cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7145870.v4
title: Erythrocyte indices, anaemia levels and types in Kenyan injection and non-injection substance users

description: Abstract The impact of injection and non-injection substance use in HIV infections is an area of great public importance especially with respect to hematologic and immune profiles. Evaluations of hematologic and immune status are critical for better disease classification and clinical management especially of HIV positive substance users. However, not much information is known about the hematologic and immune derangements in HIV infected injection and non-injection substance users. This study, therefore, aimed at determining the laboratory markers of hematologic and immune derangements in HIV infected substance users. Hematologic and immune profiles were evaluated on venous blood specimens obtained from injection substance users, ISU (HIV-infected, n=62 and -uninfected, n=213) and non-injection substance users (HIV-infected, n=33 and -uninfected, n=186); and non-substance using controls (n=56) from Mombasa, coastal town of Kenya. The prevalence of anemia was higher in HIV infected ISU (48.4%) and non-ISU (63.6%) (p&lt;0.0001); and HIV uninfected ISUs (56.3%) compared to HIV-uninfected non-ISUs (39.2%) and non-substance using controls (28.6%; p=0.0028). Hypochromic anaemia was more prevalent in the HIV-infected ISU (50.0%) and non-ISU (61.9%), and HIV-negative ISU (63.3%) relative to the HIV-negative non-ISU (39.7%) and non-substance using controls (56.3%; p=0.0007). Mild immunodeficiency dominated in the HIV infected individuals (HIV-infected ISU, 32.3% and non-ISU, 21.2%) versus HIV-uninfected ISU (16.9%); non-ISU (12.9%); and non-substance users (14.3%) while severe immunosuppression prevailed in HIV infected substance users (ISU, 14.5% and non-ISU, 15.2%) against HIV uninfected substance users (ISU, 5.2% and non-ISU, 3.8%); thus immunosuppression in substance users is aggravated with HIV infection. Moreover, drug-induced immunosuppression is associated with a higher likelihood of anaemia in HIV-uninfected substance users; ISU (OR=3.95, CI=1.934-8.077, p&lt;0.0001) and non-ISU (OR=3.63, CI=1.571-8.39, p=0.003). Altogether, hypochromic anaemia, normochromic anaemia and CD4+ T-helper cytopenia are the most prevalent hemocytopenias in HIV infected and uninfected injection and non-injection substance users.
DOI: 10.7284/117043
title: INS (Inertial Navigation System) data collected during research cruise WS1406 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7145846
title: GCAP MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for GCAP/GCIP sequences
DOI: 10.6084/m9.figshare.7145846.v1
title: GCAP MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for GCAP/GCIP sequences
DOI: 10.7284/117166
title: Multiplexed data collected during research cruise WS1407 using a Miami VIDS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7145840
title: NCKX MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for NCKX sequences
DOI: 10.7284/117058
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1407 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7145837
title: Recoverin/Visinin MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for recoverin/visinin sequences
DOI: 10.6084/m9.figshare.7145840.v1
title: NCKX MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for NCKX sequences
DOI: 10.6084/m9.figshare.7145834
title: GC MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for guanylyl cyclase sequences
DOI: 10.6084/m9.figshare.7145837.v1
title: Recoverin/Visinin MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for recoverin/visinin sequences
DOI: 10.6084/m9.figshare.7145834.v1
title: GC MSAs from Evolution of the calcium feedback steps of vertebrate phototransduction

description: Multiple sequence alignments for guanylyl cyclase sequences
DOI: 10.7284/117059
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1407 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7145825
title: Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical <i>Pristimantis</i> leaf litter frogs

description: The Neotropical leaf litter frog genus <i>Pristimantis</i> is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in <i>Pristimantis</i>. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 <i>Pristimantis</i> presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of <i>Pristimantis</i> at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in <i>Pristimantis</i> phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within <i>Pristimantis</i>. Diversification rates decrease towards the present following a density-dependent pattern for <i>Pristimantis</i> overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of <i>Pristimantis</i> and thus contributed to the origins of evolutionary independent phylogenetic clusters.
DOI: 10.6084/m9.figshare.7145813
title: An updated phylogeny of <i>Deprea</i> (Solanaceae) with a new species from Colombia: interspecific relationships, conservation assessment, and a key for Colombian species

description: <i>Deprea</i> is a neotropical genus that comprises 51 species. Recent work based on molecular data has explored its monophyly and interspecific relationships, but the relationships amongst <i>Deprea</i> species were not entirely elucidated. The inclusion of more accessions and molecular markers in phylogenetic analysis is likely to produce more supported hypotheses. Therefore, the main objective of this study was to perform a combined phylogenetic analysis of <i>Deprea</i> including seven new samples representing six species and one more DNA plastid marker than in previous studies. In that process, a new species of <i>Deprea</i> from Colombia was discovered and is described and illustrated here. <i>Deprea teresitae</i> Deanna & A. Orejuela, sp. nov. is morphologically similar to <i>D. dilloniana</i> and phylogenetically closely related to <i>D. hawkesii</i> and <i>D. harlingiana</i>. This new species is distinguished by the combination of short calyx lobes, non-mucronate anthers, long staminal filaments and corolla lobes, and elongated appressed fruiting calyx around a subglobose green berry. The new phylogenetic results are presented, including discussion on phylogenetic interspecific relationships, taxonomy, geographic distribution, and conservation status from <i>D. teresitae</i>. The synonymy of <i>Deprea sylvarum</i> subsp. <i>novogranatensis</i> under <i>D. glabra</i> is also proposed and an identification key to the 10 <i>Deprea</i> species distributed in Colombia is included.
DOI: 10.6084/m9.figshare.7145813.v1
title: An updated phylogeny of <i>Deprea</i> (Solanaceae) with a new species from Colombia: interspecific relationships, conservation assessment, and a key for Colombian species

description: <i>Deprea</i> is a neotropical genus that comprises 51 species. Recent work based on molecular data has explored its monophyly and interspecific relationships, but the relationships amongst <i>Deprea</i> species were not entirely elucidated. The inclusion of more accessions and molecular markers in phylogenetic analysis is likely to produce more supported hypotheses. Therefore, the main objective of this study was to perform a combined phylogenetic analysis of <i>Deprea</i> including seven new samples representing six species and one more DNA plastid marker than in previous studies. In that process, a new species of <i>Deprea</i> from Colombia was discovered and is described and illustrated here. <i>Deprea teresitae</i> Deanna & A. Orejuela, sp. nov. is morphologically similar to <i>D. dilloniana</i> and phylogenetically closely related to <i>D. hawkesii</i> and <i>D. harlingiana</i>. This new species is distinguished by the combination of short calyx lobes, non-mucronate anthers, long staminal filaments and corolla lobes, and elongated appressed fruiting calyx around a subglobose green berry. The new phylogenetic results are presented, including discussion on phylogenetic interspecific relationships, taxonomy, geographic distribution, and conservation status from <i>D. teresitae</i>. The synonymy of <i>Deprea sylvarum</i> subsp. <i>novogranatensis</i> under <i>D. glabra</i> is also proposed and an identification key to the 10 <i>Deprea</i> species distributed in Colombia is included.
DOI: 10.7284/117044
title: INS (Inertial Navigation System) data collected during research cruise WS1407 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7145810
title: Supplementary Material for: Value of a Marker Lesion in Non-Muscle-Invasive Bladder Cancer Patients Treated with Interleukin-2 Instillations: A Randomized Controlled Multicentre Trial

description: <b><i>Purpose:</i></b> To compare the effect of intravesical interleukin-2 (IL-2) instillations with and without a marker lesion on time to recurrence (TTR) in non-muscle-invasive bladder cancer (NMIBC) patients. <b><i>Methods:</i></b> A prospective randomized, controlled trial was conducted. Patients with multiple non-muscle-invasive tumours were randomized for a complete or incomplete transurethral resection (TURBT), followed by 3 IL-2 instillations. The primary end point was TTR. <b><i>Results:</i></b> These are the results of an interim analysis, which was performed due to slow accrual after which the study was closed prematurely. Twenty-eight patients were randomized of which 17 were eligible on an intention-to-treat basis. Median TTR or last follow-up was 3 months (interquartile range [IQR] 3–10 months) for the complete and 4 months (IQR 3–8 months) for the incomplete TURBT group. The TTR between the 2 groups did not differ significantly (log-rank, <i>p</i> = 0.54). ­<b><i>Conclusions:</i></b> These data do not support the hypothesis that a marker lesion enhances the therapeutic effect of IL-2 instillations in patients with NMIBC.
DOI: 10.6084/m9.figshare.7145825.v1
title: Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical <i>Pristimantis</i> leaf litter frogs

description: The Neotropical leaf litter frog genus <i>Pristimantis</i> is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in <i>Pristimantis</i>. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 <i>Pristimantis</i> presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of <i>Pristimantis</i> at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in <i>Pristimantis</i> phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within <i>Pristimantis</i>. Diversification rates decrease towards the present following a density-dependent pattern for <i>Pristimantis</i> overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of <i>Pristimantis</i> and thus contributed to the origins of evolutionary independent phylogenetic clusters.
DOI: 10.6084/m9.figshare.7145825.v3
title: Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical <i>Pristimantis</i> leaf litter frogs

description: The Neotropical leaf litter frog genus <i>Pristimantis</i> is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in <i>Pristimantis</i>. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 <i>Pristimantis</i> presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of <i>Pristimantis</i> at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in <i>Pristimantis</i> phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within <i>Pristimantis</i>. Diversification rates decrease towards the present following a density-dependent pattern for <i>Pristimantis</i> overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of <i>Pristimantis</i> and thus contributed to the origins of evolutionary independent phylogenetic clusters.
DOI: 10.6084/m9.figshare.7145810.v1
title: Supplementary Material for: Value of a Marker Lesion in Non-Muscle-Invasive Bladder Cancer Patients Treated with Interleukin-2 Instillations: A Randomized Controlled Multicentre Trial

description: <b><i>Purpose:</i></b> To compare the effect of intravesical interleukin-2 (IL-2) instillations with and without a marker lesion on time to recurrence (TTR) in non-muscle-invasive bladder cancer (NMIBC) patients. <b><i>Methods:</i></b> A prospective randomized, controlled trial was conducted. Patients with multiple non-muscle-invasive tumours were randomized for a complete or incomplete transurethral resection (TURBT), followed by 3 IL-2 instillations. The primary end point was TTR. <b><i>Results:</i></b> These are the results of an interim analysis, which was performed due to slow accrual after which the study was closed prematurely. Twenty-eight patients were randomized of which 17 were eligible on an intention-to-treat basis. Median TTR or last follow-up was 3 months (interquartile range [IQR] 3–10 months) for the complete and 4 months (IQR 3–8 months) for the incomplete TURBT group. The TTR between the 2 groups did not differ significantly (log-rank, <i>p</i> = 0.54). ­<b><i>Conclusions:</i></b> These data do not support the hypothesis that a marker lesion enhances the therapeutic effect of IL-2 instillations in patients with NMIBC.
DOI: 10.7284/117060
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1408 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith
DOI: 10.6084/m9.figshare.7145789
title: Data for Fig 2 from Novel elucidation and treatment of pancreatic chronic graft-versus-host disease in mice

description: Chronic graft-versus-host disease (cGVHD) is a severe complication of allogeneic haematopoietic stem cell transplantation. There is a growing understanding of cGVHD, and several effective therapies for cGVHD have been reported. However, pancreatic cGVHD is a potentially untapped study field. Our thought-provoking study using a mouse model of cGVHD suggested that the pancreas could be impaired by cGVHD-induced inflammation and fibrosis and that endoplasmic reticulum (ER) stress was augmented in the pancreas affected by cGVHD. These findings urged us to treat pancreatic cGVHD through reduction of ER stress, and we used 4-phenylbutyric acid (PBA) as an ER stress reducer. A series of experiments have indicated that PBA can suppress cGVHD-elicited ER stress in the pancreas and accordingly alleviate pancreatic cGVHD. Furthermore, we focused on a correlation between epithelial to mesenchymal transition (EMT) and fibrosis in the cGVHD-affected pancreas, because EMT was conceivably implicated in various fibrosis-associated diseases. Our investigation has suggested that the expression of EMT markers was increased in the cGVHD-disordered pancreas and that it could be reduced by PBA. Taken together, we have provided a clue to elucidate the pathogenic process of pancreatic cGVHD and created a potentially effective treatment of this disease using the ER stress alleviator PBA.
DOI: 10.6084/m9.figshare.7145789.v1
title: Data for Fig 2 from Novel elucidation and treatment of pancreatic chronic graft-versus-host disease in mice

description: Chronic graft-versus-host disease (cGVHD) is a severe complication of allogeneic haematopoietic stem cell transplantation. There is a growing understanding of cGVHD, and several effective therapies for cGVHD have been reported. However, pancreatic cGVHD is a potentially untapped study field. Our thought-provoking study using a mouse model of cGVHD suggested that the pancreas could be impaired by cGVHD-induced inflammation and fibrosis and that endoplasmic reticulum (ER) stress was augmented in the pancreas affected by cGVHD. These findings urged us to treat pancreatic cGVHD through reduction of ER stress, and we used 4-phenylbutyric acid (PBA) as an ER stress reducer. A series of experiments have indicated that PBA can suppress cGVHD-elicited ER stress in the pancreas and accordingly alleviate pancreatic cGVHD. Furthermore, we focused on a correlation between epithelial to mesenchymal transition (EMT) and fibrosis in the cGVHD-affected pancreas, because EMT was conceivably implicated in various fibrosis-associated diseases. Our investigation has suggested that the expression of EMT markers was increased in the cGVHD-disordered pancreas and that it could be reduced by PBA. Taken together, we have provided a clue to elucidate the pathogenic process of pancreatic cGVHD and created a potentially effective treatment of this disease using the ER stress alleviator PBA.
DOI: 10.7284/117046
title: INS (Inertial Navigation System) data collected during research cruise WS1408 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7145783
title: Data for Fig 4 from Novel elucidation and treatment of pancreatic chronic graft-versus-host disease in mice

description: Chronic graft-versus-host disease (cGVHD) is a severe complication of allogeneic haematopoietic stem cell transplantation. There is a growing understanding of cGVHD, and several effective therapies for cGVHD have been reported. However, pancreatic cGVHD is a potentially untapped study field. Our thought-provoking study using a mouse model of cGVHD suggested that the pancreas could be impaired by cGVHD-induced inflammation and fibrosis and that endoplasmic reticulum (ER) stress was augmented in the pancreas affected by cGVHD. These findings urged us to treat pancreatic cGVHD through reduction of ER stress, and we used 4-phenylbutyric acid (PBA) as an ER stress reducer. A series of experiments have indicated that PBA can suppress cGVHD-elicited ER stress in the pancreas and accordingly alleviate pancreatic cGVHD. Furthermore, we focused on a correlation between epithelial to mesenchymal transition (EMT) and fibrosis in the cGVHD-affected pancreas, because EMT was conceivably implicated in various fibrosis-associated diseases. Our investigation has suggested that the expression of EMT markers was increased in the cGVHD-disordered pancreas and that it could be reduced by PBA. Taken together, we have provided a clue to elucidate the pathogenic process of pancreatic cGVHD and created a potentially effective treatment of this disease using the ER stress alleviator PBA.
DOI: 10.6084/m9.figshare.7145783.v1
title: Data for Fig 4 from Novel elucidation and treatment of pancreatic chronic graft-versus-host disease in mice

description: Chronic graft-versus-host disease (cGVHD) is a severe complication of allogeneic haematopoietic stem cell transplantation. There is a growing understanding of cGVHD, and several effective therapies for cGVHD have been reported. However, pancreatic cGVHD is a potentially untapped study field. Our thought-provoking study using a mouse model of cGVHD suggested that the pancreas could be impaired by cGVHD-induced inflammation and fibrosis and that endoplasmic reticulum (ER) stress was augmented in the pancreas affected by cGVHD. These findings urged us to treat pancreatic cGVHD through reduction of ER stress, and we used 4-phenylbutyric acid (PBA) as an ER stress reducer. A series of experiments have indicated that PBA can suppress cGVHD-elicited ER stress in the pancreas and accordingly alleviate pancreatic cGVHD. Furthermore, we focused on a correlation between epithelial to mesenchymal transition (EMT) and fibrosis in the cGVHD-affected pancreas, because EMT was conceivably implicated in various fibrosis-associated diseases. Our investigation has suggested that the expression of EMT markers was increased in the cGVHD-disordered pancreas and that it could be reduced by PBA. Taken together, we have provided a clue to elucidate the pathogenic process of pancreatic cGVHD and created a potentially effective treatment of this disease using the ER stress alleviator PBA.