cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10497625
title: ATAC-Seq Invivo Control HFD Diet

description: Liver tissue was homogenized in PBS via mortar and pestle on ice. Samples were centrifuged at 300 rpm for 5 minutes at 4°C. Cells were resuspended in 1 ml ATAC lysis buffer provided in the ATAC-Seq kit (Active Motif, 105310). Nuclei were counted and 5x104 nuclei per reaction were used. ATAC-Seq was performed using the ATAC-Seq kit (Active Motif, 105310) following the protocol provided by the manufacturer. Therefore, the tagmentation reaction was performed by adding 50 µl of Tagmentation Master Mix to each sample. The reaction was incubated at 37°C for 30 minutes in a Thermoshaker (Life Technologies). Samples were transferred to new tubes and 250 µl DNA Purification Binding Buffer and 5 µl 3 M sodium acetate was added to each sample. No pH adjustments had to be performed. DNA purification was performed using DNA purification columns provided by the kit. The purified DNA was quantified using the Qubit instrument (Thermo Scientific). Sequencing libraries were prepared using NEBNext Ultra library preparation kit for PCR amplification following the manufacturer’s instructions. DNA clean-up was performed using 1.2x the sample volume of SPRI beads provided by the kit. The purified DNA was assessed for quality and quantity via the BioAnalyzer (Agilent). Generated libraries were sequenced on an Illumina NovaSeq instrument with an average depth of 50 million reads per library (150 bp, paired-end).
DOI: 10.25919/3q4j-n127
title: Parkes observations for project P1219 semester 2023OCTS_14

description: The magnetic field potentially regulates the process of star formation and the evolution of molecular clouds. It is inherently difficult to measure interstellar magnetic field strengths, with the measurement of Zeeman splitting a unique method to estimate the magnetic field strength along the line of sight directly. Despite the detection of Zeeman splitting in other mediums, there are as yet no Zeeman detections against compact background sources in quiescent molecular clouds or the cold neutral medium. Pulsars with extremely small solid angles and relatively high transverse velocities are ideal background sources to study the magnetic field in molecular clouds, providing a distinct signal to measure splitting against. There are four pulsars with OH absorption detections, namely PSR B1849+00, B1641-45, B1718-35, and B1749-28. We propose to utilize these four pulsars to explore the properties of the magnetic field and its variations within molecular clouds through both the Zeeman splitting of OH absorption and rotation measure estimations, between epochs. If a detection is confirmed, it will open a new window on the hard-to-measure magnetic fields in molecular clouds, independent of interpretation, thus shedding light on the physics of star formation and the interstellar medium.
DOI: 10.25919/b32m-f485
title: Parkes observations for project P456 semester 2023OCTS_07

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. We are now in an exciting regime where a signal detected in our (and other data sets) has the form expected for a gravitational wave background. We are therefore now attempting to confirm, or deny, this exciting result. With this proposal we aim to maintain our pre-eminent position in the field.

Unlike most observing proposals, this is a continuing proposal for which the observations will continue to improve bounds on ultra-low-frequency gravitational waves until they are finally detected. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected we will want to continue observations in support of the nascent field of gravitational wave astronomy!
DOI: 10.34740/kaggle/dsv/7501321
title: crypto-data-daily-updates
DOI: 10.25919/jb07-zb36
title: Parkes observations for project P1189 semester 2023OCTS_02

description: The solar wind and space weather events have a crucial influence on the solar system, and can present a hazard to space and Earth-based technologies. Understanding the origins of the solar wind and space weather is therefore crucial, so that we can better understand how these events are driven, and to improve space weather prediction efforts. In particular, magnetic structures such as coronal holes, helmet streamers, and prominences in the lower corona are thought to be crucial drivers of the winds and coronal mass ejections (CMEs). However, there are very few observational constraints on the solar wind and space weather events at low solar altitudes (&lt; 20 solar radii), as this region is inaccessible to space probes. In this proposal, we seek to monitor a set of pulsars as they pass within 5.7 degrees of the Sun. We will use the UWL receiver on the Parkes Radio Telescope to make precision measurements of the dispersive group delay and Faraday rotation of the pulses. This will enable us to probe the densities and magnetic fields of the coronal structures driving the wind, and probe $6 \pm 4$ CMEs as they pass by the pulsars serendipitously. We will tie this information together with complementary efforts to probe the solar wind via interplanetary scintillation, constraints from space probes, and simulations. This will give us an exciting opportunity to form a holistic picture of the solar wind and space weather.
DOI: 10.34740/kaggle/dsv/7501337
title: AI recognition dataset
DOI: 10.5519/qd.6uc0hlf6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (21 records)
DOI: 10.5281/zenodo.10578564
title: Approaches to Managing Periferal Nerve Lesions of the Arm and  Forearm Actual Treatment and Literature Review

description: Peripheral nerve injuries are frequently seen in clinical practice, and the absence of a readily accessible algorithm for achieving favorable treatment outcomes is a recurrent challenge. The frequency of incomplete injuries is most prevalent. Seddon's classification system classified nerve damage into three distinct groups, namely neurapraxia, axonotmesis, and neurotmesis. Following a full axonal transection, the neuron experiences a series of degenerative mechanisms, subsequently followed by endeavors at regeneration. The distal growth cone actively strives to establish connections with the degraded distal fiber. The prevailing surgical practice involves employing a nylon suture for epineural repair. Nerve-cable interfascicular autografts are utilized to address gaps that cannot be effectively bridged by primary repair due to severe stress. Extensive research is currently being conducted on pharmacologic drugs, immune system modulators, boosting factors, and entubulation chambers. The ongoing advancements resulting from these investigations hold promise for enhancing the outcomes of nerve injury treatment in clinical settings
DOI: 10.5281/zenodo.10578565
title: Approaches to Managing Periferal Nerve Lesions of the Arm and  Forearm Actual Treatment and Literature Review

description: Peripheral nerve injuries are frequently seen in clinical practice, and the absence of a readily accessible algorithm for achieving favorable treatment outcomes is a recurrent challenge. The frequency of incomplete injuries is most prevalent. Seddon's classification system classified nerve damage into three distinct groups, namely neurapraxia, axonotmesis, and neurotmesis. Following a full axonal transection, the neuron experiences a series of degenerative mechanisms, subsequently followed by endeavors at regeneration. The distal growth cone actively strives to establish connections with the degraded distal fiber. The prevailing surgical practice involves employing a nylon suture for epineural repair. Nerve-cable interfascicular autografts are utilized to address gaps that cannot be effectively bridged by primary repair due to severe stress. Extensive research is currently being conducted on pharmacologic drugs, immune system modulators, boosting factors, and entubulation chambers. The ongoing advancements resulting from these investigations hold promise for enhancing the outcomes of nerve injury treatment in clinical settings
DOI: 10.5517/ccdc.csd.cc2bqm7y
title: CCDC 2166690: Experimental Crystal Structure Determination

description: Related Article: Maryam Taghizadeh Shool, Hadi Amiri Rudbari, José V. Cuevas-Vicario, Andrea Rodríguez-Rubio, Claudio Stagno, Nunzio Iraci, Thomas Efferth, Ejlal A. Omer, Tanja Schirmeister, Olivier Blacque, Nakisa Moini, Esmail Sheibani, Nicola Micale|2023|Inorg.Chem.|63|1083|doi:10.1021/acs.inorgchem.3c03414
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bqm8z
title: CCDC 2166691: Experimental Crystal Structure Determination

description: Related Article: Maryam Taghizadeh Shool, Hadi Amiri Rudbari, José V. Cuevas-Vicario, Andrea Rodríguez-Rubio, Claudio Stagno, Nunzio Iraci, Thomas Efferth, Ejlal A. Omer, Tanja Schirmeister, Olivier Blacque, Nakisa Moini, Esmail Sheibani, Nicola Micale|2023|Inorg.Chem.|63|1083|doi:10.1021/acs.inorgchem.3c03414
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bqm90
title: CCDC 2166692: Experimental Crystal Structure Determination

description: Related Article: Maryam Taghizadeh Shool, Hadi Amiri Rudbari, José V. Cuevas-Vicario, Andrea Rodríguez-Rubio, Claudio Stagno, Nunzio Iraci, Thomas Efferth, Ejlal A. Omer, Tanja Schirmeister, Olivier Blacque, Nakisa Moini, Esmail Sheibani, Nicola Micale|2023|Inorg.Chem.|63|1083|doi:10.1021/acs.inorgchem.3c03414
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d04q9
title: CCDC 2204680: Experimental Crystal Structure Determination

description: Related Article: Maryam Taghizadeh Shool, Hadi Amiri Rudbari, José V. Cuevas-Vicario, Andrea Rodríguez-Rubio, Claudio Stagno, Nunzio Iraci, Thomas Efferth, Ejlal A. Omer, Tanja Schirmeister, Olivier Blacque, Nakisa Moini, Esmail Sheibani, Nicola Micale|2023|Inorg.Chem.|63|1083|doi:10.1021/acs.inorgchem.3c03414
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.10578583
title: MD5_fasta
DOI: 10.5281/zenodo.10578584
title: MD5_fasta
DOI: 10.25919/new4-0b27
title: Pronunciamien to Sobre La Aplicacion de Calicivirus y Virus Mixoma Para Control de Conejo Europeo En Islas de Areas Silvestres Protegidas Del Estado. Ord. No 274/2015

description: Answer from the Chilean Agricultural and Livestock Service to use RHDV for rabbit biocontrol
DOI: 10.25919/6zzp-b607
title: Chromosomal genome assembly for Apis mellifera populations from Arista Research Group

description: Genome assembly for Apis mellifera populations from the Arista Research Group

The genome data was generated from Australian strains of honey bees using Oxford Nanopore Promethion long reads and short Illumina reads.
DOI: 10.25919/998c-ye18
title: Chromosomal genome assembly for Apis mellifera populations from Australia

description: Genome assembly for Apis mellifera populations from Australia

The genome data was generated from Australian strains of honey bees using Oxford Nanopore Promethion long reads and short Illumina reads.
DOI: 10.6084/m9.figshare.22691715
title: Pharmacophore-guided drug design using LdNMT as a model drug target for leishmaniasis

description: Leishmaniasis is caused by <i>Leishmania</i> genus parasites and has a high mortality rate. The available drugs to treat leishmaniasis fail due to acquired resistance in parasites. Several enzymes of the <i>Leishmania</i> parasite have been used to design new therapeutic molecules against leishmaniasis. This study uses a pharmacophore-guided approach to design the drug candidate by targeting <i>Leishmania</i> N-Myristoyl transferase (LdNMT). From the initial sequence analysis of LdNMT, we have identified a unique 20 amino acid stretch exploited for screening and designing the small molecules. The pharmacophore for the myristate binding site on LdNMT was elucidated, and a heatmap was constructed. The leishmanial NMT pharmacophore has similarities with other pathogenic microorganisms. Moreover, substituting alanine in pharmacophoric residues elevates the affinity of myristate with NMT. Furthermore, a molecular dynamics (MD) simulation study was conducted to ascertain the stability of the mutants and or wild type. The wild-type NMT has a comparatively low affinity to myristate compared to alanine mutants, indicating that hydrophobic residues favor the myristate binding. The molecules were initially designed by using pharmacophore as a sieving mechanism. In subsequent steps, the selected molecules screened against leishmanial unique amino acid stretch and subsequently with human, leishmanial full-size NMTs. The compounds BP5, TYI, DMU, 3PE and 4UL were the top hits and chemical features similar to the myristate. The molecule 4UL was found to be highly specific towards leishmanial NMT over human NMT, suggesting the molecule is a strong leishmanial NMT inhibitor. The molecule can be taken further to assess it in in-vitro conditions.
DOI: 10.6084/m9.figshare.22691715.v1
title: Pharmacophore-guided drug design using LdNMT as a model drug target for leishmaniasis

description: Leishmaniasis is caused by <i>Leishmania</i> genus parasites and has a high mortality rate. The available drugs to treat leishmaniasis fail due to acquired resistance in parasites. Several enzymes of the <i>Leishmania</i> parasite have been used to design new therapeutic molecules against leishmaniasis. This study uses a pharmacophore-guided approach to design the drug candidate by targeting <i>Leishmania</i> N-Myristoyl transferase (LdNMT). From the initial sequence analysis of LdNMT, we have identified a unique 20 amino acid stretch exploited for screening and designing the small molecules. The pharmacophore for the myristate binding site on LdNMT was elucidated, and a heatmap was constructed. The leishmanial NMT pharmacophore has similarities with other pathogenic microorganisms. Moreover, substituting alanine in pharmacophoric residues elevates the affinity of myristate with NMT. Furthermore, a molecular dynamics (MD) simulation study was conducted to ascertain the stability of the mutants and or wild type. The wild-type NMT has a comparatively low affinity to myristate compared to alanine mutants, indicating that hydrophobic residues favor the myristate binding. The molecules were initially designed by using pharmacophore as a sieving mechanism. In subsequent steps, the selected molecules screened against leishmanial unique amino acid stretch and subsequently with human, leishmanial full-size NMTs. The compounds BP5, TYI, DMU, 3PE and 4UL were the top hits and chemical features similar to the myristate. The molecule 4UL was found to be highly specific towards leishmanial NMT over human NMT, suggesting the molecule is a strong leishmanial NMT inhibitor. The molecule can be taken further to assess it in in-vitro conditions.
DOI: 10.6084/m9.figshare.22598319
title: Identification of common candidate genes and pathways for Spina Bifida and Wilm’s Tumor using an integrative bioinformatics analysis

description: Spina Bifida (SB) and Wilm’s Tumor (WT) are conditions, both associated with children. Several studies have shown that WT later develops in SB patients, which led us to elucidate common key genes and linked pathways of both conditions, aimed at their concurrent therapeutic management. For this, integrated bioinformatics analysis was employed. A comprehensive manual curation of genes identified 133 and 139 genes associated with SB and WT, respectively, which were used to construct a single protein-protein interaction (PPI) network. Topological parameters analysis of the network showed its scale-free and hierarchical nature. Centrality-based analysis of the network identified 116 hubs, of which, 6 were called the key genes attributed to being common between SB and WT besides being the hubs. Gene enrichment analysis of the 5 most essential modules, identified important biological processes and pathways possibly linking SB to WT. Additionally, miRNA-key gene-transcription factor (TF) regulatory network elucidated a few important miRNAs and TFs that regulate our key genes. In closing, we put forward TP53, DICER1, NCAM1, PAX3, PTCH1, MTHFR; hsa-mir-107, hsa-mir-137, hsa-mir-122, hsa-let-7d; and YY1, SOX4, MYC, STAT3; key genes, miRNAs and TFs, respectively, as the key regulators. Further, MD simulation studies of wild and Glu429Ala forms of MTHFR proteins showed that there is a slight change in MTHFR protein structure due to Glu429Ala polymorphism. We anticipate that the interplay of these three entities will be an interesting area of research to explore the regulatory mechanism of SB and WT and may serve as candidate target molecules to diagnose, monitor, and treat SB and WT, parallelly. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22598319.v1
title: Identification of common candidate genes and pathways for Spina Bifida and Wilm’s Tumor using an integrative bioinformatics analysis

description: Spina Bifida (SB) and Wilm’s Tumor (WT) are conditions, both associated with children. Several studies have shown that WT later develops in SB patients, which led us to elucidate common key genes and linked pathways of both conditions, aimed at their concurrent therapeutic management. For this, integrated bioinformatics analysis was employed. A comprehensive manual curation of genes identified 133 and 139 genes associated with SB and WT, respectively, which were used to construct a single protein-protein interaction (PPI) network. Topological parameters analysis of the network showed its scale-free and hierarchical nature. Centrality-based analysis of the network identified 116 hubs, of which, 6 were called the key genes attributed to being common between SB and WT besides being the hubs. Gene enrichment analysis of the 5 most essential modules, identified important biological processes and pathways possibly linking SB to WT. Additionally, miRNA-key gene-transcription factor (TF) regulatory network elucidated a few important miRNAs and TFs that regulate our key genes. In closing, we put forward TP53, DICER1, NCAM1, PAX3, PTCH1, MTHFR; hsa-mir-107, hsa-mir-137, hsa-mir-122, hsa-let-7d; and YY1, SOX4, MYC, STAT3; key genes, miRNAs and TFs, respectively, as the key regulators. Further, MD simulation studies of wild and Glu429Ala forms of MTHFR proteins showed that there is a slight change in MTHFR protein structure due to Glu429Ala polymorphism. We anticipate that the interplay of these three entities will be an interesting area of research to explore the regulatory mechanism of SB and WT and may serve as candidate target molecules to diagnose, monitor, and treat SB and WT, parallelly. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22691793
title: Exploration of molecular interactions between scoparone and associated compounds with Constitutive androstane receptor (CAR) leading to gallstone prevention: an in silico investigation

description: Scoparone (6, 7 dimethylesculetin) is a biologically active compound derived from the herb <i>Artemisia capillaris</i> having anti-inflammatory, anti-lipemic, and anti-allergic roles. Activation of the constitutive androstane receptor (CAR) in primary hepatocytes of both wild-type and humanized CAR mice by scoparone, accelerates bilirubin and cholesterol clearance <i>in vivo</i>. This can prevent gallstones which is a dreaded gastrointestinal disease. To date, surgery is regarded as the gold standard for treating gallstones. The molecular interactions between scoparone and CAR leading to gallstone prevention are not yet explored. In this study, we have analyzed these interactions through an <i>insilico</i> approach. After extracting the CAR structures (mice and human) from the protein databank and 6, 7-dimethylesuletin from PubChem, energy minimization of both the receptors was done to make them stable followed by docking. Next, a simulation was performed to stabilize the docked complexes. Through docking, H-bonds and pi-pi interactions were found in the complexes, which imply a stable interaction, thus activating the CAR. A similarity search for scoparone was performed and the selected compounds were docked with the CAR receptors. Esculentin acetate and scopoletin acetate interacted with human CAR through pi-alkyl and H-bond respectively. While Fraxidin methyl ether, fraxinol methyl ether, and 6, 7 diethoxycoumarin interacted with mice CAR through H-bond and Pi-Pi T-shaped bonds. The selected complexes were simulated further. Our results are in accordance with the hypothesis in the literature. We have also analyzed the drug likeliness, absorption, non-carcinogenicity, and other properties of scoparone which can support further <i>in vivo</i> studies. Communicated by Ramaswamy H. Sarma