cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7718246
title: MC Simulations (AD and HG) for 'Homegardens and the future of food and nutrition security in southwest Uganda'

description: Data for: Whitney, Cory W., John R. S. Tabuti, Oliver Hensel, Ching-Hua Yeh, Jens Gebauer, and Eike Luedeling. “Homegardens and the Future of Food and Nutrition Security in Southwest Uganda.” <i>Agricultural Systems</i> 154 (2017): 133–44. https://doi.org/10.1016/j.agsy.2017.03.009.
DOI: 10.6084/m9.figshare.7718246.v1
title: MC Simulations (AD and HG) for 'Homegardens and the future of food and nutrition security in southwest Uganda'

description: Data for: Whitney, Cory W., John R. S. Tabuti, Oliver Hensel, Ching-Hua Yeh, Jens Gebauer, and Eike Luedeling. “Homegardens and the Future of Food and Nutrition Security in Southwest Uganda.” <i>Agricultural Systems</i> 154 (2017): 133–44. https://doi.org/10.1016/j.agsy.2017.03.009.
DOI: 10.6084/m9.figshare.7718192
title: Permutation Test R Code from Common noctules exploit low levels of the aerosphere

description: Permutation Test R Code
DOI: 10.6084/m9.figshare.7718207
title: Inferring global species richness from megatransect data and undetected species estimates: supplementary material

description: Ratio-like approaches for estimating global species richness have been criticised for their unjustified extrapolation from regional to global patterns. Here we explore the use of cumulative percentages of ‘new’ (i.e., not formally described) species over large geographic areas (‘megatransects’) as a means to overcome this problem. In addition, we take into account undetected species and illustrate these combined methods by applying them to a family of spiders (Pholcidae) that currently contains some 1,700 described species. The raw global cumulative percentage of new species (‘new’ as of the end of 2008, when 1,001 species were formally described) is 75.1%, and is relatively constant across large biogeographic regions. Undetected species are estimated using the <i>Chao2</i> <i>estimator</i> based on species incidence data (date by species and locality by species matrices). The estimated percentage of new species based on the date by species matrices is 76.0% with an estimated standard error (s.e.) of 2.6%. This leads to an estimated global species richness of about 4,200 with a 95% confidence interval of (3,300, 5,000). The corresponding values based on locality by species matrices are 84.2% (s.e. 3.0%) and 6,300 with a 95% confidence interval of (4,000, 8,600). Our results suggest that the currently known 1,700 species of Pholcidae may represent no more than about 25–40% of the total species richness. The impact of further biasing factors like geography, species size and distribution, cryptic species, and model assumptions needs to be explored.
DOI: 10.7284/101518
title: Gravimeter data collected during research cruise AT15-56 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718192.v1
title: Permutation Test R Code from Common noctules exploit low levels of the aerosphere

description: Permutation Test R Code
DOI: 10.6084/m9.figshare.7718207.v1
title: Inferring global species richness from megatransect data and undetected species estimates: supplementary material

description: Ratio-like approaches for estimating global species richness have been criticised for their unjustified extrapolation from regional to global patterns. Here we explore the use of cumulative percentages of ‘new’ (i.e., not formally described) species over large geographic areas (‘megatransects’) as a means to overcome this problem. In addition, we take into account undetected species and illustrate these combined methods by applying them to a family of spiders (Pholcidae) that currently contains some 1,700 described species. The raw global cumulative percentage of new species (‘new’ as of the end of 2008, when 1,001 species were formally described) is 75.1%, and is relatively constant across large biogeographic regions. Undetected species are estimated using the <i>Chao2</i> <i>estimator</i> based on species incidence data (date by species and locality by species matrices). The estimated percentage of new species based on the date by species matrices is 76.0% with an estimated standard error (s.e.) of 2.6%. This leads to an estimated global species richness of about 4,200 with a 95% confidence interval of (3,300, 5,000). The corresponding values based on locality by species matrices are 84.2% (s.e. 3.0%) and 6,300 with a 95% confidence interval of (4,000, 8,600). Our results suggest that the currently known 1,700 species of Pholcidae may represent no more than about 25–40% of the total species richness. The impact of further biasing factors like geography, species size and distribution, cryptic species, and model assumptions needs to be explored.
DOI: 10.7284/101513
title: Multiplexed data collected during research cruise AT15-57 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101512
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-57 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718147
title: Supplementary Material for: Liver Fibrosis, Not Steatosis, Associates with Long-Term Outcomes in Ischaemic Stroke Patients

description: <b><i>Background:</i></b> To investigate whether there are differences in long-term all-cause and cardiovascular mortality according to the burden of liver fibrosis or steatosis in patients with ischaemic stroke or transient ischaemic attack (TIA). ­<b><i>Methods:</i></b> Consecutive patients with acute ischaemic stroke or TIA who underwent transient elastography (TE) from January 2014 to December 2014 were considered eligible. The influence of liver fibrosis or steatosis, assessed via TE, on long-term outcomes was investigated using Cox proportional hazard models. <b><i>Results:</i></b> Among 395 patients included in this study, there were 37 (9%) patients with significant fibrosis (&gt; 8.0 kPa) and 164 (41.5%) patients with fatty liver (&gt; 250 dB/m). During the follow-up period (median 2.7 years), all-cause and cardiovascular mortality occurred in 28 (7.1%) and 20 (5.1%) patients. On multivariate analyses, significant liver fibrosis was independently associated with increased risk of all-cause (hazard ratio [HR] 8.14, 95% CI 3.03–21.90, <i>p</i> p = 0.036) mortality, whereas fatty liver was not (all <i>p</i> &gt; 0.05). <b><i>Conclusions:</i></b> This study found that the burden of liver fibrosis but not that of steatosis, assessed via TE, was an independent predictor of all-cause and cardiovascular mortality during long-term follow-up in patients with ischaemic stroke.
DOI: 10.7284/101511
title: Gravimeter data collected during research cruise AT15-57 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101523
title: Multiplexed data collected during research cruise AT15-58 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718072
title: Supplementary Material for: Associations of High Intensities on Magnetization-Prepared Rapid Acquisition with Gradient Echo with Aortic Complicated Lesions in Ischemic Stroke Patients

description: <b><i>Background:</i></b> Aortic complicated lesions (ACLs) are key parameters for evaluating aortic embolic sources in embolic stroke, and are usually diagnosed using transesophageal echocardiography (TEE). However, alternative methods for diagnosing ACLs have not been well established. We investigated associations between high-intensity areas on T1-weighted imaging (T1WI) with magnetization-prepared rapid acquisition with gradient echo (MPRAGE) and ACLs on TEE among ischemic stroke patients. <b><i>Methods:</i></b> Participants comprised 135 patients (mean age, 71 years; 35 women) with ischemic stroke or transient ischemic attack who underwent TEE for evaluation of embolic sources and plaque imaging using MPRAGE for evaluation of aortic or carotid plaques. Aortic plaque with signal intensity ≥200% of sternocleidomastoid intensity on MPRAGE was categorized as “high intensity”. ACLs on TEE were defined by focal increases in intima-media thickness (IMT) ≥4.0 mm or the presence of ulcerated or mobile plaques. <b><i>Results:</i></b> Fifty-six patients (42%) showed high-intensity areas on MPRAGE at the aortic arch. Aortic maximum IMT was significantly higher in patients with high intensities than in those without (<i>p</i> &lt; 0.001). Incidences of ACLs (66 vs. 20%, <i>p</i> &lt; 0.001) or ulcerated or mobile plaques (30 vs. 6%, <i>p</i> &lt; 0.001) were significantly higher in patients with high intensities than in patients without. Multivariable logistic regression analysis showed that high intensities on MPRAGE were independently associated with the presence of ACLs (OR 5.72; 95% CI 2.38–13.70) and ulcerated or mobile plaques (OR 4.18; 95% CI 1.29–13.50). <b><i>Conclusions:</i></b> High intensities on T1WI with MPRAGE in the aortic arch were significantly associated with the presence of ACLs. An evaluation of the aortic arch using MPRAGE may be useful for predicting ACLs.
DOI: 10.7284/101522
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-58 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7717889
title: Supplementary Material for: Prevalence and Characteristics of Restless Legs Syndrome in Korean Adults: A Study in Two Independent Samples of the General Population

description: <b><i>Background:</i></b> Restless legs syndrome (RLS) is a common sleep disorder, although it has a low prevalence in Asian populations. However, the reported RLS prevalence in ­Korean adults is mostly 4.5–12.1%, which is higher than that reported in other Asian populations. This study aimed to diagnose RLS and exclude mimicking conditions in 2 independent samples of Korean adults, and to compare its prevalence to that from previous studies performed in Asian countries. <b><i>Methods:</i></b> Study populations included a (1) nationwide stratified random sample (<i>n</i> = 2,824; age 19–79 years) and (2) community-based cohort (<i>n</i> = 2,685; age 47–79 years). We applied the Cambridge-Hopkins diagnostic questionnaire to diagnose RLS and differentiate it from RLS mimics. Sleep-related symptoms, mood, and medical conditions were compared between the RLS and non-RLS groups. Prior studies of the RLS prevalence in Asia were systematically reviewed and compared to our findings. <b><i>Results:</i></b> The adjusted RLS prevalence was 0.4 and 1.3% in populations 1 and 2, respectively. In both populations, subjects with RLS had more depression. The prevalence of RLS mimics was 5.1 and 2.6%, in populations 1 and 2, respectively. The RLS prevalence in Asia was higher when RLS was defined by the presence of essential clinical features and lower when a differential diagnosis was additionally implemented. <b><i>Conclusions:</i></b> The RLS prevalence in Korean adults considering RLS mimics is comparable to that in adults from other Asian countries (&lt; 2%). The reported RLS prevalence varies depending on the diagnostic method employed.
DOI: 10.6084/m9.figshare.7717910
title: Supplementary Material for: Comparison of All-Cause and Cause-Specific Mortality of Persons with Traumatic Spinal Cord Injuries to the General Swiss Population: Results from a National Cohort Study

description: <b><i>Background:</i></b> Traumatic spinal cord injuries (TSCI) are a neurological condition associated with reduced well-being, increased morbidity and reductions in life expectancy. Estimates of all-cause and cause-specific mortality can aid in identifying targets for prevention and management of contributors for premature mortality. <b><i>Objectives:</i></b> To compare all-cause and cause-specific rates of mortality to that of the Swiss general population; to identify differentials in risk of cause-specific mortality according to lesion characteristics. <b><i>Methods:</i></b> All-cause and cause-specific standardized mortality ratios (SMRs) were calculated using data from the Swiss Spinal Cord Injury cohort study. Cause-specific subhazard ratios were estimated within a competing risk framework using flexible parametric survival models. <b><i>Results:</i></b> Between 1990 and 2011, 2,492 persons sustained a TSCI, of which 379 died. Persons with TSCI had a mortality rate more than 2 times higher than that of the Swiss general population (SMR 2.32; 95% CI 2.10–2.56). Tetraplegic lesions were associated with an increased risk of mortality due to respiratory and cardiovascular diseases, infections, and accidents. Cause-specific SMRs were notably elevated for SCI-related conditions such as urinary tract infections (UTIs) and septicemia. <b><i>Conclusions:</i></b> Elevated SMRs due to cardiovascular disease, UTIs and septicemia-related mortality suggest the need for innovation when managing associated secondary health conditions.
DOI: 10.7284/101521
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT15-58 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7717889.v1
title: Supplementary Material for: Prevalence and Characteristics of Restless Legs Syndrome in Korean Adults: A Study in Two Independent Samples of the General Population

description: <b><i>Background:</i></b> Restless legs syndrome (RLS) is a common sleep disorder, although it has a low prevalence in Asian populations. However, the reported RLS prevalence in ­Korean adults is mostly 4.5–12.1%, which is higher than that reported in other Asian populations. This study aimed to diagnose RLS and exclude mimicking conditions in 2 independent samples of Korean adults, and to compare its prevalence to that from previous studies performed in Asian countries. <b><i>Methods:</i></b> Study populations included a (1) nationwide stratified random sample (<i>n</i> = 2,824; age 19–79 years) and (2) community-based cohort (<i>n</i> = 2,685; age 47–79 years). We applied the Cambridge-Hopkins diagnostic questionnaire to diagnose RLS and differentiate it from RLS mimics. Sleep-related symptoms, mood, and medical conditions were compared between the RLS and non-RLS groups. Prior studies of the RLS prevalence in Asia were systematically reviewed and compared to our findings. <b><i>Results:</i></b> The adjusted RLS prevalence was 0.4 and 1.3% in populations 1 and 2, respectively. In both populations, subjects with RLS had more depression. The prevalence of RLS mimics was 5.1 and 2.6%, in populations 1 and 2, respectively. The RLS prevalence in Asia was higher when RLS was defined by the presence of essential clinical features and lower when a differential diagnosis was additionally implemented. <b><i>Conclusions:</i></b> The RLS prevalence in Korean adults considering RLS mimics is comparable to that in adults from other Asian countries (&lt; 2%). The reported RLS prevalence varies depending on the diagnostic method employed.
DOI: 10.6084/m9.figshare.7717910.v1
title: Supplementary Material for: Comparison of All-Cause and Cause-Specific Mortality of Persons with Traumatic Spinal Cord Injuries to the General Swiss Population: Results from a National Cohort Study

description: <b><i>Background:</i></b> Traumatic spinal cord injuries (TSCI) are a neurological condition associated with reduced well-being, increased morbidity and reductions in life expectancy. Estimates of all-cause and cause-specific mortality can aid in identifying targets for prevention and management of contributors for premature mortality. <b><i>Objectives:</i></b> To compare all-cause and cause-specific rates of mortality to that of the Swiss general population; to identify differentials in risk of cause-specific mortality according to lesion characteristics. <b><i>Methods:</i></b> All-cause and cause-specific standardized mortality ratios (SMRs) were calculated using data from the Swiss Spinal Cord Injury cohort study. Cause-specific subhazard ratios were estimated within a competing risk framework using flexible parametric survival models. <b><i>Results:</i></b> Between 1990 and 2011, 2,492 persons sustained a TSCI, of which 379 died. Persons with TSCI had a mortality rate more than 2 times higher than that of the Swiss general population (SMR 2.32; 95% CI 2.10–2.56). Tetraplegic lesions were associated with an increased risk of mortality due to respiratory and cardiovascular diseases, infections, and accidents. Cause-specific SMRs were notably elevated for SCI-related conditions such as urinary tract infections (UTIs) and septicemia. <b><i>Conclusions:</i></b> Elevated SMRs due to cardiovascular disease, UTIs and septicemia-related mortality suggest the need for innovation when managing associated secondary health conditions.
DOI: 10.7284/102185
title: Multiplexed data collected during research cruise AT15-59 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7717880
title: Supplementary Material for: Loss of RUNX3 Immunoreactivity in Non-Neoplastic Rectal Mucosa May Predict the Occurrence of Ulcerative Colitis-Associated Colorectal Cancer

description: <b><i>Background/Aims:</i></b> Runt-related transcription factor (RUNX) 3 is a tumor suppressor whose expression is reduced in non-neoplastic rectal mucosa of patients with ulcerative colitis (UC) with coexisting colitis-associated cancer (CAC). We aimed to evaluate RUNX3 utility as a predictive marker for CAC using immunohistochemistry (IHC) for non-neoplastic UC mucosa. <b><i>Methods:</i></b> We retrospectively compared the RUNX3 expression detected by IHC between non-neoplastic rectal biopsy specimens from 20 cases with invasive cancer (CAC group) and 20 cases selected from 138 patients without CAC (non-CAC group) that were treated during the same period (2006–2017) and were matched for sex, duration, extension, and age. We validated the results using tissue microarrays (TMA) of 44 operated cases with CAC. The RUNX3 expression level was determined by calculating the percentage of RUNX3-positive-cells. <b><i>Results:</i></b> The RUNX3 expression was lower in the CAC than that in the non-CAC group (35.6 vs. 70.7%, <i>p</i> = 0.03). For a cutoff value of 58%, the sensitivity and specificity for predicting CAC were 75.0 and 70.0% respectively. The immunostaining results for the TMA showed the same trend; 74% of cases with CAC were negative for the RUNX3 expression. <b><i>Conclusion:</i></b> RUNX3 immunostaining of non-neoplastic mucosa is useful for identifying UC patients at a high risk of developing CAC.
DOI: 10.7284/102187
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-59 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7717844
title: Supplementary Material for: Identification and Assessment of Drug-User Groups Among Nightlife Attendees: Self-Reports, Breathalyzer-Tests and Oral Fluid Drug Tests

description: <b><i>Background and Objectives:</i></b> Even though nightlife studies with potentially intoxicated participants provide the much needed information on drug use, they face additional methodological challenges. This study aimed to explore the utility of such studies by (i) classifying nightlife attendees based on their self-reported drug use and by (ii) examining whether these classifications were meaningful when assessed against other sources of data, including oral fluid drug tests. <b><i>Methods:</i></b> Self-reported questionnaires, oral fluid samples and blood alcohol concentration readings were collected in a sample of 1,085 nightlife patrons recruited outside 12 popular nightclubs in Oslo, Norway, in 2014. Patrons were classified using multiple approaches, including latent class analysis. Group differences were examined by logistic regression models. <b><i>Results:</i></b> Participants were classified into 5 mutually exclusive groups: 2 among <i>current non-users</i> (“Never-users”; “Previous users”), 2 among <i>current users</i> (“Multiple drugs”; “Cannabis mainly”) and one “Incomplete information” group. Meaningful differences across these groups were observed. For instance, positive tests for any illicit drug were more common in “Multiple drugs” group than in “Cannabis mainly” (62.7 vs. 29.1%, adjusted OR [aOR] 3.77 [2.42–5.84]) or “Incomplete information” groups (62.7 vs. 34.4%, aOR 2.46 [1.26–4.79]). Despite their self-declared non-use, illicit substances were detected in oral fluids of “Never-users” (13.1%; 95% CI 9.9–17.2) and “Previous users” (7.9%; 95% CI 5.1–12.1). <b><i>Conclusions:</i></b> Despite some discrepancies between self-reports and biological tests, self-reports proved both suitable and useful in identification of substantively different drug-user typologies, potentially informing targeted policy responses. Still, methodological challenges associated with onsite studies of illicit drug use should be further explored.
DOI: 10.6084/m9.figshare.7717844.v1
title: Supplementary Material for: Identification and Assessment of Drug-User Groups Among Nightlife Attendees: Self-Reports, Breathalyzer-Tests and Oral Fluid Drug Tests

description: <b><i>Background and Objectives:</i></b> Even though nightlife studies with potentially intoxicated participants provide the much needed information on drug use, they face additional methodological challenges. This study aimed to explore the utility of such studies by (i) classifying nightlife attendees based on their self-reported drug use and by (ii) examining whether these classifications were meaningful when assessed against other sources of data, including oral fluid drug tests. <b><i>Methods:</i></b> Self-reported questionnaires, oral fluid samples and blood alcohol concentration readings were collected in a sample of 1,085 nightlife patrons recruited outside 12 popular nightclubs in Oslo, Norway, in 2014. Patrons were classified using multiple approaches, including latent class analysis. Group differences were examined by logistic regression models. <b><i>Results:</i></b> Participants were classified into 5 mutually exclusive groups: 2 among <i>current non-users</i> (“Never-users”; “Previous users”), 2 among <i>current users</i> (“Multiple drugs”; “Cannabis mainly”) and one “Incomplete information” group. Meaningful differences across these groups were observed. For instance, positive tests for any illicit drug were more common in “Multiple drugs” group than in “Cannabis mainly” (62.7 vs. 29.1%, adjusted OR [aOR] 3.77 [2.42–5.84]) or “Incomplete information” groups (62.7 vs. 34.4%, aOR 2.46 [1.26–4.79]). Despite their self-declared non-use, illicit substances were detected in oral fluids of “Never-users” (13.1%; 95% CI 9.9–17.2) and “Previous users” (7.9%; 95% CI 5.1–12.1). <b><i>Conclusions:</i></b> Despite some discrepancies between self-reports and biological tests, self-reports proved both suitable and useful in identification of substantively different drug-user typologies, potentially informing targeted policy responses. Still, methodological challenges associated with onsite studies of illicit drug use should be further explored.
DOI: 10.7284/102186
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT15-59 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition