cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ps7ede
title: Occurrence Download

description: A dataset containing 62070 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-79.88820024573366 -4.387765396315229, -79.8858394121526 -4.387680468448415, -79.88510067584266 -4.387552733716885, -79.88479441354741 -4.387470870279506, -79.88437237407824 -4.386466235877938, -79.86576301138173 -4.313806168011958, -79.86664332554223 -4.313820384635354, -79.88279667011382 -4.314624862727437, -79.88703525313782 -4.316327597522515, -79.88883236412252 -4.317794516959427, -79.92510011308556 -4.354754741404345, -79.92820726697533 -4.36037263840867, -79.92788953855948 -4.365834588177667, -79.92705017734204 -4.368669060298981, -79.9067056708373 -4.382597124814489, -79.89595048084641 -4.387665199313759, -79.88820024573366 -4.387765396315229))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 62070 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027095-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/usctheses-ouc11399khd1
title: Theory and Design of Algorithms for Quantum Systems
DOI: 10.15468/dl.vbs8hy
title: Occurrence Download

description: A dataset containing 726425 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pyrocephalus rubinus (Boddaert, 1783)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 726425 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027106-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/usctheses-ouc11399khdx
title: Modern Workplace Environment Pre- and Post-Occupant Satisfaction in Modern Office Hot-Desking Systems: A Comparative Study of Workplace Environments
DOI: 10.15468/dl.w7bemq
title: Occurrence Download

description: A dataset containing 422 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scytalopus iraiensis Bornschein, Reinert & Pichorim, 1998"
 ]
}

 The dataset includes 422 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027111-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28184100
title: Optimizing conditions for carbofuran degrading isolates: a pathway to sustainable bioremediation in agricultural settings

description: Agriculture, driven by the escalating global demand for food, heavily relies on pesticides to ensure high yields and pest-free produce. The carbamate group of pesticides, including the widely used carbofuran, presents advantages such as low retention, high efficacy, and broad application. However, the associated health concerns categorize these pesticides as hidden threats. In response, biological remediation emerges as a more cost-efficient and environmentally friendly alternative to chemical or physical approaches. Our prior investigation identified 17 highly potential carbofuran degraders, forming the basis for this research. The focus lies on optimizing the isolates’ growth conditions, exploring temperatures (30 °C and 37 °C) and pH levels (7 and 9) in Bushnell Haas Agar. It was observed that all four pesticide doses (250, 500, 750, and 1000 mg/L) in Bushnell Haas Agar medium were supported by the majority of isolates at 30 °C and pH 9, whereas 750 and 1000 mg/L were favored at pH 7 (30 °C) and at both pH 7 and 9 (37 °C). Despite limited biofilm-forming ability rendered due to presence of <i>omp</i>A along with or with not <i>bap</i> gene, the isolates’ extracellular polymeric substance (EPS) composition indicated a polymeric nature. Also 13 of the isolates’ EPS production accelerates at 250 mg/L pesticide concentration. Metabolic pathway analyses revealed a preference for hydrolytic degradation, while molecular examinations confirmed the presence of plasmid and the absence of specific genes <i>mcd</i> and <i>ceh</i>A responsible for carbamate – hydrolase on the chromosome. Concern is raised by the presence of colistin and tetracycline resistant genes (mcr2 (47.05%), tetA (29.41%), and qnrs (23.53%) in the genomic content of some isolates, in addition to ESBL resistance genes found in varying frequencies, such as blaIMP3 (5.89%), blaVIM (70.59%), blaKPC (88.25%), blaOXA-1 (11.76%), bla-SHV (23.53%) & blaOXA1 (11.76%), bla-CTMX15 (17.65%), necessitating alternative mechanisms. The findings demonstrate the isolates’ dual function as repositories of antibiotic resistance and prospective bioremediation agents, requiring careful handling and application. Developing safe and efficient bioremediation systems will need addressing resistance issues while maximizing degrading efficiency.
DOI: 10.6084/m9.figshare.28184100.v1
title: Optimizing conditions for carbofuran degrading isolates: a pathway to sustainable bioremediation in agricultural settings

description: Agriculture, driven by the escalating global demand for food, heavily relies on pesticides to ensure high yields and pest-free produce. The carbamate group of pesticides, including the widely used carbofuran, presents advantages such as low retention, high efficacy, and broad application. However, the associated health concerns categorize these pesticides as hidden threats. In response, biological remediation emerges as a more cost-efficient and environmentally friendly alternative to chemical or physical approaches. Our prior investigation identified 17 highly potential carbofuran degraders, forming the basis for this research. The focus lies on optimizing the isolates’ growth conditions, exploring temperatures (30 °C and 37 °C) and pH levels (7 and 9) in Bushnell Haas Agar. It was observed that all four pesticide doses (250, 500, 750, and 1000 mg/L) in Bushnell Haas Agar medium were supported by the majority of isolates at 30 °C and pH 9, whereas 750 and 1000 mg/L were favored at pH 7 (30 °C) and at both pH 7 and 9 (37 °C). Despite limited biofilm-forming ability rendered due to presence of <i>omp</i>A along with or with not <i>bap</i> gene, the isolates’ extracellular polymeric substance (EPS) composition indicated a polymeric nature. Also 13 of the isolates’ EPS production accelerates at 250 mg/L pesticide concentration. Metabolic pathway analyses revealed a preference for hydrolytic degradation, while molecular examinations confirmed the presence of plasmid and the absence of specific genes <i>mcd</i> and <i>ceh</i>A responsible for carbamate – hydrolase on the chromosome. Concern is raised by the presence of colistin and tetracycline resistant genes (mcr2 (47.05%), tetA (29.41%), and qnrs (23.53%) in the genomic content of some isolates, in addition to ESBL resistance genes found in varying frequencies, such as blaIMP3 (5.89%), blaVIM (70.59%), blaKPC (88.25%), blaOXA-1 (11.76%), bla-SHV (23.53%) & blaOXA1 (11.76%), bla-CTMX15 (17.65%), necessitating alternative mechanisms. The findings demonstrate the isolates’ dual function as repositories of antibiotic resistance and prospective bioremediation agents, requiring careful handling and application. Developing safe and efficient bioremediation systems will need addressing resistance issues while maximizing degrading efficiency.
DOI: 10.6084/m9.figshare.27073989
title: Structural insights into polyethylene terephthalate (PET)-degrading archaeal lipase enzyme: An <i>insilico</i> approach

description: Biodegradation of plastic is the most eco-friendly degradation process conferred by various microbial enzymes, especially the lipase enzymes. The lipase enzymes depict a broad substrate range, high regio/stereoselectivity, and stability in organic solvents. However, enhancing the catalytic activity of lipases for industrial production remains a challenge, predominantly due to the need for their extensive mechanistic characterization. Here, we employed a multidisciplinary approach to illustrate the comprehensive physiochemical and mechanical properties of 102 lipase sequences from six different groups of plastic-degrading microorganisms. Molecular docking-based evaluation of the binding efficiencies of selected lipases with the most common plastic polymers- polyurethane (PUR) and polyethylene terephthalate (PET), revealed that the archaeal lipase had the lowest binding energy of −7.1 kcal/mol with PET. Remarkably, the molecular dynamic simulation studies (up to 100 ns) and very low RMSD (0.3 nm) and RMSF (0.25 nm) values further ascertained the stability of archaeal lipase after binding with PET polymer. Further, a 2.19 nm radius of gyration (Rg) within 100 ns simulation time, binding free energy ΔG<sub>TOTAL</sub> with −24.36 kcal/mol and entropy factor -TΔS 7.65 kcal/mol also indicated strong binding of archaeal lipase with PET polymer. The mechanistic exploration of archaeal lipase yielded valuable insights into its effective binding with PET polymer, paving the way for future lipase enzyme engineering and harnessing its industrial potential for plastic biodegradation.
DOI: 10.6084/m9.figshare.27073989.v1
title: Structural insights into polyethylene terephthalate (PET)-degrading archaeal lipase enzyme: An <i>insilico</i> approach

description: Biodegradation of plastic is the most eco-friendly degradation process conferred by various microbial enzymes, especially the lipase enzymes. The lipase enzymes depict a broad substrate range, high regio/stereoselectivity, and stability in organic solvents. However, enhancing the catalytic activity of lipases for industrial production remains a challenge, predominantly due to the need for their extensive mechanistic characterization. Here, we employed a multidisciplinary approach to illustrate the comprehensive physiochemical and mechanical properties of 102 lipase sequences from six different groups of plastic-degrading microorganisms. Molecular docking-based evaluation of the binding efficiencies of selected lipases with the most common plastic polymers- polyurethane (PUR) and polyethylene terephthalate (PET), revealed that the archaeal lipase had the lowest binding energy of −7.1 kcal/mol with PET. Remarkably, the molecular dynamic simulation studies (up to 100 ns) and very low RMSD (0.3 nm) and RMSF (0.25 nm) values further ascertained the stability of archaeal lipase after binding with PET polymer. Further, a 2.19 nm radius of gyration (Rg) within 100 ns simulation time, binding free energy ΔG<sub>TOTAL</sub> with −24.36 kcal/mol and entropy factor -TΔS 7.65 kcal/mol also indicated strong binding of archaeal lipase with PET polymer. The mechanistic exploration of archaeal lipase yielded valuable insights into its effective binding with PET polymer, paving the way for future lipase enzyme engineering and harnessing its industrial potential for plastic biodegradation.
DOI: 10.6084/m9.figshare.27862066
title: Computational insights into mercuric reductase from <i>Pseudomonas fluorescens</i>: a bioinformatic and molecular dynamics approach for mercury detoxification

description: Mercury (Hg) pollution poses significant threats to human health and ecosystems worldwide due to its persistence, bioaccumulation, and toxic effects. This study focuses on mercuric reductase from <i>Pseudomonas fluorescens</i> (UniProt ID Q51772), a key enzyme involved in detoxifying mercury through reduction to its less toxic elemental form, Hg(0). This study aims to explore the potential of this enzyme for bioremediation applications, focusing on structural insights, functional mechanisms, and biotechnological enhancements to facilitate mercury detoxification. The protein sequence of Q51772 was analyzed using bioinformatics tools to determine its structural and functional attributes. Physiochemical properties, including molecular weight, isoelectric point, and secondary structure predictions, were assessed. Virulence prediction tools confirmed the protein’s nontoxic and nonpathogenic nature. Homology modeling and docking studies provided insights into its three-dimensional structure and binding interactions with mercury substrates. Q51772 consists of 548 amino acids and belongs to the Pyridine nucleotide-disulphide oxidoreductase family, class I. It features specific domains crucial for mercury reduction, identified through Pfam and InterPro analyses. Physiochemical analysis indicated a stable protein with hydrophilic tendencies conducive to enzymatic function. Structural modeling validated by ProQ and PROCHECK confirmed the reliability of the predicted structure. Molecular docking of organic mercury compound with wild-type and mutant mercuric reductase revealed strong binding affinities, with key hydrogen bonds involving residues Gly95, Thr122, and Asp390. Mercuric reductase Q51772 from <i>Pseudomonas fluorescens</i> emerges as a promising candidate for bioremediation of mercury-contaminated environments. Future research should focus on optimizing its performance under diverse environmental conditions to advance sustainable solutions for mercury pollution control.
DOI: 10.6084/m9.figshare.27862066.v2
title: Computational insights into mercuric reductase from <i>Pseudomonas fluorescens</i>: a bioinformatic and molecular dynamics approach for mercury detoxification

description: Mercury (Hg) pollution poses significant threats to human health and ecosystems worldwide due to its persistence, bioaccumulation, and toxic effects. This study focuses on mercuric reductase from <i>Pseudomonas fluorescens</i> (UniProt ID Q51772), a key enzyme involved in detoxifying mercury through reduction to its less toxic elemental form, Hg(0). This study aims to explore the potential of this enzyme for bioremediation applications, focusing on structural insights, functional mechanisms, and biotechnological enhancements to facilitate mercury detoxification. The protein sequence of Q51772 was analyzed using bioinformatics tools to determine its structural and functional attributes. Physiochemical properties, including molecular weight, isoelectric point, and secondary structure predictions, were assessed. Virulence prediction tools confirmed the protein’s nontoxic and nonpathogenic nature. Homology modeling and docking studies provided insights into its three-dimensional structure and binding interactions with mercury substrates. Q51772 consists of 548 amino acids and belongs to the Pyridine nucleotide-disulphide oxidoreductase family, class I. It features specific domains crucial for mercury reduction, identified through Pfam and InterPro analyses. Physiochemical analysis indicated a stable protein with hydrophilic tendencies conducive to enzymatic function. Structural modeling validated by ProQ and PROCHECK confirmed the reliability of the predicted structure. Molecular docking of organic mercury compound with wild-type and mutant mercuric reductase revealed strong binding affinities, with key hydrogen bonds involving residues Gly95, Thr122, and Asp390. Mercuric reductase Q51772 from <i>Pseudomonas fluorescens</i> emerges as a promising candidate for bioremediation of mercury-contaminated environments. Future research should focus on optimizing its performance under diverse environmental conditions to advance sustainable solutions for mercury pollution control.
DOI: 10.6084/m9.figshare.27862066.v1
title: Computational insights into mercuric reductase from <i>Pseudomonas fluorescens</i>: a bioinformatic and molecular dynamics approach for mercury detoxification

description: Mercury (Hg) pollution poses significant threats to human health and ecosystems worldwide due to its persistence, bioaccumulation, and toxic effects. This study focuses on mercuric reductase from <i>Pseudomonas fluorescens</i> (UniProt ID Q51772), a key enzyme involved in detoxifying mercury through reduction to its less toxic elemental form, Hg(0). This study aims to explore the potential of this enzyme for bioremediation applications, focusing on structural insights, functional mechanisms, and biotechnological enhancements to facilitate mercury detoxification. The protein sequence of Q51772 was analyzed using bioinformatics tools to determine its structural and functional attributes. Physiochemical properties, including molecular weight, isoelectric point, and secondary structure predictions, were assessed. Virulence prediction tools confirmed the protein’s nontoxic and nonpathogenic nature. Homology modeling and docking studies provided insights into its three-dimensional structure and binding interactions with mercury substrates. Q51772 consists of 548 amino acids and belongs to the Pyridine nucleotide-disulphide oxidoreductase family, class I. It features specific domains crucial for mercury reduction, identified through Pfam and InterPro analyses. Physiochemical analysis indicated a stable protein with hydrophilic tendencies conducive to enzymatic function. Structural modeling validated by ProQ and PROCHECK confirmed the reliability of the predicted structure. Molecular docking of organic mercury compound with wild-type and mutant mercuric reductase revealed strong binding affinities, with key hydrogen bonds involving residues Gly95, Thr122, and Asp390. Mercuric reductase Q51772 from <i>Pseudomonas fluorescens</i> emerges as a promising candidate for bioremediation of mercury-contaminated environments. Future research should focus on optimizing its performance under diverse environmental conditions to advance sustainable solutions for mercury pollution control.
DOI: 10.6084/m9.figshare.24638692
title: Efficacy of 3-day versus 5-day aprepitant regimens for long-delayed chemotherapy-induced nausea and vomiting in patients receiving cisplatin-based chemotherapy

description: Chemotherapy-induced nausea and vomiting (CINV) is an ongoing problem. While effectiveness of triplet antiemetic regimens in the delayed CINV phase (24–120 hours after administration of chemotherapy) has been studied, their effectiveness in the long-delayed phase (120–168 hours post-administration) is unknown. We compared the efficacy of 3- and 5-day courses of a triplet antiemetic prophylaxis containing aprepitant (APR) in controlling long-delayed CINV after cisplatin (CDDP)-based chemotherapy. We obtained patient-level data from a nationwide, multicenter, prospective observational study in Japan. The incidence and timing of CINV after 3- and 5-day APR-containing regimens were compared using inverse probability treatment weighting. The analysis included 380 patients. The incidence rates of long-delayed nausea and vomiting were significantly reduced for the 5-day compared with the 3-day regimen (29.1% vs. 22.2%, <i>p</i> = 0.0042; 6.7% vs. 0%, <i>p</i> &lt; 0.0001, respectively). Among those without CINV, vomiting was not reported after day 2 in the 5-day APR group but increased after day 4 in the 3-day APR group. A 5-day regimen triplet antiemetic prophylaxis with APR decreased long-delayed vomiting compared with a 3-day regimen in patients receiving CDDP-based chemotherapy. However, the 5-day regimen showed no advantage over the 3-day regimen against long-delayed nausea.
DOI: 10.6084/m9.figshare.24638692.v1
title: Efficacy of 3-day versus 5-day aprepitant regimens for long-delayed chemotherapy-induced nausea and vomiting in patients receiving cisplatin-based chemotherapy

description: Chemotherapy-induced nausea and vomiting (CINV) is an ongoing problem. While effectiveness of triplet antiemetic regimens in the delayed CINV phase (24–120 hours after administration of chemotherapy) has been studied, their effectiveness in the long-delayed phase (120–168 hours post-administration) is unknown. We compared the efficacy of 3- and 5-day courses of a triplet antiemetic prophylaxis containing aprepitant (APR) in controlling long-delayed CINV after cisplatin (CDDP)-based chemotherapy. We obtained patient-level data from a nationwide, multicenter, prospective observational study in Japan. The incidence and timing of CINV after 3- and 5-day APR-containing regimens were compared using inverse probability treatment weighting. The analysis included 380 patients. The incidence rates of long-delayed nausea and vomiting were significantly reduced for the 5-day compared with the 3-day regimen (29.1% vs. 22.2%, <i>p</i> = 0.0042; 6.7% vs. 0%, <i>p</i> &lt; 0.0001, respectively). Among those without CINV, vomiting was not reported after day 2 in the 5-day APR group but increased after day 4 in the 3-day APR group. A 5-day regimen triplet antiemetic prophylaxis with APR decreased long-delayed vomiting compared with a 3-day regimen in patients receiving CDDP-based chemotherapy. However, the 5-day regimen showed no advantage over the 3-day regimen against long-delayed nausea.
DOI: 10.6084/m9.figshare.24747612
title: Use of sacubitril/valsartan in patients with heart failure: evidence from the real world

description: To characterize the use of sacubitril/valsartan in a group of patients with heart failure in Colombia. Follow-up study of patients with heart failure who started sacubitril/valsartan and were affiliated with the Colombian health system between 2019 and 2021. Sociodemographic, clinical, and pharmacological variables and adherence and persistence of use were identified. A total of 514 patients were identified, with a mean age of 65.7 years, 73.7% of whom started sacubitril/valsartan at low doses, and only 12.5% reached the maximum dose. Adherence was 78.2% and persistence was 56.8% at 1 year of follow-up. The increase in systolic blood pressure (odds ratio (OR): 1.01; 95% CI: 1.00–1.03) and the use of β-blockers (OR: 2.63; 95% CI: 1.42–4.85) were correlated with a greater persistence, while receiving furosemide (OR: 0.59; 95% CI: 0.39–0.89) and not having received renin – angiotensin – aldosterone system inhibitors in the 3 months before starting sacubitril/valsartan (OR: 0.48; 95% CI: 0.31–0.76) were associated with lower persistence. The persistence of treatment 1 year after starting sacubitril/valsartan was not high, and a small proportion of patients reached the target dose of the drug. Nontitration of the drug dose was common.
DOI: 10.6084/m9.figshare.24747612.v1
title: Use of sacubitril/valsartan in patients with heart failure: evidence from the real world

description: To characterize the use of sacubitril/valsartan in a group of patients with heart failure in Colombia. Follow-up study of patients with heart failure who started sacubitril/valsartan and were affiliated with the Colombian health system between 2019 and 2021. Sociodemographic, clinical, and pharmacological variables and adherence and persistence of use were identified. A total of 514 patients were identified, with a mean age of 65.7 years, 73.7% of whom started sacubitril/valsartan at low doses, and only 12.5% reached the maximum dose. Adherence was 78.2% and persistence was 56.8% at 1 year of follow-up. The increase in systolic blood pressure (odds ratio (OR): 1.01; 95% CI: 1.00–1.03) and the use of β-blockers (OR: 2.63; 95% CI: 1.42–4.85) were correlated with a greater persistence, while receiving furosemide (OR: 0.59; 95% CI: 0.39–0.89) and not having received renin – angiotensin – aldosterone system inhibitors in the 3 months before starting sacubitril/valsartan (OR: 0.48; 95% CI: 0.31–0.76) were associated with lower persistence. The persistence of treatment 1 year after starting sacubitril/valsartan was not high, and a small proportion of patients reached the target dose of the drug. Nontitration of the drug dose was common.