cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1955250.08fu
title: SH1955250.08FU

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/sh1955251.08fu
title: SH1955251.08FU

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/sh1491786.08fu
title: SH1491786.08FU

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/sh1491787.08fu
title: SH1491787.08FU

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/sh1955252.08fu
title: SH1955252.08FU

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/sh1955253.08fu
title: SH1955253.08FU

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: 10.6084/m9.figshare.21030341
title: Rates and types of urine drug screen false negative results compared with confirmatory toxicology testing in major trauma patients

description: Trauma centers are required to screen patients for alcohol use, and if necessary, intervene and refer to treatment (SBIRT). Similar screening for illicit drug use is recommended but not required. Urine drug screening (UDS) underestimates problematic substance use. This study aimed to estimate the types and rates of UDS false negatives (FN) compared to comprehensive testing by liquid chromatography-mass spectrometry (LC-MS) in trauma patients. We performed a prospective cohort study of deidentified urine samples from adult trauma and burn activation patients. Both UDS and LC-MS comprehensive testing of &gt;200 analytes were performed by a reference laboratory on all samples. Iatrogenic medications were excluded from the FN count. Crosstab analyses were conducted for UDS versus LC-MS outcomes to establish FN types and rates. We dichotomized the results by creating an “intentionality” variable (intentional injuries by self/others versus accidental injuries). A series of crosstabs with odds ratios considered intentionality by substance class and demographics. Statistically significant variables by Chi-Square were assessed by logistic regression. Psychoactive FN were detected in 56/100 urine samples analyzed; the most frequent included anticonvulsants (primarily gabapentin, <i>N</i> = 13), opioid agonists (<i>N</i> = 12), antihistamines (primarily diphenhydramine, <i>N</i> = 10), and phenethylamines (primarily bupropion, <i>N</i> = 5). Nonpsychoactive FN were detected in 70/100 samples; the most common were nicotine (<i>N</i> = 33), caffeine (<i>N</i> = 23), acetaminophen (<i>N</i> = 22), and antidepressants (<i>N</i> = 12). Of substance classes included in the UDS and also tested by LC-MS, FN occurred for opiates (3%), amphetamines (5%) and opioids (25%). Polypharmacy was associated with fall injuries in elderly patients. Cocaine (<i>p</i> = 0.015) and cannabinoids (<i>p</i> = 0.002) were significantly associated with intentionality. Our results indicate that FN for potentially important psychoactive and nonpsychoactive substances are common when toxicologic testing is limited to routine UDS in trauma patients. We recommend expanding SBIRT in this patient population to include misuse of tobacco products, prescription analgesics, and over-the-counter antihistamines.
DOI: 10.6084/m9.figshare.21030341.v1
title: Rates and types of urine drug screen false negative results compared with confirmatory toxicology testing in major trauma patients

description: Trauma centers are required to screen patients for alcohol use, and if necessary, intervene and refer to treatment (SBIRT). Similar screening for illicit drug use is recommended but not required. Urine drug screening (UDS) underestimates problematic substance use. This study aimed to estimate the types and rates of UDS false negatives (FN) compared to comprehensive testing by liquid chromatography-mass spectrometry (LC-MS) in trauma patients. We performed a prospective cohort study of deidentified urine samples from adult trauma and burn activation patients. Both UDS and LC-MS comprehensive testing of &gt;200 analytes were performed by a reference laboratory on all samples. Iatrogenic medications were excluded from the FN count. Crosstab analyses were conducted for UDS versus LC-MS outcomes to establish FN types and rates. We dichotomized the results by creating an “intentionality” variable (intentional injuries by self/others versus accidental injuries). A series of crosstabs with odds ratios considered intentionality by substance class and demographics. Statistically significant variables by Chi-Square were assessed by logistic regression. Psychoactive FN were detected in 56/100 urine samples analyzed; the most frequent included anticonvulsants (primarily gabapentin, <i>N</i> = 13), opioid agonists (<i>N</i> = 12), antihistamines (primarily diphenhydramine, <i>N</i> = 10), and phenethylamines (primarily bupropion, <i>N</i> = 5). Nonpsychoactive FN were detected in 70/100 samples; the most common were nicotine (<i>N</i> = 33), caffeine (<i>N</i> = 23), acetaminophen (<i>N</i> = 22), and antidepressants (<i>N</i> = 12). Of substance classes included in the UDS and also tested by LC-MS, FN occurred for opiates (3%), amphetamines (5%) and opioids (25%). Polypharmacy was associated with fall injuries in elderly patients. Cocaine (<i>p</i> = 0.015) and cannabinoids (<i>p</i> = 0.002) were significantly associated with intentionality. Our results indicate that FN for potentially important psychoactive and nonpsychoactive substances are common when toxicologic testing is limited to routine UDS in trauma patients. We recommend expanding SBIRT in this patient population to include misuse of tobacco products, prescription analgesics, and over-the-counter antihistamines.
DOI: 10.6084/m9.figshare.21120171
title: Population pharmacokinetic analysis of acetaminophen overdose with immediate release, extended release and modified release formulations

description: The introduction of delayed release formulations of acetaminophen (APAP) has created concern about the role of formulation in overdose. We examined the APAP overdose pharmacokinetic (PK) profiles to assess the role of dose, coingestants and formulation: immediate release (IR), extended release (ER), and modified release (MR) on APAP pharmacokinetic measures. We collected by-subject APAP PK data: subject description, timed blood APAP concentrations, dose, and coingestants. We sought both overdose and randomized controlled trials (RCTs) for supratherapeutic doses involving ER or MR formulations. Data analysis and simulation used the non-linear mixed-effects modeling program NONMEM-version 7.4. The final dataset comprised 3,033 [APAP] from 356 subjects and 15 sources including 3 RCTs (179 subjects receiving IR, 122 ER, 65 MR). The final population PK (PopPK) model was a linear 2-compartment model with first-order (oral) absorption. Covariate relationships included: APAP absorption rate and bioavailability decreased with increased oral dose (<i>p</i> &lt; 0.00005) for all 3 formulations (MR &gt; ER &gt; IR). Post hoc analyses showed opioid coingestant increased exposure (area under the curve, AUC) by factor of 1.6. Simulations of 100 g vs 10 g doses for IR, ER and MR showed overdose of the ER formulation exhibits slower absorption and lower <i>C</i><sub>max</sub>, overall exposure (AUC) is less than 80% of an equivalent dose of IR acetaminophen. The overall exposure for the MR formulation is less than 70% of an equivalent dose of IR. Acetaminophen ER and MR formulations have slower absorption and decreased bioavailability leading to a lower <i>C</i><sub>max</sub> and later <i>T</i><sub>max</sub> than the IR formulation. These results have potential clinical implications because delayed absorption could confound use of the Rumack-Matthew nomogram by underestimating the severity of ingestion early in the course of treatment.
DOI: 10.6084/m9.figshare.21120171.v1
title: Population pharmacokinetic analysis of acetaminophen overdose with immediate release, extended release and modified release formulations

description: The introduction of delayed release formulations of acetaminophen (APAP) has created concern about the role of formulation in overdose. We examined the APAP overdose pharmacokinetic (PK) profiles to assess the role of dose, coingestants and formulation: immediate release (IR), extended release (ER), and modified release (MR) on APAP pharmacokinetic measures. We collected by-subject APAP PK data: subject description, timed blood APAP concentrations, dose, and coingestants. We sought both overdose and randomized controlled trials (RCTs) for supratherapeutic doses involving ER or MR formulations. Data analysis and simulation used the non-linear mixed-effects modeling program NONMEM-version 7.4. The final dataset comprised 3,033 [APAP] from 356 subjects and 15 sources including 3 RCTs (179 subjects receiving IR, 122 ER, 65 MR). The final population PK (PopPK) model was a linear 2-compartment model with first-order (oral) absorption. Covariate relationships included: APAP absorption rate and bioavailability decreased with increased oral dose (<i>p</i> &lt; 0.00005) for all 3 formulations (MR &gt; ER &gt; IR). Post hoc analyses showed opioid coingestant increased exposure (area under the curve, AUC) by factor of 1.6. Simulations of 100 g vs 10 g doses for IR, ER and MR showed overdose of the ER formulation exhibits slower absorption and lower <i>C</i><sub>max</sub>, overall exposure (AUC) is less than 80% of an equivalent dose of IR acetaminophen. The overall exposure for the MR formulation is less than 70% of an equivalent dose of IR. Acetaminophen ER and MR formulations have slower absorption and decreased bioavailability leading to a lower <i>C</i><sub>max</sub> and later <i>T</i><sub>max</sub> than the IR formulation. These results have potential clinical implications because delayed absorption could confound use of the Rumack-Matthew nomogram by underestimating the severity of ingestion early in the course of treatment.
DOI: 10.15156/bio/sh1491788.08fu
title: SH1491788.08FU

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/sh1491789.08fu
title: SH1491789.08FU

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/sh1491790.08fu
title: SH1491790.08FU

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/sh1955254.08fu
title: SH1955254.08FU

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: 10.6084/m9.figshare.21287822
title: Haff disease associated with consumption of buffalofish (<i>Ictiobus</i> spp.) in the United States, 2010–2020, with confirmation of the causative species

description: In the United States, buffalofish (<i>Ictiobus</i> spp.) are sporadically associated with sudden onset muscle pain and weakness due to rhabdomyolysis within 24 h of fish consumption (Haff disease). Previous genetic analyses of case-associated samples were unable to distinguish the three species of buffalofish that occur in the US, <i>Ictiobus cyprinellus</i> (bigmouth buffalo), <i>Ictiobus bubalus</i> (smallmouth buffalo), and <i>Ictiobus niger</i> (black buffalo). Ten events were investigated between 2010 and 2020 and demographic and clinical information was collected for 24 individuals. Meal remnants were collected from 5 of 10 events with additional associated samples (<i>n</i> = 24) collected from another five of 10 events. Low-coverage whole-genome sequencing (genome skimming) was used to identify meal remnants. Patients (26–75 years of age) ranged from 1–4 per event, with 90% involving ≥2 individuals. Reported symptoms included muscle tenderness and weakness, nausea/vomiting, and brown/tea-colored urine. Median incubation period was 8 h. Ninety-six percent of cases were hospitalized with a median duration of four days. The most commonly reported laboratory finding was elevated creatine phosphokinase and liver transaminases. Treatment was supportive including intravenous fluids to prevent renal failure. Events occurred in California (1), Illinois (2), Louisiana (1), New York (1), Mississippi (1), Missouri (2), New Jersey (1), and Texas (1) with location of harvest, when known, being Illinois, Louisiana, Mississippi, Missouri, Texas, and Wisconsin. Meal remnants were identified as <i>I. bubalus</i> (<i>n</i> = 4) and <i>I. niger</i> (<i>n</i> = 1). Associated samples were identified as <i>I. bubalus</i> (<i>n</i> = 16), <i>I. cyprinellus</i> (<i>n</i> = 5), and <i>I. niger</i> (<i>n</i> = 3). Time course, presentation of illness, and clinical findings were all consistent with previous domestic cases of buffalofish-associated Haff disease. In contrast to previous reports that <i>I. cyprinellus</i> is the causative species in US cases, data indicate that all three buffalofish species are harvested but <i>I. bubalus</i> is most often associated with illness.