cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.aq6uc3
title: Occurrence Download

description: A dataset containing 2131 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pinus torreyana Parry ex Carrière",
 "HasCoordinate is true",
 "BasisOfRecord is Human Observation",
 "Continent is North America"
 ]
}

 The dataset includes 2131 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007094-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8b9qjv
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Costa Rica",
 "TaxonKey is Aeschynomene ciliata Vogel"
 ]
}

 The dataset includes 83 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007095-250127130748423/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.28024426
title: Bacterial Dynamics in the Northern Indian Ocean Region: Understanding from the Pre-genomics to Present-Day OMICS Era

description: The Northern Indian Ocean (NIO) is one of the most characteristic regions of the world oceans with diverse oceanographic features. Understanding of the microbial community structure in these unique habitats has rapidly increased in the last decade, especially with the advent of molecular tools and the application of NGS technologies. Studies on marine microbial ecology in the NIO regions, from the pre-genomics era relied on culture techniques, microscopic observations, qualitative plate assays and biochemical tests. Molecular techniques and 16S rRNA gene sequencing introduced after the late 1990s significantly enhanced the understanding of bacterial diversity. These molecular tools revealed the presence of bacterial phyla and provided insights into their functional characteristics. Recent, NGS-based metagenomic studies further expanded the understanding of bacterial community structures, especially in the oxygen minimum zones and deep-sea sediments. These tools have identified bacterial taxa in-depth, revealing the existence of numerous Candidatus taxa known only by their genomic makeup. Despite these advancements, a large part of the bacterial diversity from the NIO remains unexplored, with many unanswered questions related to microbial carbon pump. Further transcriptome based studies can greatly improve the understanding of the microbial processes in the NIO, which is a dynamic, oceanographic habitat.
DOI: 10.6084/m9.figshare.28024426.v2
title: Bacterial Dynamics in the Northern Indian Ocean Region: Understanding from the Pre-genomics to Present-Day OMICS Era

description: The Northern Indian Ocean (NIO) is one of the most characteristic regions of the world oceans with diverse oceanographic features. Understanding of the microbial community structure in these unique habitats has rapidly increased in the last decade, especially with the advent of molecular tools and the application of NGS technologies. Studies on marine microbial ecology in the NIO regions, from the pre-genomics era relied on culture techniques, microscopic observations, qualitative plate assays and biochemical tests. Molecular techniques and 16S rRNA gene sequencing introduced after the late 1990s significantly enhanced the understanding of bacterial diversity. These molecular tools revealed the presence of bacterial phyla and provided insights into their functional characteristics. Recent, NGS-based metagenomic studies further expanded the understanding of bacterial community structures, especially in the oxygen minimum zones and deep-sea sediments. These tools have identified bacterial taxa in-depth, revealing the existence of numerous Candidatus taxa known only by their genomic makeup. Despite these advancements, a large part of the bacterial diversity from the NIO remains unexplored, with many unanswered questions related to microbial carbon pump. Further transcriptome based studies can greatly improve the understanding of the microbial processes in the NIO, which is a dynamic, oceanographic habitat.
DOI: 10.6084/m9.figshare.28024426.v1
title: Bacterial Dynamics in the Northern Indian Ocean Region: Understanding from the Pre-genomics to Present-Day OMICS Era

description: The Northern Indian Ocean (NIO) is one of the most characteristic regions of the world oceans with diverse oceanographic features. Understanding of the microbial community structure in these unique habitats has rapidly increased in the last decade, especially with the advent of molecular tools and the application of NGS technologies. Studies on marine microbial ecology in the NIO regions, from the pre-genomics era relied on culture techniques, microscopic observations, qualitative plate assays and biochemical tests. Molecular techniques and 16S rRNA gene sequencing introduced after the late 1990s significantly enhanced the understanding of bacterial diversity. These molecular tools revealed the presence of bacterial phyla and provided insights into their functional characteristics. Recent, NGS-based metagenomic studies further expanded the understanding of bacterial community structures, especially in the oxygen minimum zones and deep-sea sediments. These tools have identified bacterial taxa in-depth, revealing the existence of numerous Candidatus taxa known only by their genomic makeup. Despite these advancements, a large part of the bacterial diversity from the NIO remains unexplored, with many unanswered questions related to microbial carbon pump. Further transcriptome based studies can greatly improve the understanding of the microbial processes in the NIO, which is a dynamic, oceanographic habitat.
DOI: 10.6084/m9.figshare.27910511
title: Multidrug-resistant keratinolytic dermatophytes and non-dermatophytes causing onychomycosis in outpatients

description: This study identified and determined antibiograms of keratinolytic dermatophytes (DM), non-dermatophytic molds (NDM), and yeasts causing onychomycosis. Morphological, cultural, and biochemical characteristics were used to identify DM and NDM. The keratinolytic activity (KA) and antibiograms were conducted with keratin azure and the agar diffusion method, respectively. The minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) were determined using the microdilution method. Onychomycosis was more prevalent in males (53%) than females, toenails (57%) than fingernails, and commercial employees (40%) than other employees or unemployed. Fungal growth was observed in 92.5% nail samples. DM, NDM, and yeasts caused 46%, 35%, and 19% onychomycosis, respectively. <i>Trichophyton rubrum</i> and <i>Trichophyton mentagrophytes</i> were the common DM. Five different genus of NDM and three different yeasts were isolated. The KA of DM was 30–45% higher than that of NDM and yeasts. All fungal isolates (FI) were resistant to griseofulvin and fluconazole. However, 71%, 64%, and 36% of FI were sensitive to terbinafine hydrochloride, nystatin, and ketoconazole, respectively, while 84% of DM and 46% of NDM were multidrug-resistant. The MIC and MFC of these antifungals against FI ranged from micrograms to milligrams. Multidrug resistance is growing in keratinolytic DM and NDM. This study looks at what causes nail infections. We found that the infection was more common in men than women, and approximately 90% of nail samples showed infections. The fungi that caused the infections were often resistant to two drugs commonly used to treat infections and between 40% and 70% were sensitive to three drugs. The finding suggests that a large number of fungi were resistant to multiple drugs, and new drugs are needed to treat nail infections.
DOI: 10.6084/m9.figshare.27910511.v1
title: Multidrug-resistant keratinolytic dermatophytes and non-dermatophytes causing onychomycosis in outpatients

description: This study identified and determined antibiograms of keratinolytic dermatophytes (DM), non-dermatophytic molds (NDM), and yeasts causing onychomycosis. Morphological, cultural, and biochemical characteristics were used to identify DM and NDM. The keratinolytic activity (KA) and antibiograms were conducted with keratin azure and the agar diffusion method, respectively. The minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) were determined using the microdilution method. Onychomycosis was more prevalent in males (53%) than females, toenails (57%) than fingernails, and commercial employees (40%) than other employees or unemployed. Fungal growth was observed in 92.5% nail samples. DM, NDM, and yeasts caused 46%, 35%, and 19% onychomycosis, respectively. <i>Trichophyton rubrum</i> and <i>Trichophyton mentagrophytes</i> were the common DM. Five different genus of NDM and three different yeasts were isolated. The KA of DM was 30–45% higher than that of NDM and yeasts. All fungal isolates (FI) were resistant to griseofulvin and fluconazole. However, 71%, 64%, and 36% of FI were sensitive to terbinafine hydrochloride, nystatin, and ketoconazole, respectively, while 84% of DM and 46% of NDM were multidrug-resistant. The MIC and MFC of these antifungals against FI ranged from micrograms to milligrams. Multidrug resistance is growing in keratinolytic DM and NDM. This study looks at what causes nail infections. We found that the infection was more common in men than women, and approximately 90% of nail samples showed infections. The fungi that caused the infections were often resistant to two drugs commonly used to treat infections and between 40% and 70% were sensitive to three drugs. The finding suggests that a large number of fungi were resistant to multiple drugs, and new drugs are needed to treat nail infections.
DOI: 10.6084/m9.figshare.27950671
title: Detection of MPT-64 protein in pleural tuberculosis cases by magnetic bead-gold nanoparticle-PCR amplified immunoassay

description: Diagnosis of pleural tuberculosis (TB) is challenging; thus, an efficient method is urgently needed. We developed a magnetic-bead-gold nanoparticle-PCR amplified immunoassay (MB-AuNP-I-PCR, liquid system) to detect the <i>Mycobacterium tuberculosis</i> MPT-64 protein in pleural TB patients. AuNPs functionalized with detection antibodies/oligonucleotides were characterized by UV-vis spectroscopy, Transmission/Scanning electron microscopy, Fourier-transform infrared spectrometer, ELISA, and PCR, whereas MBs conjugated with detection antibodies were validated by magneto-ELISA/UV-vis spectroscopy. We utilized the MB-AuNP-I-PCR for MPT-64 detection in 99 clinical specimens which displayed 85.2% sensitivity and 97.8% specificity to diagnose pleural TB cases. Markedly, the sensitivity achieved by MB-AuNP-I-PCR was noticeably higher (<i>p</i> &lt; 0.01) than magneto-ELISA and GeneXpert. This is a preliminary report to diagnose pleural TB cases by MB-AuNP-I-PCR with promising results that require further corroboration in a higher number of specimens. Pleural tuberculosis is a sickness that is hard for doctors to diagnose because it doesn’t show clear signs. The current tests that doctors use don’t work very well, so we designed a new test using nanoparticles. This test showed promise in comparison to the other tests, but our findings need to be confirmed with a larger sample size.
DOI: 10.6084/m9.figshare.27950671.v1
title: Detection of MPT-64 protein in pleural tuberculosis cases by magnetic bead-gold nanoparticle-PCR amplified immunoassay

description: Diagnosis of pleural tuberculosis (TB) is challenging; thus, an efficient method is urgently needed. We developed a magnetic-bead-gold nanoparticle-PCR amplified immunoassay (MB-AuNP-I-PCR, liquid system) to detect the <i>Mycobacterium tuberculosis</i> MPT-64 protein in pleural TB patients. AuNPs functionalized with detection antibodies/oligonucleotides were characterized by UV-vis spectroscopy, Transmission/Scanning electron microscopy, Fourier-transform infrared spectrometer, ELISA, and PCR, whereas MBs conjugated with detection antibodies were validated by magneto-ELISA/UV-vis spectroscopy. We utilized the MB-AuNP-I-PCR for MPT-64 detection in 99 clinical specimens which displayed 85.2% sensitivity and 97.8% specificity to diagnose pleural TB cases. Markedly, the sensitivity achieved by MB-AuNP-I-PCR was noticeably higher (<i>p</i> &lt; 0.01) than magneto-ELISA and GeneXpert. This is a preliminary report to diagnose pleural TB cases by MB-AuNP-I-PCR with promising results that require further corroboration in a higher number of specimens. Pleural tuberculosis is a sickness that is hard for doctors to diagnose because it doesn’t show clear signs. The current tests that doctors use don’t work very well, so we designed a new test using nanoparticles. This test showed promise in comparison to the other tests, but our findings need to be confirmed with a larger sample size.
DOI: 10.6084/m9.figshare.27620580
title: Ultrastructural polymicrobial <i>Staphylococcus aureus–Pseudomonas aeruginosa</i> interactions and antimicrobial resistance in <i>ex vivo</i> cornea model

description: <b>Aim:</b> To investigate antagonistic interactions among pathogens, in <i>ex vivo</i> donor corneas infected with monomicrobial or polymicrobial combinations of antibiotic susceptible and resistant clinical isolates of <i>Staphylococcus aureus</i> (MSSA, MRSA) and <i>Pseudomonas aeruginosa</i> (S-PA, MDR-PA). <b>Materials & methods:</b> Scanning electron microscopy and antimicrobial susceptibility testing (AST, broth microdilution for minimum inhibitory and bactericidal concentrations [MIC/MBC]) pre-and post-polymicrobial interactions, in infected donor corneas. <b>Results:</b> MSSA lost viability with S-PA/MDR-PA, while MRSA formed larger cells, biofilm and lower MIC (teicoplanin) with S-PA, but lost viability with MDR-PA. S-PA had lower MIC (ceftazidime, meropenem, chloramphenicol) with MSSA, and lower MBC (cefoperazone, ciprofloxacin) and fewer cells with MRSA. MDR-PA had abundant cells and no change in AST with MSSA or MRSA. <b>Conclusion:</b> Significant antagonistic interactions occur in ocular polymicrobial infections, affecting antibiotic susceptible isolates more than resistant ones. Bacteria that cause human disease are becoming difficult to treat using common antibiotics due to resistance. One alternative way of treating infections being researched is by looking at how different bacteria interact. Just like humans, bacteria exist in communities and have ‘friends’ and ‘enemies’, against whom they compete for food and space. We wanted to see if this was also true at an infection site. We looked at two harmful bacteria, <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>. We found that these bacteria did interact and were made weaker in some respects when they were together at an infection site. How they become weaker and how this could be used to improve treatment requires further research. This study investigates polymicrobial interactions between ocular isolates of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> in an <i>ex vivo</i> cornea model. Scanning electron microscopy was used to observe morphological changes, and broth microdilution for antimicrobial susceptibility testing. Antagonistic/competitive polymicrobial interactions reduce antimicrobial resistance and virulence among co-infectants. Drug-susceptible isolates were more affected by these antagonistic interactions compared to drug-resistant counterparts. Our results potentially offer a new approach to combating antimicrobial resistance in ocular infections.
DOI: 10.6084/m9.figshare.27620580.v1
title: Ultrastructural polymicrobial <i>Staphylococcus aureus–Pseudomonas aeruginosa</i> interactions and antimicrobial resistance in <i>ex vivo</i> cornea model

description: <b>Aim:</b> To investigate antagonistic interactions among pathogens, in <i>ex vivo</i> donor corneas infected with monomicrobial or polymicrobial combinations of antibiotic susceptible and resistant clinical isolates of <i>Staphylococcus aureus</i> (MSSA, MRSA) and <i>Pseudomonas aeruginosa</i> (S-PA, MDR-PA). <b>Materials & methods:</b> Scanning electron microscopy and antimicrobial susceptibility testing (AST, broth microdilution for minimum inhibitory and bactericidal concentrations [MIC/MBC]) pre-and post-polymicrobial interactions, in infected donor corneas. <b>Results:</b> MSSA lost viability with S-PA/MDR-PA, while MRSA formed larger cells, biofilm and lower MIC (teicoplanin) with S-PA, but lost viability with MDR-PA. S-PA had lower MIC (ceftazidime, meropenem, chloramphenicol) with MSSA, and lower MBC (cefoperazone, ciprofloxacin) and fewer cells with MRSA. MDR-PA had abundant cells and no change in AST with MSSA or MRSA. <b>Conclusion:</b> Significant antagonistic interactions occur in ocular polymicrobial infections, affecting antibiotic susceptible isolates more than resistant ones. Bacteria that cause human disease are becoming difficult to treat using common antibiotics due to resistance. One alternative way of treating infections being researched is by looking at how different bacteria interact. Just like humans, bacteria exist in communities and have ‘friends’ and ‘enemies’, against whom they compete for food and space. We wanted to see if this was also true at an infection site. We looked at two harmful bacteria, <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>. We found that these bacteria did interact and were made weaker in some respects when they were together at an infection site. How they become weaker and how this could be used to improve treatment requires further research. This study investigates polymicrobial interactions between ocular isolates of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> in an <i>ex vivo</i> cornea model. Scanning electron microscopy was used to observe morphological changes, and broth microdilution for antimicrobial susceptibility testing. Antagonistic/competitive polymicrobial interactions reduce antimicrobial resistance and virulence among co-infectants. Drug-susceptible isolates were more affected by these antagonistic interactions compared to drug-resistant counterparts. Our results potentially offer a new approach to combating antimicrobial resistance in ocular infections.
DOI: 10.6084/m9.figshare.28075380
title: METTL4 and METTL5 as biomarkers for recurrence-free survival in hepatocellular carcinoma patients

description: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths, with high rates of postoperative recurrence. Identifying reliable biomarkers for predicting recurrence is critical for improving patient outcomes. This study investigates the predictive value of m6A methylation-related genes, METTL4 and METTL5, on HCC recurrence after surgery. We analyzed METTL4 and METTL5 expression in HCC and adjacent non-cancerous tissues using the TCGA database and evaluated their levels in surgical samples from 67 hCC patients. A recurrence risk model was developed and validated in an external cohort of 65 patients. METTL4 and METTL5 were significantly overexpressed in HCC tissues. High expression correlated with shorter recurrence-free survival (RFS). The model stratified patients into high, medium, and low-risk groups with 3-year RFS rates of 18.75%, 69.70%, and 93.75%, respectively. METTL4 and METTL5 expression levels are strong predictors of HCC recurrence. The risk model offers a novel approach for postoperative management of HCC.
DOI: 10.6084/m9.figshare.28075380.v1
title: METTL4 and METTL5 as biomarkers for recurrence-free survival in hepatocellular carcinoma patients

description: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths, with high rates of postoperative recurrence. Identifying reliable biomarkers for predicting recurrence is critical for improving patient outcomes. This study investigates the predictive value of m6A methylation-related genes, METTL4 and METTL5, on HCC recurrence after surgery. We analyzed METTL4 and METTL5 expression in HCC and adjacent non-cancerous tissues using the TCGA database and evaluated their levels in surgical samples from 67 hCC patients. A recurrence risk model was developed and validated in an external cohort of 65 patients. METTL4 and METTL5 were significantly overexpressed in HCC tissues. High expression correlated with shorter recurrence-free survival (RFS). The model stratified patients into high, medium, and low-risk groups with 3-year RFS rates of 18.75%, 69.70%, and 93.75%, respectively. METTL4 and METTL5 expression levels are strong predictors of HCC recurrence. The risk model offers a novel approach for postoperative management of HCC.
DOI: 10.15468/dl.ej2ena
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oxyura jamaicensis (J.F.Gmelin, 1789)",
 "DatasetKey is one of (Invasive species - Ruddy duck (Oxyura jamaicensis) in Flanders, Belgium)"
 ]
}

 The dataset includes 104 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007096-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vnpkg9
title: Occurrence Download

description: A dataset containing 1116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-119.98 42.01,-91.23 42.01,-91.23 49.31,-119.98 49.31,-119.98 42.01))",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochrophyta"
 ]
}

 The dataset includes 1116 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007097-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/00007078
title: Role of Body Mass Index and concomitant medication use in metastatic urothelial carcinoma

description: The obesity paradox is a peculiar phenomenon whereby patients that are obese tend to survive longer, if affected by certain diseases, such as cancer. 
While this phenomenon has been demonstrated in certain malignancies, the obesity paradox in patients with metastatic urothelial carcinoma (e.g. bladder cancer that has spread to other parts of the body) has not yet been investigated. If proven true, body mass index (BMI) categories, as per the World Health Organization (WHO), could represent a novel stratification factor for randomization for patients enrolled in future prospective trials and aid in study design. 
Beta blockers are medications that are given to treat hypertension or following coronary artery disease (e.g. miocardial infaction). It has been demonstrated in patients with metastatic melanoma a synergistic effect of beta blockers and immunotherapy, meaning that patients that receive beta blockers and are on immunotherapy tend to achieve a greater degree of response to immunothreapy. This is due to the fact that beta blockers can enhance the activity of white blood cells that are the same target of immunotherapy for cancer. If proven true, in the context of metastatic urothelial carcinoma, one could advise on the use of beta blockers to all patients with hypertension or coronary syndromes instead of other alternative medications. The investigators are going to explore also the role of concomitant use of corticosterois, especially in case of the occurrence of ummune-related adverse events and anti-histamine medications.