Grand Falls Dune Field, Arizona

description: Grand Falls dune field (GFDF) is located on the Navajo Nation, ~70 km NE of Flagstaff, AZ. This active dune field displays a range of morphologies, including barchans, smaller dunes, and ripples, and is bimodal in composition. The felsic component is likely derived from the Little Colorado River, and the mafic component (basaltic grains) is locally sourced from nearby cinder cones [1]. GFDF is an excellent analog site for both active dunes on Mars and other planetary bodies that have dune-like features (e.g., Venus and Titan). We have set up a meteorological station within the dune field that records temperature, barometric pressure, relative humidity, wind direction, wind speed, solar radiation, and precipitation. In addition, an array of temperature and relative humidity sensors were deployed at five different depths within the soil to capture diurnal temperatures and humidity variations. This array is located near the meteorological station and both sets of instruments collect data every 15 minutes. A set of cameras have been positioned near an active ripple field, ~7 m southeast of the meteorological station. The cameras take images every 10 minutes to monitor ripple movement. A series of images were also taken using a NIKON D250 camera, in which data were then processed using the software Agisoft Metashope Professional to create a digital elevation model of the ripple field. [1] Hayward, R. K. et al. (2010) 2nd Int. Plan. Dunes Wrkshp., Abstract #2004.
DOI: 10.6084/m9.figshare.12853266
title: Vaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools

description: Carcinoembryonic antigen-related cell adhesion (CEACAM) molecules belong to a family of membrane glycoproteins that mediate intercellular interactions influencing cellular growth, immune cell activation, apoptosis, and tumor suppression. Several family members (CEACAM1, CEACAM5, and CEACAM6) are highly expressed in cancers, and they share a conserved N-terminal domain that serves as an attractive target for cancer immunotherapy. A multi-epitope vaccine candidate against this conserved domain has been developed using immunoinformatics tools. Specifically, several epitopes predicted to interact with MHC class I and II molecules were linked together with appropriate linkers. The tertiary structure of the vaccine is generated by homology and <i>ab initio</i> modeling. Molecular docking of epitopes to MHC structures have revealed that the lowest energy conformations are the epitopes bound to the antigen-binding groove of the MHC molecules. Subsequent molecular dynamics simulation has confirmed the stability of the binding conformations in solution. The predicted vaccine has relatively high antigenicity and low allergenicity, suggesting that it is an ideal candidate for further refinement and development. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853266.v1
title: Vaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools

description: Carcinoembryonic antigen-related cell adhesion (CEACAM) molecules belong to a family of membrane glycoproteins that mediate intercellular interactions influencing cellular growth, immune cell activation, apoptosis, and tumor suppression. Several family members (CEACAM1, CEACAM5, and CEACAM6) are highly expressed in cancers, and they share a conserved N-terminal domain that serves as an attractive target for cancer immunotherapy. A multi-epitope vaccine candidate against this conserved domain has been developed using immunoinformatics tools. Specifically, several epitopes predicted to interact with MHC class I and II molecules were linked together with appropriate linkers. The tertiary structure of the vaccine is generated by homology and <i>ab initio</i> modeling. Molecular docking of epitopes to MHC structures have revealed that the lowest energy conformations are the epitopes bound to the antigen-binding groove of the MHC molecules. Subsequent molecular dynamics simulation has confirmed the stability of the binding conformations in solution. The predicted vaccine has relatively high antigenicity and low allergenicity, suggesting that it is an ideal candidate for further refinement and development. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853185
title: Computational evaluation of a fusion protein consisted of pertussis toxin and filamentous hemagglutinin from <i>Bordetella pertussis</i> to target Claudin-4 using C-terminal fragment of <i>Clostridium perfringens</i> enterotoxin

description: Pertussis, caused by <i>Bordetella pertussis</i> is still one of the controversial diseases worldwide due to its high prevalence in both the developed and the developing countries, especially among young children. As currently approved vaccines are not protective enough and provide Th2-type immune responses, there is an urgent need to develop new vaccines. In the current study, we applied the C-terminal fragment of <i>Clostridium perferingens</i> enterotoxin (C-CPE) as a delivery system and F1S1 fragment (Filamentous hemagglutinin (F1) and subunit 1 of pertussis toxin (S1) of <i>B. pertussis</i> to design a novel chimeric protein <i>in silico</i>, to target Claudin-4 receptors in mice lung cells. To achieve this goal, the primary, secondary and tertiary structures of the fusion protein were evaluated and the interaction of this protein with Claudin-4 receptors was studied. Molecular dynamic (MD) simulation analysis was performed to investigate the physical movement of atoms in a fixed period. According to the results; the full-length fusion protein has consisted of 807 amino acid residues which could be classified as a stable protein. There was a convenient consistency between the 3D predicted structure and the secondary structure prediction. An acceptable percentage of the residues were also detected in the most favored and allowed regions for the model. Based on HADDOCK results, there were no considerable differences between the interactions and MD simulation analysis, indicating that the predicted structures were stable during the simulation. Altogether, the data reported in this study represents the first step toward developing a nasal vaccine candidate against <i>B. pertussis</i> infection. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853185.v1
title: Computational evaluation of a fusion protein consisted of pertussis toxin and filamentous hemagglutinin from <i>Bordetella pertussis</i> to target Claudin-4 using C-terminal fragment of <i>Clostridium perfringens</i> enterotoxin

description: Pertussis, caused by <i>Bordetella pertussis</i> is still one of the controversial diseases worldwide due to its high prevalence in both the developed and the developing countries, especially among young children. As currently approved vaccines are not protective enough and provide Th2-type immune responses, there is an urgent need to develop new vaccines. In the current study, we applied the C-terminal fragment of <i>Clostridium perferingens</i> enterotoxin (C-CPE) as a delivery system and F1S1 fragment (Filamentous hemagglutinin (F1) and subunit 1 of pertussis toxin (S1) of <i>B. pertussis</i> to design a novel chimeric protein <i>in silico</i>, to target Claudin-4 receptors in mice lung cells. To achieve this goal, the primary, secondary and tertiary structures of the fusion protein were evaluated and the interaction of this protein with Claudin-4 receptors was studied. Molecular dynamic (MD) simulation analysis was performed to investigate the physical movement of atoms in a fixed period. According to the results; the full-length fusion protein has consisted of 807 amino acid residues which could be classified as a stable protein. There was a convenient consistency between the 3D predicted structure and the secondary structure prediction. An acceptable percentage of the residues were also detected in the most favored and allowed regions for the model. Based on HADDOCK results, there were no considerable differences between the interactions and MD simulation analysis, indicating that the predicted structures were stable during the simulation. Altogether, the data reported in this study represents the first step toward developing a nasal vaccine candidate against <i>B. pertussis</i> infection. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853317
title: Exploring 3-Benzyloxyflavones as new lead cholinesterase inhibitors: synthesis, structure–activity relationship and molecular modelling simulations

description: In this protocol, a series of 3-benzyloxyflavone derivatives have been designed, synthesized, characterized and investigated <i>in vitro</i> as cholinesterase inhibitors. The findings showed that all the synthesized target compounds (<b>1–10</b>) are potent dual inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes with varying IC<sub>50</sub> values. In comparison, they are more active against AChE than BChE. Remarkably, amongst the series, the compound <b>2</b> was identified as the most active inhibitor of both AChE (IC<sub>50</sub> = 0.05 ± 0.01 μM) and BChE (IC<sub>50</sub> = 0.09 ± 0.02 μM) relative to the standard Donepezil (IC<sub>50</sub> = 0.09 ± 0.01 for AChE and 0.13 ± 0.04 μM for BChE). Moreover, the derivatives <b>5</b> (IC<sub>50</sub> = 0.07 ± 0.02 μM) and <b>10</b> (0.08 ± 0.02 μM) exhibited the highest selective inhibition against AChE as compared to the standard. Preliminary structure-activity relationship was established and thus found that cholinesterase inhibitory activities of these compounds are highly dependent on the nature and position of various substituents on Ring-B of the 3-Benzyloxyflavone scaffolds. In order to find out the nature of binding interactions of the compounds and active sites of the enzymes, molecular docking studies were carried out. HIGHLIGHTS3-benzyloxyflavone analogues were designed, synthesized and characterized.The target molecules (<b>1–10</b>) were evaluated for their inhibitory potential against AChE and BChE inhibitory activities.Limited structure-activity relationship was developed based on the different substituent patterns on aryl part.Molecular docking studies were conducted to correlate the <i>in vitro</i> results and to identify possible mode of interactions at the active pocket site of the enzyme. 3-benzyloxyflavone analogues were designed, synthesized and characterized. The target molecules (<b>1–10</b>) were evaluated for their inhibitory potential against AChE and BChE inhibitory activities. Limited structure-activity relationship was developed based on the different substituent patterns on aryl part. Molecular docking studies were conducted to correlate the <i>in vitro</i> results and to identify possible mode of interactions at the active pocket site of the enzyme. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853317.v1
title: Exploring 3-Benzyloxyflavones as new lead cholinesterase inhibitors: synthesis, structure–activity relationship and molecular modelling simulations

description: In this protocol, a series of 3-benzyloxyflavone derivatives have been designed, synthesized, characterized and investigated <i>in vitro</i> as cholinesterase inhibitors. The findings showed that all the synthesized target compounds (<b>1–10</b>) are potent dual inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes with varying IC<sub>50</sub> values. In comparison, they are more active against AChE than BChE. Remarkably, amongst the series, the compound <b>2</b> was identified as the most active inhibitor of both AChE (IC<sub>50</sub> = 0.05 ± 0.01 μM) and BChE (IC<sub>50</sub> = 0.09 ± 0.02 μM) relative to the standard Donepezil (IC<sub>50</sub> = 0.09 ± 0.01 for AChE and 0.13 ± 0.04 μM for BChE). Moreover, the derivatives <b>5</b> (IC<sub>50</sub> = 0.07 ± 0.02 μM) and <b>10</b> (0.08 ± 0.02 μM) exhibited the highest selective inhibition against AChE as compared to the standard. Preliminary structure-activity relationship was established and thus found that cholinesterase inhibitory activities of these compounds are highly dependent on the nature and position of various substituents on Ring-B of the 3-Benzyloxyflavone scaffolds. In order to find out the nature of binding interactions of the compounds and active sites of the enzymes, molecular docking studies were carried out. HIGHLIGHTS3-benzyloxyflavone analogues were designed, synthesized and characterized.The target molecules (<b>1–10</b>) were evaluated for their inhibitory potential against AChE and BChE inhibitory activities.Limited structure-activity relationship was developed based on the different substituent patterns on aryl part.Molecular docking studies were conducted to correlate the <i>in vitro</i> results and to identify possible mode of interactions at the active pocket site of the enzyme. 3-benzyloxyflavone analogues were designed, synthesized and characterized. The target molecules (<b>1–10</b>) were evaluated for their inhibitory potential against AChE and BChE inhibitory activities. Limited structure-activity relationship was developed based on the different substituent patterns on aryl part. Molecular docking studies were conducted to correlate the <i>in vitro</i> results and to identify possible mode of interactions at the active pocket site of the enzyme. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853320
title: <i>In vitro</i> and <i>in silico</i> analysis of <i>L. donovani</i> enoyl acyl carrier protein reductase - A possible drug target

description: The emergence of increased resistance to the available drugs has created a situation that demands to find out more specific molecular drug targets for Leishmaniasis. The enoyl acyl carrier protein reductase (ENR), a regulatory enzyme in type II fatty acid synthesis, was confirmed as a novel drug target and triclosan as its specific inhibitor in many microorganisms. In this study, the triclosan was tested for the leishmanicidal property against <i>Leishmania donovani</i> (<i>L. donovani</i>) and the results of <i>in vitro</i> and <i>ex vivo</i> drug assays on promastigotes and amastigotes showed that triclosan possessed antileishmanial activity with a half minimal inhibitory concentration (IC<sub>50</sub>) of 30 µM. Consequently, adopting <i>in silico</i> approach, we have tested the triclosan’s ability to bind with the <i>L. donovani</i> enoyl acyl carrier protein reductase (<i>Ld</i>ENR). The 3D structure of <i>Ld</i>ENR was modelled, triclosan and cofactors were docked in <i>Ld</i>ENR model and molecular dynamic simulations were performed to observe the protein-ligands interactions, stability, compactness and binding energy calculation of the ligands-<i>Ld</i>ENR complexes. The observation showed that triclosan stably interacted with <i>Ld</i>ENR in presence of both the cofactors (NADPH and NADH), however, simulation results favor NADH as a preferred co-factor for <i>Ld</i>ENR. These results support that the reduction of <i>L. donovani</i> growth in the <i>in vitro</i> and <i>ex vivo</i> drug assays may be due to the interaction of triclosan with <i>Ld</i>ENR, which should be confirmed through enzymatic assays. The results of this study suggest that <i>Ld</i>ENR could be a potential drug target and triclosan as a lead for Leishmaniasis. Communicated by Ramaswamy H. Sarma