cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26362421
title: The landscape of clinical trials research in inherited ophthalmic disease

description: To describe the current status of clinical trials of genetic eye diseases with identified molecular targets for future areas of research. Data analysis of the clinical trials database on clinicaltrials.gov with keywords for eight common, genetically tractable inherited eye diseases and their common molecular targets was performed during the period from 20 March 2021 to 31 December 2023. Two hundred and eighty-eight trials involving our keywords have been identified, excluding 25 (8.7%) trials which were unknown (verification expired with no update), 14 (4.9%) trials which were terminated early and 6(2.1%) trials which were withdrawn. In total there were 243 (84.4%) trials included. Out of the 243 trials, 120 trials were completed, 76 trials were active and still open to recruitment and 44 trials were active without any more recruitment on the way. There were only 32 (13.2%) trials with posted results. A low percentage of results were posted for completed trials. However, current and future clinical trials in the genetic eye diseases with molecular targets identified, have a promising future. The results of these trials will enhance and allow a better understanding of the potential to develop treatments for these conditions.
DOI: 10.6084/m9.figshare.26362421.v1
title: The landscape of clinical trials research in inherited ophthalmic disease

description: To describe the current status of clinical trials of genetic eye diseases with identified molecular targets for future areas of research. Data analysis of the clinical trials database on clinicaltrials.gov with keywords for eight common, genetically tractable inherited eye diseases and their common molecular targets was performed during the period from 20 March 2021 to 31 December 2023. Two hundred and eighty-eight trials involving our keywords have been identified, excluding 25 (8.7%) trials which were unknown (verification expired with no update), 14 (4.9%) trials which were terminated early and 6(2.1%) trials which were withdrawn. In total there were 243 (84.4%) trials included. Out of the 243 trials, 120 trials were completed, 76 trials were active and still open to recruitment and 44 trials were active without any more recruitment on the way. There were only 32 (13.2%) trials with posted results. A low percentage of results were posted for completed trials. However, current and future clinical trials in the genetic eye diseases with molecular targets identified, have a promising future. The results of these trials will enhance and allow a better understanding of the potential to develop treatments for these conditions.
DOI: 10.6084/m9.figshare.26364678.v1
title: Comparative analysis of eleven SARS-CoV-2 immunoassays and neutralisation data: time to enhance standardisation and correlation of protection

description: To infer a reliable SARS-CoV-2 antibody protection level from a serological test, an appropriate quantitative threshold and solid equivalence across serological tests are needed. Additionally, tests should show a solid correlation with neutralising assays and with the protection observed in large population cohorts even against emerging variants. We studied convalescent and vaccinated populations using 11 commercial antibody assays. Results were compared to evaluate discrepancies across tests. Neutralisation capacity was measured in a subset of the samples with a lentiviral-based assay. Serum from convalescent (<i>n</i> = 121) and vaccinated individuals (<i>n</i> = 471, 260 with Comirnaty, 110 with Spikevax, and 96 with Vaxzevria) was assessed using 11 different assays, including two from Abbott, Euroimmun, Liaison, Roche, and Vircell, and one from Siemens. A spike protein-lentiviral vector with a fluorescent reporter was used for neutralisation assay of serum from convalescent (<i>n</i> = 26) and vaccinated (<i>n</i> = 39) individuals. Positivity ranged between 81.3 and 94.3% after infection and 99.4 and 99.7% after vaccination, depending on the assay. Both cohorts showed a high level of qualitative agreement across tests (Fleiss’ kappa = 0.598 and 0.719 for convalescent and vaccinated respectively). Spikevax vaccine recipients showed the highest level of antibodies in all tests. Effectiveness of each test predicting SARS-CoV-2 neutralising capacity depended on assay type and target, with CLIA and anti-S being more effective than ELISA and anti-N assays, respectively. High-throughput immunoassays are good predictors of neutralising capacity. Updated targets and better standardisation would be required to find an effective correlate of protection, especially to account for antibodies against new variants.
DOI: 10.6084/m9.figshare.26364678
title: Comparative analysis of eleven SARS-CoV-2 immunoassays and neutralisation data: time to enhance standardisation and correlation of protection

description: To infer a reliable SARS-CoV-2 antibody protection level from a serological test, an appropriate quantitative threshold and solid equivalence across serological tests are needed. Additionally, tests should show a solid correlation with neutralising assays and with the protection observed in large population cohorts even against emerging variants. We studied convalescent and vaccinated populations using 11 commercial antibody assays. Results were compared to evaluate discrepancies across tests. Neutralisation capacity was measured in a subset of the samples with a lentiviral-based assay. Serum from convalescent (<i>n</i> = 121) and vaccinated individuals (<i>n</i> = 471, 260 with Comirnaty, 110 with Spikevax, and 96 with Vaxzevria) was assessed using 11 different assays, including two from Abbott, Euroimmun, Liaison, Roche, and Vircell, and one from Siemens. A spike protein-lentiviral vector with a fluorescent reporter was used for neutralisation assay of serum from convalescent (<i>n</i> = 26) and vaccinated (<i>n</i> = 39) individuals. Positivity ranged between 81.3 and 94.3% after infection and 99.4 and 99.7% after vaccination, depending on the assay. Both cohorts showed a high level of qualitative agreement across tests (Fleiss’ kappa = 0.598 and 0.719 for convalescent and vaccinated respectively). Spikevax vaccine recipients showed the highest level of antibodies in all tests. Effectiveness of each test predicting SARS-CoV-2 neutralising capacity depended on assay type and target, with CLIA and anti-S being more effective than ELISA and anti-N assays, respectively. High-throughput immunoassays are good predictors of neutralising capacity. Updated targets and better standardisation would be required to find an effective correlate of protection, especially to account for antibodies against new variants.
DOI: 10.6084/m9.figshare.26764031.v1
title: Operational feasibility and multi-centric evaluation of ‘TB<i>Detect</i> sputum microscopy kit’ for the direct detection of <i>Mycobacterium tuberculosis</i> in field settings

description: India relies primarily on direct smear microscopy for tuberculosis (TB) diagnosis. However, the low sensitivity of smear microscopy emphasizes the need to improve its performance. We recently described the development of ‘TB<i>Detect</i>’ kit which showed improved performance over direct smear microscopy at National Reference Laboratories (NRLs) in India. The present study was aimed to assess the operational feasibility of ‘TB<i>Detect</i>’ microscopy in field settings. This was evaluated by (i) assessing the performance of ‘TB<i>Detect</i>’ microscopy <i>vs.</i> LED-fluorescence microscopy (LED-FM) on consecutive presumptive pulmonary TB patients (<i>n</i> = 5300) who attended Designated Microscopy Centres (DMCs, <i>n</i> = 13) under 4 NRLs at Bhubaneswar, Bhopal, Chennai, and New Delhi, and (ii) obtaining feedback from Scientists (<i>n</i> = 10) and laboratory technicians (<i>n</i> = 42) using semi-structured questionnaires under the following parameters: feasibility of initiation of ‘TB<i>Detect’</i> microscopy in DMCs, sample preparation and testing, training, time-to-result, logistics, and troubleshooting. A scoring questionnaire was also used to assess ‘TB<i>Detect</i>’ microscopy <i>vs</i>. LED-FM and statistical significance of the scores was calculated using paired <i>t</i>-test. The overall positivity of ‘TB<i>Detect</i>’ microscopy was 10.32% (547/5300) <i>vs.</i> 8.96% (475/5300) of LED-FM at all sites and the increment in positivity was significant (<i>p</i> = 0.019). In addition, ‘TB<i>Detect</i>’ microscopy yielded an increment in smear grade status over LED-FM (<i>p</i> = 0.043). The feedback from the study-in-charge and kit users indicated that ‘TB<i>Detect</i>’ microscopy was easily adapted in point-of-care settings. An analysis of scoring feedback suggested that it was easy to perform and observe in comparison to LED-FM (<i>p</i> &lt; 0.005). This study established the feasibility of ‘TB<i>Detect</i>’ microscopy in field settings.
DOI: 10.6084/m9.figshare.26764031
title: Operational feasibility and multi-centric evaluation of ‘TB<i>Detect</i> sputum microscopy kit’ for the direct detection of <i>Mycobacterium tuberculosis</i> in field settings

description: India relies primarily on direct smear microscopy for tuberculosis (TB) diagnosis. However, the low sensitivity of smear microscopy emphasizes the need to improve its performance. We recently described the development of ‘TB<i>Detect</i>’ kit which showed improved performance over direct smear microscopy at National Reference Laboratories (NRLs) in India. The present study was aimed to assess the operational feasibility of ‘TB<i>Detect</i>’ microscopy in field settings. This was evaluated by (i) assessing the performance of ‘TB<i>Detect</i>’ microscopy <i>vs.</i> LED-fluorescence microscopy (LED-FM) on consecutive presumptive pulmonary TB patients (<i>n</i> = 5300) who attended Designated Microscopy Centres (DMCs, <i>n</i> = 13) under 4 NRLs at Bhubaneswar, Bhopal, Chennai, and New Delhi, and (ii) obtaining feedback from Scientists (<i>n</i> = 10) and laboratory technicians (<i>n</i> = 42) using semi-structured questionnaires under the following parameters: feasibility of initiation of ‘TB<i>Detect’</i> microscopy in DMCs, sample preparation and testing, training, time-to-result, logistics, and troubleshooting. A scoring questionnaire was also used to assess ‘TB<i>Detect</i>’ microscopy <i>vs</i>. LED-FM and statistical significance of the scores was calculated using paired <i>t</i>-test. The overall positivity of ‘TB<i>Detect</i>’ microscopy was 10.32% (547/5300) <i>vs.</i> 8.96% (475/5300) of LED-FM at all sites and the increment in positivity was significant (<i>p</i> = 0.019). In addition, ‘TB<i>Detect</i>’ microscopy yielded an increment in smear grade status over LED-FM (<i>p</i> = 0.043). The feedback from the study-in-charge and kit users indicated that ‘TB<i>Detect</i>’ microscopy was easily adapted in point-of-care settings. An analysis of scoring feedback suggested that it was easy to perform and observe in comparison to LED-FM (<i>p</i> &lt; 0.005). This study established the feasibility of ‘TB<i>Detect</i>’ microscopy in field settings.
DOI: 10.6084/m9.figshare.26763062
title: Clinical usefulness of urine Gram stain for diagnosing urinary tract infections at the emergency department

description: Diagnosis of urinary tract infections (UTIs) is a frequent challenge at the emergency department (ED). The clinical usefulness of the urine Gram stain (GS) is uncertain. We studied the GS performance to clarify its clinical utility at the ED. Urine dipstick (UD), automated urinalysis (UF-1000<i>i</i>), GS and urine culture (UC) were performed in a cohort of consecutive adults presenting at the ED suspected of a UTI. GS performance was assessed and compared to UD and UF-1000<i>i.</i> A UTI diagnosis was established in 487/1358 (35.9%) episodes. Sensitivity and specificity for ‘many’ GS leucocytes was 33.7% and 95.4%; for ‘many’ GS bacteria 51.3% and 91.0%. GS diagnostic performance by ROC analysis was 0.796 for leucocytes and 0.823 for bacteria. GS bacteria performed better than UD nitrite comparable to UF-1000<i>i</i> bacteria. GS leucocytes underperformed compared to UD leucocyte esterase and UF-1000<i>i</i> leucocytes. UC was positive in 455 episodes. GS correctly predicted urine culture of gram-negative rods (PPV 84.6%). Prediction was poor for gram-positive bacteria (PPV 38.4% (cocci), 1.0% (rods)). With the exception of a moderate prediction of gram-negative bacteria in the UC, urine GS does not improve UTI diagnosis at the ED compared to other urine parameters.
DOI: 10.6084/m9.figshare.26763062.v2
title: Clinical usefulness of urine Gram stain for diagnosing urinary tract infections at the emergency department

description: Diagnosis of urinary tract infections (UTIs) is a frequent challenge at the emergency department (ED). The clinical usefulness of the urine Gram stain (GS) is uncertain. We studied the GS performance to clarify its clinical utility at the ED. Urine dipstick (UD), automated urinalysis (UF-1000<i>i</i>), GS and urine culture (UC) were performed in a cohort of consecutive adults presenting at the ED suspected of a UTI. GS performance was assessed and compared to UD and UF-1000<i>i.</i> A UTI diagnosis was established in 487/1358 (35.9%) episodes. Sensitivity and specificity for ‘many’ GS leucocytes was 33.7% and 95.4%; for ‘many’ GS bacteria 51.3% and 91.0%. GS diagnostic performance by ROC analysis was 0.796 for leucocytes and 0.823 for bacteria. GS bacteria performed better than UD nitrite comparable to UF-1000<i>i</i> bacteria. GS leucocytes underperformed compared to UD leucocyte esterase and UF-1000<i>i</i> leucocytes. UC was positive in 455 episodes. GS correctly predicted urine culture of gram-negative rods (PPV 84.6%). Prediction was poor for gram-positive bacteria (PPV 38.4% (cocci), 1.0% (rods)). With the exception of a moderate prediction of gram-negative bacteria in the UC, urine GS does not improve UTI diagnosis at the ED compared to other urine parameters.
DOI: 10.6084/m9.figshare.27907065.v1
title: Evaluation of the specificity of the 2023 European Society of Cardiology classification for infective endocarditis

description: The 2023 Duke-ISCVID and 2023 ESC classifications have recently issued independent diagnostic criteria for infective endocarditis (IE), updating the 2015 ESC criteria. The specificity of the 2023 ESC criteria should be evaluated and compared to the two other classifications in IE suspected patients. We retrospectively collected the characteristics of patients hospitalised in Bichat University Hospital, in 2021, who had been evaluated for suspicion of IE, and in whom IE diagnosis was finally rejected. All were classified by 2015 ESC, 2023 Duke-ISCVID, and 2023 ESC. In total 130 patients were analysed. Mean age was 62 years, 64.6% were male, 30.0% had prosthetic cardiac valve or valve repair, 16.2% had cardiac implanted electronic device, and 23.1% other cardiac conditions. Overall, 2, 5 and 5 patients were falsely classified as definite IE with the 2015 ESC, 2023 Duke-ISCVID and 2023 ESC criteria, respectively. The corresponding specificities were 99% (95% CI [94%; 100%], 96% (95% CI [91%; 99%]), and 96% (95% CI [91%; 99%]). The 2023 ESC and the 2023 Duke-ISCVID criteria are highly specific, although slightly less than the 2015 ESC criteria, for ruling out the diagnosis of definite IE.HIGHLIGHTS2023 Duke-ISCVID and 2023 ESC criteria are recently issued diagnostic classifications2023 ESC criteria have an excellent specificity, equivalent to the 2023 Duke-ISCVID one2023 ESC criteria and the 2023 Duke-ISCVID are less specific than the 2015 ESC criteriaSpecificities were quite similar according to the nature of the cardiac valve (native or prosthetic valve) or the duration of antibiotic therapy 2023 Duke-ISCVID and 2023 ESC criteria are recently issued diagnostic classifications 2023 ESC criteria have an excellent specificity, equivalent to the 2023 Duke-ISCVID one 2023 ESC criteria and the 2023 Duke-ISCVID are less specific than the 2015 ESC criteria Specificities were quite similar according to the nature of the cardiac valve (native or prosthetic valve) or the duration of antibiotic therapy
DOI: 10.6084/m9.figshare.27907065
title: Evaluation of the specificity of the 2023 European Society of Cardiology classification for infective endocarditis

description: The 2023 Duke-ISCVID and 2023 ESC classifications have recently issued independent diagnostic criteria for infective endocarditis (IE), updating the 2015 ESC criteria. The specificity of the 2023 ESC criteria should be evaluated and compared to the two other classifications in IE suspected patients. We retrospectively collected the characteristics of patients hospitalised in Bichat University Hospital, in 2021, who had been evaluated for suspicion of IE, and in whom IE diagnosis was finally rejected. All were classified by 2015 ESC, 2023 Duke-ISCVID, and 2023 ESC. In total 130 patients were analysed. Mean age was 62 years, 64.6% were male, 30.0% had prosthetic cardiac valve or valve repair, 16.2% had cardiac implanted electronic device, and 23.1% other cardiac conditions. Overall, 2, 5 and 5 patients were falsely classified as definite IE with the 2015 ESC, 2023 Duke-ISCVID and 2023 ESC criteria, respectively. The corresponding specificities were 99% (95% CI [94%; 100%], 96% (95% CI [91%; 99%]), and 96% (95% CI [91%; 99%]). The 2023 ESC and the 2023 Duke-ISCVID criteria are highly specific, although slightly less than the 2015 ESC criteria, for ruling out the diagnosis of definite IE.HIGHLIGHTS2023 Duke-ISCVID and 2023 ESC criteria are recently issued diagnostic classifications2023 ESC criteria have an excellent specificity, equivalent to the 2023 Duke-ISCVID one2023 ESC criteria and the 2023 Duke-ISCVID are less specific than the 2015 ESC criteriaSpecificities were quite similar according to the nature of the cardiac valve (native or prosthetic valve) or the duration of antibiotic therapy 2023 Duke-ISCVID and 2023 ESC criteria are recently issued diagnostic classifications 2023 ESC criteria have an excellent specificity, equivalent to the 2023 Duke-ISCVID one 2023 ESC criteria and the 2023 Duke-ISCVID are less specific than the 2015 ESC criteria Specificities were quite similar according to the nature of the cardiac valve (native or prosthetic valve) or the duration of antibiotic therapy
DOI: 10.15468/dl.tg7tgr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Petrocodon longgangensis W.H.Wu & W.B.Xu)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001396-241125135418005/datasets/export for details.
DOI: 10.15468/dl.fjtvqh
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aucuba filicauda Chun & F.C.How)"
 ]
}

 The dataset includes 73 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001397-241125135418005/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.26049079
title: An SST-based velocity diagnostic model for TIW velocities

description: This is a code to calculate sea surface meridional velocities of tropical instability waves (TIWs) in Pacific Ocean from satellite SST for the period between 1981-2023.The input is satellite SST from NOAA OISSTv2 (3-day and 0.5deg latitude x 1deg longitude resolution), and two space-varying paramters: best-fit mean zonal flows and damping rates for SST variability.The output is the surface meridional velcoties of TIWs.The dataset 'u_v_ssh_recon' is reconstrcuted from the SST-derived meridional velocities, including zonal and meridional components of velocities, and SSH associated with TIWs.
DOI: 10.6084/m9.figshare.26049079.v1
title: An SST-based velocity diagnostic model for TIW velocities

description: This is a code to calculate sea surface meridional velocities of tropical instability waves (TIWs) in Pacific Ocean from satellite SST for the period between 1981-2024. The input is satellite SST from NOAA OISSTv2 (3-day and 0.5deg latitude x 1deg longitude resolution), and two space-varying paramters: best-fit mean zonal flows and damping rates for SST variability.The output is the surface meridional velcoties of TIWs.
DOI: 10.15468/dl.8qw9xa
title: Occurrence Download

description: A dataset containing 634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aucuba himalaica Hook.f. & Thomson)"
 ]
}

 The dataset includes 634 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001399-241125135418005/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ndy4ja
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Petrocodon longgangensis W.H.Wu & W.B.Xu)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001400-241125135418005/datasets/export for details.
DOI: 10.15468/dl.cpmxb2
title: Occurrence Download

description: A dataset containing 12328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aucuba japonica Thunb.)"
 ]
}

 The dataset includes 12328 records from 229 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001401-241125135418005/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y6wuwg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Petrocodon longitubus Cong R.Li & Yang Luo)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001402-241125135418005/datasets/export for details.
DOI: 10.15468/dl.cnp58v
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aucuba obcordata (Rehder) K.T.Fu)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001403-241125135418005/datasets/export for details.