cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28554154.v2
title: High glucose heightens vulnerability to <i>Leishmania braziliensis</i> infection in human macrophages by hampering the production of reactive oxygen species through TLR2 and TLR4

description: Diabetes increases susceptibility to infections, including <i>Leishmania braziliensis</i> (<i>Lb</i>). Our group previously demonstrated that diabetic patients with cutaneous leishmaniasis (CL) take longer to heal lesions compared to non-diabetics. Since macrophages play a critical role in CL pathogenesis, we investigated how high glucose levels impact their response during <i>Lb</i> infection. Macrophages cultured in high glucose conditions showed increased parasite load than those in normal glucose conditions. The production of inflammatory mediators was similar between glucose conditions, but basal reactive oxygen species (ROS) production was elevated under high glucose conditions and remained unchanged after <i>Lb</i> infection, indicating glucose-induced oxidative stress does not control the parasite. In contrast, macrophages in normal glucose conditions, exhibited increased ROS production only after infection<i>.</i> Additionally, high glucose reduced TLR2 and TLR4 expression, which was also observed after <i>Lb</i> infection. TLR2/4 inhibition increased <i>Lb</i> infection in normal glucose conditions, mediated by TLR-dependent ROS production. However, this mechanism was absent under high glucose conditions, where elevated basal ROS production appeared TLR-independent. Biopsies from diabetic CL patients corroborated these findings, showing decreased TLR2 and TLR4 expression compared to non-diabetics. These findings suggest that high glucose levels induce oxidative stress and reduces TLR expression, impairing macrophage functions and rendering them less effective at controlling Lb infection.
DOI: 10.6084/m9.figshare.28607943
title: Monocyte distribution width (MDW) as a reliable diagnostic biomarker for sepsis in patients with HIV

description: Sepsis is a leading cause of death among patients with HIV, but early diagnosis remains a challenge. This study evaluates the diagnostic performance of monocyte distribution width (MDW) in detecting sepsis in patients with HIV. A prospective observational study was conducted at Shanghai Public Health Center, involving 488 hospitalized patients with HIV aged 18–65 between December 2022 and August 2023. MDW was measured at admission, and its diagnostic accuracy was compared with Sepsis-3 criteria. Survival rates on day 28 and 90 were also recorded. Additionally, five machine learning (ML) models were tested to enhance diagnostic efficacy. Of 488 subjects, 90 were in the sepsis group and 398 in the control group. MDW showed a diagnostic area under the curve (AUC) of 0.82, comparable to C-reactive protein (CRP) and Procalcitonin (PCT) with AUCs of 0.78 and 0.82, respectively. With a cut-off value of 25.25, MDW had a sensitivity of 0.83 and specificity of 0.76. The positive and negative predictive values were 44% and 95%, respectively. When MDW was combined with platelet count, serum albumin, and hemoglobin in a random forest model, the AUC improved to 0.931. The model achieved a sensitivity of 1.00 and specificity of 0.732. MDW is a useful diagnostic marker for sepsis in patients with HIV, with strong sensitivity and specificity. Combining MDW with other lab markers can further enhance diagnostic accuracy. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT05036928..
DOI: 10.6084/m9.figshare.28607943.v1
title: Monocyte distribution width (MDW) as a reliable diagnostic biomarker for sepsis in patients with HIV

description: Sepsis is a leading cause of death among patients with HIV, but early diagnosis remains a challenge. This study evaluates the diagnostic performance of monocyte distribution width (MDW) in detecting sepsis in patients with HIV. A prospective observational study was conducted at Shanghai Public Health Center, involving 488 hospitalized patients with HIV aged 18–65 between December 2022 and August 2023. MDW was measured at admission, and its diagnostic accuracy was compared with Sepsis-3 criteria. Survival rates on day 28 and 90 were also recorded. Additionally, five machine learning (ML) models were tested to enhance diagnostic efficacy. Of 488 subjects, 90 were in the sepsis group and 398 in the control group. MDW showed a diagnostic area under the curve (AUC) of 0.82, comparable to C-reactive protein (CRP) and Procalcitonin (PCT) with AUCs of 0.78 and 0.82, respectively. With a cut-off value of 25.25, MDW had a sensitivity of 0.83 and specificity of 0.76. The positive and negative predictive values were 44% and 95%, respectively. When MDW was combined with platelet count, serum albumin, and hemoglobin in a random forest model, the AUC improved to 0.931. The model achieved a sensitivity of 1.00 and specificity of 0.732. MDW is a useful diagnostic marker for sepsis in patients with HIV, with strong sensitivity and specificity. Combining MDW with other lab markers can further enhance diagnostic accuracy. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT05036928..
DOI: 10.6084/m9.figshare.28557000
title: Natural occurrence of semicarbazide in heather honey

description: Regulatory bodies aim to protect consumers from harmful substances. The use of certain antibiotics is prohibited in food-producing animals in the EU due to their potential detrimental effects on humans. Among these are nitrofuran antibiotics, which degrade rapidly so that their metabolites are used as markers in screening for their illegal use. The use of one metabolite, semicarbazide (SEM), as a marker for detecting the antibiotic nitrofurazone, has been criticized due to the many pathways it can be formed by and its natural occurrence in some food items. A recent change in the reference point of action (RPA) for SEM, as stated in Commission Regulation (EU) 2019/1871, due to a reassessment of sensitivity of the analyses, poses a problem for the export of heather honey in Norway. Norwegian heather honey seems to exceed the lowered RPA in numerous cases. Here we show that Norwegian heather honey samples, but not polyfloral ‘summer’ honey samples from the same hives, contain SEM. The simplest explanation for the demonstrated pattern is a natural source of SEM in heather honey, not the use of a banned antibiotic. Based on our results, we propose that an exception to the EU regulation should be added, exempting heather honey derived from <i>Calluna vulgaris</i> unless other nitrofurans or their metabolites are found together with SEM.
DOI: 10.6084/m9.figshare.28557000.v1
title: Natural occurrence of semicarbazide in heather honey

description: Regulatory bodies aim to protect consumers from harmful substances. The use of certain antibiotics is prohibited in food-producing animals in the EU due to their potential detrimental effects on humans. Among these are nitrofuran antibiotics, which degrade rapidly so that their metabolites are used as markers in screening for their illegal use. The use of one metabolite, semicarbazide (SEM), as a marker for detecting the antibiotic nitrofurazone, has been criticized due to the many pathways it can be formed by and its natural occurrence in some food items. A recent change in the reference point of action (RPA) for SEM, as stated in Commission Regulation (EU) 2019/1871, due to a reassessment of sensitivity of the analyses, poses a problem for the export of heather honey in Norway. Norwegian heather honey seems to exceed the lowered RPA in numerous cases. Here we show that Norwegian heather honey samples, but not polyfloral ‘summer’ honey samples from the same hives, contain SEM. The simplest explanation for the demonstrated pattern is a natural source of SEM in heather honey, not the use of a banned antibiotic. Based on our results, we propose that an exception to the EU regulation should be added, exempting heather honey derived from <i>Calluna vulgaris</i> unless other nitrofurans or their metabolites are found together with SEM.
DOI: 10.6084/m9.figshare.27256120
title: Inequality and Poverty of Privately Owned Forests Farmers in Rural Areas of Indonesia

description: Land limitation dramatically affects people with land-based livelihoods, such as farmers, and is often an obstacle to earning sufficient income for their family’s needs. Privately owned forests (POFs) are a land-based farming activity with a long history in Indonesian society. This study aimed to determine the socio-economic conditions, inequality, poverty, and livelihood dynamics of POF farmers. The research was conducted in three villages in Ciamis Regency, West Java Province, Indonesia. The research was conducted from February to May 2022 through structured, questionnaire-based interviews and in-depth interviews. The number of respondents was 170 POF farmers selected by simple random sampling in each village: 60 in Kalijaya village (18% of 325 farmers), 55 in Mekarjaya village (35% of 154 farmers), and 55 in Hujungtiwu village (37% of 148 farmers). The data obtained were processed using the Gini index and Poverty Line calculations, and analyzed descriptively. The results of this study show that POF farmers are dominated by productive age, long farming experience and low education. POF is the most dominant land use in the three research locations, but the income and contribution of POF are high only in Kalijaya village and lower in Mekarjaya and Hujungtiwu villages. Regression analysis indicates that land has a strong positive impact on farmers’ income. Land inequality was present in farmland, paddy fields, and POF land. The overall level of income and land inequality was less equitable in all locations. Land and income from POFs and non-POFs worked together to reduce POF farmers’ income and land inequality for POF farmers. Poverty was also more widespread among POF farmers in Mekarjaya and Hujungtiwu communities, where average land ownership was low. Farmers’ strategies to deal with this condition include continuing to farm the land but also diversifying their work both within and outside the village. Policymakers can utilise this information to promote or incentivize POF farmers to optimize POF management and improve their families’ living standards.
DOI: 10.6084/m9.figshare.27256120.v1
title: Inequality and Poverty of Privately Owned Forests Farmers in Rural Areas of Indonesia

description: Land limitation dramatically affects people with land-based livelihoods, such as farmers, and is often an obstacle to earning sufficient income for their family’s needs. Privately owned forests (POFs) are a land-based farming activity with a long history in Indonesian society. This study aimed to determine the socio-economic conditions, inequality, poverty, and livelihood dynamics of POF farmers. The research was conducted in three villages in Ciamis Regency, West Java Province, Indonesia. The research was conducted from February to May 2022 through structured, questionnaire-based interviews and in-depth interviews. The number of respondents was 170 POF farmers selected by simple random sampling in each village: 60 in Kalijaya village (18% of 325 farmers), 55 in Mekarjaya village (35% of 154 farmers), and 55 in Hujungtiwu village (37% of 148 farmers). The data obtained were processed using the Gini index and Poverty Line calculations, and analyzed descriptively. The results of this study show that POF farmers are dominated by productive age, long farming experience and low education. POF is the most dominant land use in the three research locations, but the income and contribution of POF are high only in Kalijaya village and lower in Mekarjaya and Hujungtiwu villages. Regression analysis indicates that land has a strong positive impact on farmers’ income. Land inequality was present in farmland, paddy fields, and POF land. The overall level of income and land inequality was less equitable in all locations. Land and income from POFs and non-POFs worked together to reduce POF farmers’ income and land inequality for POF farmers. Poverty was also more widespread among POF farmers in Mekarjaya and Hujungtiwu communities, where average land ownership was low. Farmers’ strategies to deal with this condition include continuing to farm the land but also diversifying their work both within and outside the village. Policymakers can utilise this information to promote or incentivize POF farmers to optimize POF management and improve their families’ living standards.
DOI: 10.15468/dl.kbnv8u
title: Occurrence Download

description: A dataset containing 4591 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is WII Herbarium Dataset"
 ]
}

 The dataset includes 4591 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016836-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0198342.10fu
title: SH0198342.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0198343.10fu
title: SH0198343.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0198344.10fu
title: SH0198344.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0198345.10fu
title: SH0198345.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0198346.10fu
title: SH0198346.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5281/zenodo.18203225
title: Replication Package for "An Investigation into Open Source Robustness Tool Sustainability"

description: This replication package contains the datasets and scripts used to analyze the sustainability of open-source robustness tools hosted on GitHub. The package supports the empirical analyses reported in the accompanying paper.
DOI: 10.15156/bio/sh0198347.10fu
title: SH0198347.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5281/zenodo.18203224
title: Replication Package for "An Investigation into Open Source Robustness Tool Sustainability"

description: This replication package contains the datasets and scripts used to analyze the sustainability of open-source robustness tools hosted on GitHub. The package supports the empirical analyses reported in the accompanying paper.
DOI: 10.15156/bio/sh0198348.10fu
title: SH0198348.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0198349.10fu
title: SH0198349.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0198350.10fu
title: SH0198350.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.