cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2hn8dv
title: CCDC 2313387: Experimental Crystal Structure Determination

description: Related Article: Michael Weiser, Ádám Márk Pálvölgyi, Matthias Weil, Katharina Bica-Schröder|2024|J.Org.Chem.|89|8906|doi:10.1021/acs.joc.4c00759
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: 10.5066/p968oent
title: Digital orthophotos and field measurements of flow velocity from the Tanana and Nenana Rivers, Alaska, from August 2021 (ver. 2.0, June 2024)

description: This data release includes digital orthophotos acquired from a fixed-wing aircraft and field measurements of flow velocity from the Tanana and Nenana Rivers near Nenana, Alaska, obtained on August 18 and 19, 2021.  This parent data release includes links to child pages for two data sets produced during the study:

1. Acoustic Doppler Current Profiler (ADCP) field measurements of flow velocity from the Tanana and Nenana Rivers, Alaska, collected on August 18, 2021.
2. Digital orthophotos of the Tanana and Nenana Rivers, Alaska, acquired from a fixed-wing aircraft on August 19, 2021. 

Please refer to the individual child pages for further detail about each data set.  

Overall, these data were used to assess the potential to estimate surface flow velocities in sediment-laden rivers from optical image sequences acquired from a fixed-wing aircraft flying along the river by tracking water surface features via particle image velocimetry (PIV). The field measurements of flow velocity were used for accuracy assessment. Remote sensing of flow velocities could provide a more efficient, cost-effective alternative to conventional field-based methods of measuring channel hydraulics and thus become an important component of non-contact approaches to streamgaging. Moreover, the ability to collect such data from a moving aircraft opens up the possibility of examining longer river reaches via remote sensing.
DOI: 10.15468/dl.88vawv
title: Occurrence Download

description: A dataset containing 207076 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "Geometry POLYGON((-180 -90,-95 -90,-95 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera",
 "Year 2020-2020"
 ]
}

 The dataset includes 207076 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000057-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ka5gcp
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Budorcas taxicolor Hodgson, 1850",
 "Year 1970-2024"
 ]
}

 The dataset includes 70 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000078-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cc4ds5
title: Occurrence Download

description: A dataset containing 30187 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is one of (France, United Kingdom of Great Britain and Northern Ireland, Netherlands, Germany, Switzerland, Belgium, Denmark, Andorra, Austria, Cyprus, Czechia, Ireland, Italy, Jordan, Luxembourg, Poland, Romania, Slovenia, Spain, Turkmenistan)",
 "PublishingOrg is 396d5f30-dea9-11db-8ab4-b8a03c50a862",
 "TaxonKey is one of (Liliaceae, Amaryllidaceae, Asteraceae)",
 "Year 1965-2020"
 ]
}

 The dataset includes 30187 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000080-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds005107.v1.0.2
title: OPM-FACE
DOI: 10.5281/zenodo.12547978
title: The Enhanced Teleconnection of Maritime Continent Deforestation on North Pacific Climate During La Niña Conditions
DOI: 10.5281/zenodo.12547979
title: The Enhanced Teleconnection of Maritime Continent Deforestation on North Pacific Climate During La Niña Conditions
DOI: 10.48597/zqa5-rv4v
title: Measurement of Inorganics in precipitation at Noia

description: Measurement of Inorganics in precipitation at Noia
DOI: 10.48597/zrdg-jhe7
title: Measurement of Conductivity at Els Torms

description: Measurement of Conductivity at Els Torms
DOI: 10.48597/zur6-knnh
title: Measurement of pH at Niembro

description: Measurement of pH at Niembro
DOI: 10.48597/zym2-4bv6
title: Measurement of Conductivity at Víznar

description: Measurement of Conductivity at Víznar
DOI: 10.15468/dl.n8t8hm
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((23.82674 46.83798,26.21492 46.83798,26.21492 48.8131,23.82674 48.8131,23.82674 46.83798))",
 "TaxonKey is Streptopelia turtur (Linnaeus, 1758)"
 ]
}

 The dataset includes 49 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000081-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/wf9r-r56n
title: Inorganics in precipitation at Mahón

description: Measurement of Inorganics in precipitation at Mahón
DOI: 10.48597/s7cf-2qxs
title: Inorganics in precipitation at Noia

description: Measurement of Inorganics in precipitation at Noia
DOI: 10.48597/4q2y-fnfm
title: Measurement of Inorganics in precipitation at Mahón

description: Measurement of Inorganics in precipitation at Mahón
DOI: 10.48597/j63v-36rm
title: Inorganics in precipitation at Víznar

description: Measurement of Inorganics in precipitation at Víznar
DOI: 10.48597/732p-mqb5
title: Measurement of Inorganics in precipitation at Noia

description: Measurement of Inorganics in precipitation at Noia
DOI: 10.48597/8hf6-qfky
title: Inorganics in precipitation at San Pablo de los Montes

description: Measurement of Inorganics in precipitation at San Pablo de los Montes
DOI: 10.48597/3mbx-ra4c
title: Measurement of Inorganics in precipitation at Víznar

description: Measurement of Inorganics in precipitation at Víznar
DOI: 10.48597/ea9n-g8u4
title: Measurement of Inorganics in precipitation at Víznar

description: Measurement of Inorganics in precipitation at Víznar
DOI: 10.48597/ca8f-emre
title: Measurement of Inorganics in precipitation at Noia

description: Measurement of Inorganics in precipitation at Noia
DOI: 10.48597/xhkv-xc2b
title: Measurement of Inorganics in precipitation at San Pablo de los Montes

description: Measurement of Inorganics in precipitation at San Pablo de los Montes
DOI: 10.48597/qdre-7dhc
title: Measurement of Inorganics in precipitation at Mahón

description: Measurement of Inorganics in precipitation at Mahón
DOI: 10.48597/qyv7-ut3z
title: Measurement of Inorganics in precipitation at San Pablo de los Montes

description: Measurement of Inorganics in precipitation at San Pablo de los Montes
DOI: 10.6084/m9.figshare.25956683
title: Power inspection image enhancement based on fractional wavelet combined with improved QPSO

description: Under uneven lighting conditions, power inspection (PI) images captured by drones exhibit low contrast, lost details and severe noise, which affects the efficiency of monitoring. In response to these issues, this paper proposes a new method for enhancing PI images based on discrete fractional wavelet transform (DFRWT). Firstly, according to the image entropy feature, an appropriate fractional order of DFRWT is selected to decompose the PI image. Secondly, we introduce a low-frequency fusion enhancement method based on complex number domain. It employs different mapping functions to enhance the brightness and contrast of PI image, then the results are combined to reconstruct a new low-frequency component. Here, an improved quantum-behaved particle swarm optimization (QPSO) algorithm is proposed to determine the optimal parameters of the functions, preventing over-enhancement. Finally, an adaptive threshold function is applied to handle noise and edge coefficients in high-frequency components. Using 5 quality metrics to evaluate 8 existing algorithms on 9 datasets, the results indicate that the proposed algorithm can effectively enhance the clarity of PI images, performing excellently in noise suppression and edge detail enhancement.
DOI: 10.6084/m9.figshare.25956683.v1
title: Power inspection image enhancement based on fractional wavelet combined with improved QPSO

description: Under uneven lighting conditions, power inspection (PI) images captured by drones exhibit low contrast, lost details and severe noise, which affects the efficiency of monitoring. In response to these issues, this paper proposes a new method for enhancing PI images based on discrete fractional wavelet transform (DFRWT). Firstly, according to the image entropy feature, an appropriate fractional order of DFRWT is selected to decompose the PI image. Secondly, we introduce a low-frequency fusion enhancement method based on complex number domain. It employs different mapping functions to enhance the brightness and contrast of PI image, then the results are combined to reconstruct a new low-frequency component. Here, an improved quantum-behaved particle swarm optimization (QPSO) algorithm is proposed to determine the optimal parameters of the functions, preventing over-enhancement. Finally, an adaptive threshold function is applied to handle noise and edge coefficients in high-frequency components. Using 5 quality metrics to evaluate 8 existing algorithms on 9 datasets, the results indicate that the proposed algorithm can effectively enhance the clarity of PI images, performing excellently in noise suppression and edge detail enhancement.
DOI: 10.6084/m9.figshare.23643242
title: Role of a substrate binding pocket in the amino terminal domain of <i>Mycobacterium tuberculosis</i> caseinolytic protease B (ClpB) in its function

description: <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), the causative agent of tuberculosis when infects the host encounters several stresses within the host, resulting in aggregation of its proteins. To resolve this problem <i>Mtb</i> uses chaperones to either repair the damage or degrade the aggregated proteins<i>. Mtb</i> caseinolytic protein B (ClpB) helps in the prevention of aggregation and also resolubilization of aggregated proteins in bacteria, which is important for the survival of <i>Mtb</i> in the host. To function optimally, ClpB associates with its co-partners DnaK, DnaJ, and GrpE. The role of N-terminal domain (NTD) of <i>Mtb</i> ClpB in its function is not well understood. In this context, we investigated the interaction of three substrate mimicking peptides with the NTD of <i>Mtb</i> ClpB <i>in silico</i>. A substrate binding pocket, within the NTD of ClpB comprising of residues L136, R137, E138, K142, R144, R148, V149, Y158, and Y162 forming an ɑ-helix was thus identified. The residues L136 and R137 of the ɑ-helix were found to be important for the interaction of DnaK to ClpB. Further, nine single alanine recombinant variants of the identified residues were generated. As compared to the wild-type <i>Mtb</i> ClpB all the <i>Mtb</i> ClpB variants generated in this study were found to have reduced ATPase and protein refolding activity indicating the importance of the substrate binding pocket in ClpB function. The study demonstrates that the NTD of <i>Mtb</i> ClpB is important for its substrate interaction activity, and the substrate binding pocket identified in this study plays a crucial role in this interaction. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23643242.v1
title: Role of a substrate binding pocket in the amino terminal domain of <i>Mycobacterium tuberculosis</i> caseinolytic protease B (ClpB) in its function

description: <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), the causative agent of tuberculosis when infects the host encounters several stresses within the host, resulting in aggregation of its proteins. To resolve this problem <i>Mtb</i> uses chaperones to either repair the damage or degrade the aggregated proteins<i>. Mtb</i> caseinolytic protein B (ClpB) helps in the prevention of aggregation and also resolubilization of aggregated proteins in bacteria, which is important for the survival of <i>Mtb</i> in the host. To function optimally, ClpB associates with its co-partners DnaK, DnaJ, and GrpE. The role of N-terminal domain (NTD) of <i>Mtb</i> ClpB in its function is not well understood. In this context, we investigated the interaction of three substrate mimicking peptides with the NTD of <i>Mtb</i> ClpB <i>in silico</i>. A substrate binding pocket, within the NTD of ClpB comprising of residues L136, R137, E138, K142, R144, R148, V149, Y158, and Y162 forming an ɑ-helix was thus identified. The residues L136 and R137 of the ɑ-helix were found to be important for the interaction of DnaK to ClpB. Further, nine single alanine recombinant variants of the identified residues were generated. As compared to the wild-type <i>Mtb</i> ClpB all the <i>Mtb</i> ClpB variants generated in this study were found to have reduced ATPase and protein refolding activity indicating the importance of the substrate binding pocket in ClpB function. The study demonstrates that the NTD of <i>Mtb</i> ClpB is important for its substrate interaction activity, and the substrate binding pocket identified in this study plays a crucial role in this interaction. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23898308
title: Computational screening and MM/GBSA-based MD simulation studies reveal the high binding potential of FDA-approved drugs against <i>Cutibacterium acnes</i> sialidase

description: <i>Cutibacterium acnes</i> is an opportunistic pathogen linked with acne vulgaris, affecting 80–90% of teenagers globally. On the leukocyte (WBCs) cell surface, the cell wall anchored sialidase in <i>C. acnes</i> virulence factor, catalysing the sialoconjugates into sialic acids and nutrients for <i>C. acnes</i> resulting in human skin inflammation. The clinical use of antibiotics for acne treatments has severe adverse effects, including microbial dysbiosis and resistance. Therefore, identifying inhibitors for primary virulence factors (Sialidase) was done using molecular docking of 1030 FDA-approved drugs. Initially, based on binding energies (ΔG), Naloxone (ZINC000000389747), Fenoldopam (ZINC000022116608), Labetalol (ZINC000000403010) and Thalitone (ZINC000000057255) were identified that showed high binding energies as −10.2, −10.1, −9.9 and −9.8 kcal/mol, respectively. In 2D analysis, these drugs also showed considerable structural conformer of hydrogen and hydrophobic interactions. Further, a 100 ns MD simulation study found the lowest deviation and fluctuations with various intermolecular interactions to stabilise the complexes. Out of 4, the Naloxone molecule showed robust, steady, and stable RMSD 0.23 ± 0.18 nm. Further, MMGBSA analysis supports MD results and found strong binding energy (Δ<i>G</i>) −29.71 ± 4.97 kcal/mol. In Comparative studies with Neu5Ac2en (native substrate) revealed naloxone has a higher affinity for sialidase. The PCA analysis showed that Naloxone and Thalitone were actively located on the active site, and other compounds were flickered. Our extensive computational and statistical report demonstrates that these FDA drugs can be validated as potential sialidase inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23898308.v1
title: Computational screening and MM/GBSA-based MD simulation studies reveal the high binding potential of FDA-approved drugs against <i>Cutibacterium acnes</i> sialidase

description: <i>Cutibacterium acnes</i> is an opportunistic pathogen linked with acne vulgaris, affecting 80–90% of teenagers globally. On the leukocyte (WBCs) cell surface, the cell wall anchored sialidase in <i>C. acnes</i> virulence factor, catalysing the sialoconjugates into sialic acids and nutrients for <i>C. acnes</i> resulting in human skin inflammation. The clinical use of antibiotics for acne treatments has severe adverse effects, including microbial dysbiosis and resistance. Therefore, identifying inhibitors for primary virulence factors (Sialidase) was done using molecular docking of 1030 FDA-approved drugs. Initially, based on binding energies (ΔG), Naloxone (ZINC000000389747), Fenoldopam (ZINC000022116608), Labetalol (ZINC000000403010) and Thalitone (ZINC000000057255) were identified that showed high binding energies as −10.2, −10.1, −9.9 and −9.8 kcal/mol, respectively. In 2D analysis, these drugs also showed considerable structural conformer of hydrogen and hydrophobic interactions. Further, a 100 ns MD simulation study found the lowest deviation and fluctuations with various intermolecular interactions to stabilise the complexes. Out of 4, the Naloxone molecule showed robust, steady, and stable RMSD 0.23 ± 0.18 nm. Further, MMGBSA analysis supports MD results and found strong binding energy (Δ<i>G</i>) −29.71 ± 4.97 kcal/mol. In Comparative studies with Neu5Ac2en (native substrate) revealed naloxone has a higher affinity for sialidase. The PCA analysis showed that Naloxone and Thalitone were actively located on the active site, and other compounds were flickered. Our extensive computational and statistical report demonstrates that these FDA drugs can be validated as potential sialidase inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24069679
title: Functional characterization of novel mutations in the conserved region of EPSPS for herbicide resistance in pigeonpea: structure-based coherent design

description: Prospectively, agroecosystems for the growth of crops provide the potential fertile, productive, and tropical environment which attracts infestation by weedy plant species that compete with the primary crop plants. Infestation by weed is a major biotic stress factor faced by pigeonpea that hampers the productivity of the crop. In the modern era with the development of chemicals the problem of weed infestation is dealt with armours called herbicides. The most widely utilized, post-emergent, broad-spectrum herbicide has an essential active ingredient called glyphosate. Glyphosate mechanistically inhibits a chloroplastic enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) by competitively interacting with the PEP binding site which hinders the shikimate pathway and the production of essential aromatic amino acids (Phe, Tyr, Trp) and other secondary metabolites in plants. Moreover, herbicide spray for weed management is lethal to both the primary crop and the weeds. Therefore, it is critical to develop herbicide-resistant crops for field purposes to reduce the associated yield and economic losses. In this study, the <i>in-silico</i> analysis drove the selection and validation of the point mutations in the conserved region of the EPSPS gene, which confers efficient herbicide resistance to mutated-CcEPSPS enzyme along with the retention of the normal enzyme function. An optimized <i>in-silico</i> validation of the target mutation before the development of the genome-edited resistant plant lines is a prerequisite for testing their efficacy as a proof of concept. We validated the combination of GATIPS mutation for its no-cost effect at the enzyme level <i>via</i> molecular dynamic (MD) simulation. Communicated by Ramaswamy H. Sarma Weed infestation is a major biotic stress factor and a consistent problem in agriculture. Development of glyphosate-resistant mutation is crucial to minimize the yield loss in agriculturally or nutritionally important crops for field application. Present <i>in-silico</i> approach is a proof-of-concept for validation of the selected glyphosate-resistant mutations. The current study has validated the combination of GATIPS mutation for its glyphosate-resistant phenotype and no negative cost effect at the enzyme simulation level.
DOI: 10.6084/m9.figshare.24069679.v1
title: Functional characterization of novel mutations in the conserved region of EPSPS for herbicide resistance in pigeonpea: structure-based coherent design

description: Prospectively, agroecosystems for the growth of crops provide the potential fertile, productive, and tropical environment which attracts infestation by weedy plant species that compete with the primary crop plants. Infestation by weed is a major biotic stress factor faced by pigeonpea that hampers the productivity of the crop. In the modern era with the development of chemicals the problem of weed infestation is dealt with armours called herbicides. The most widely utilized, post-emergent, broad-spectrum herbicide has an essential active ingredient called glyphosate. Glyphosate mechanistically inhibits a chloroplastic enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) by competitively interacting with the PEP binding site which hinders the shikimate pathway and the production of essential aromatic amino acids (Phe, Tyr, Trp) and other secondary metabolites in plants. Moreover, herbicide spray for weed management is lethal to both the primary crop and the weeds. Therefore, it is critical to develop herbicide-resistant crops for field purposes to reduce the associated yield and economic losses. In this study, the <i>in-silico</i> analysis drove the selection and validation of the point mutations in the conserved region of the EPSPS gene, which confers efficient herbicide resistance to mutated-CcEPSPS enzyme along with the retention of the normal enzyme function. An optimized <i>in-silico</i> validation of the target mutation before the development of the genome-edited resistant plant lines is a prerequisite for testing their efficacy as a proof of concept. We validated the combination of GATIPS mutation for its no-cost effect at the enzyme level <i>via</i> molecular dynamic (MD) simulation. Communicated by Ramaswamy H. Sarma Weed infestation is a major biotic stress factor and a consistent problem in agriculture. Development of glyphosate-resistant mutation is crucial to minimize the yield loss in agriculturally or nutritionally important crops for field application. Present <i>in-silico</i> approach is a proof-of-concept for validation of the selected glyphosate-resistant mutations. The current study has validated the combination of GATIPS mutation for its glyphosate-resistant phenotype and no negative cost effect at the enzyme simulation level.