cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7039433.v1
title: Sanitation planning for squatter settlements as urban water management in Mumbai

description: In spite of initiatives by developing countries and the United Nations, basic sanitation is still a dream for millions. This need for capacity-building has inspired our work to scientifically determine actual-demand and indicate locations for new toilets. We took data relating to 8417 toilet-blocks in Mumbai and investigated future sanitation (latrine/toilet) development in all city-wards using a combined demand-centric and geospatial approach. We found lacunae in the present sanitation scenario, where some wards need many more toilet-blocks (600–746) than have been provisioned. Certain wards require more than 100% provisioning, such as FN ward, which requires 340% (i.e. 3.4 times) more toilets compared to what it currently has. Besides demand-analysis, a geospatial assessment was carried out to find potential locations for new toilets. This study is useful to help us explore policy amendments for metropolises having similar characteristics as Mumbai. Further research may address location optimization considering ground-reality, societal-aspects and geophysical-constraints.
DOI: 10.6084/m9.figshare.7039424
title: Table S2 (csv) from Punctuated plastome reduction and host–parasite horizontal gene transfer in the holoparasitic plant genus <i>Aphyllon</i>

description: GenBank accession numbers for A. epigalium plastomes, partial mitochondrial genomes, and rbcL sequences used in this study. Sequences reported for the first time in this study are also accompanied by voucher information, the source of DNA used, and sequencing method (Sanger or Illumina). (csv format)
DOI: 10.6084/m9.figshare.7039424.v1
title: Table S2 (csv) from Punctuated plastome reduction and host–parasite horizontal gene transfer in the holoparasitic plant genus <i>Aphyllon</i>

description: GenBank accession numbers for A. epigalium plastomes, partial mitochondrial genomes, and rbcL sequences used in this study. Sequences reported for the first time in this study are also accompanied by voucher information, the source of DNA used, and sequencing method (Sanger or Illumina). (csv format)
DOI: 10.6084/m9.figshare.7039388
title: Supplementary Material for: Patiromer to Enable Spironolactone Use in the Treatment of Patients with Resistant Hypertension and Chronic Kidney Disease: Rationale and Design of the AMBER Study

description: <b><i>Background:</i></b> While chronic kidney disease (CKD) is common in resistant hypertension (RHTN), prior studies ­evaluating mineralocorticoid receptor antagonists excluded patients with reduced kidney function due to risk of hyperkalemia. AMBER (ClinicalTrials.gov identifier NCT03071263) will evaluate if the potassium-binding polymer patiromer used concomitantly with spironolactone in patients with RHTN and CKD prevents hyperkalemia and allows more persistent spironolactone use for hypertension management. <b><i>Methods:</i></b> Randomized, double-blind, placebo-controlled parallel group 12-week study of patiromer and spironolactone versus placebo and spironolactone in patients with uncontrolled RHTN and CKD. RHTN is defined as unattended systolic automated office blood pressure (AOBP) of ­135–160 mm Hg during screening despite taking ≥3 antihypertensives, including a diuretic, and an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker ­(unless not tolerated or contraindicated). The CKD inclusion criterion is an estimated glomerular filtration rate (eGFR) of 25 to ≤45 mL/min/1.73 m<sup>2</sup>. Screening serum potassium must be 4.3–5.1 mEq/L. The primary efficacy endpoint is the between-group difference (spironolactone plus patiromer versus spironolactone plus placebo) in the proportion of patients remaining on spironolactone at Week 12. <b><i>Results:</i></b> Baseline characteristics have been analyzed as of March 2018 for 146 (of a targeted 290) patients. Mean (SD) baseline age is 69.3 (10.9) years; 52.1% are male, 99.3% White, and 47.3% have diabetes. Mean (SD) baseline serum potassium is 4.68 (0.25) mEq/L, systolic AOBP is 144.3 (6.8) mm Hg, eGFR is 35.7 (7.7) mL/min/1.73 m<sup>2</sup>. <b><i>Conclusion:</i></b> AMBER will define the ability of patiromer to facilitate the use of spironolactone, an effective antihypertensive therapy for patients with RHTN and CKD.
DOI: 10.6084/m9.figshare.7039376
title: Prelimbic cortical targets of ventromedial thalamic projections include inhibitory interneurons and corticostriatal pyramidal neurons in the rat (supplementary data)

description: This dataset contains the raw and processed image files that were used to create figures presented in Sieveritz and Arbuthnott (2020) as well as supplementary data of 4 more animals to illustrate RGS14 expression in prelimbic intratelencephalic neurons, 2 more animals to illustrate RGS14 expression in prelimbic corticothalamic neurons, 3 more animals to illustrate 5HT3aR expression in prelimbic cortical layer 1 inhibitory interneurons and 4 more animals to illustrate neurotransmitter expression (VGluT1, VGluT2 and GAD67) in ventral motor thalamic axon terminals in uppermost prelimbic cortical layer 1. In addition, supplementary data from 6 animals to illustrate 5HT3aR expression in supplementary motor cortical (M2) layer 1 are provided. All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the Okinawa Institute of Science and Technology Graduate University and were approved by the Animal Care and Use Committee of the Okinawa Institute of Science and Technology Graduate University (protocols #2016-131-00 and #2018-212).
DOI: 10.6084/m9.figshare.7039388.v1
title: Supplementary Material for: Patiromer to Enable Spironolactone Use in the Treatment of Patients with Resistant Hypertension and Chronic Kidney Disease: Rationale and Design of the AMBER Study

description: <b><i>Background:</i></b> While chronic kidney disease (CKD) is common in resistant hypertension (RHTN), prior studies ­evaluating mineralocorticoid receptor antagonists excluded patients with reduced kidney function due to risk of hyperkalemia. AMBER (ClinicalTrials.gov identifier NCT03071263) will evaluate if the potassium-binding polymer patiromer used concomitantly with spironolactone in patients with RHTN and CKD prevents hyperkalemia and allows more persistent spironolactone use for hypertension management. <b><i>Methods:</i></b> Randomized, double-blind, placebo-controlled parallel group 12-week study of patiromer and spironolactone versus placebo and spironolactone in patients with uncontrolled RHTN and CKD. RHTN is defined as unattended systolic automated office blood pressure (AOBP) of ­135–160 mm Hg during screening despite taking ≥3 antihypertensives, including a diuretic, and an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker ­(unless not tolerated or contraindicated). The CKD inclusion criterion is an estimated glomerular filtration rate (eGFR) of 25 to ≤45 mL/min/1.73 m<sup>2</sup>. Screening serum potassium must be 4.3–5.1 mEq/L. The primary efficacy endpoint is the between-group difference (spironolactone plus patiromer versus spironolactone plus placebo) in the proportion of patients remaining on spironolactone at Week 12. <b><i>Results:</i></b> Baseline characteristics have been analyzed as of March 2018 for 146 (of a targeted 290) patients. Mean (SD) baseline age is 69.3 (10.9) years; 52.1% are male, 99.3% White, and 47.3% have diabetes. Mean (SD) baseline serum potassium is 4.68 (0.25) mEq/L, systolic AOBP is 144.3 (6.8) mm Hg, eGFR is 35.7 (7.7) mL/min/1.73 m<sup>2</sup>. <b><i>Conclusion:</i></b> AMBER will define the ability of patiromer to facilitate the use of spironolactone, an effective antihypertensive therapy for patients with RHTN and CKD.
DOI: 10.6084/m9.figshare.7039388.v2
title: Supplementary Material for: Patiromer to Enable Spironolactone Use in the Treatment of Patients with Resistant Hypertension and Chronic Kidney Disease: Rationale and Design of the AMBER Study

description: <b><i>Background:</i></b> While chronic kidney disease (CKD) is common in resistant hypertension (RHTN), prior studies ­evaluating mineralocorticoid receptor antagonists excluded patients with reduced kidney function due to risk of hyperkalemia. AMBER (ClinicalTrials.gov identifier NCT03071263) will evaluate if the potassium-binding polymer patiromer used concomitantly with spironolactone in patients with RHTN and CKD prevents hyperkalemia and allows more persistent spironolactone use for hypertension management. <b><i>Methods:</i></b> Randomized, double-blind, placebo-controlled parallel group 12-week study of patiromer and spironolactone versus placebo and spironolactone in patients with uncontrolled RHTN and CKD. RHTN is defined as unattended systolic automated office blood pressure (AOBP) of ­135–160 mm Hg during screening despite taking ≥3 antihypertensives, including a diuretic, and an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker ­(unless not tolerated or contraindicated). The CKD inclusion criterion is an estimated glomerular filtration rate (eGFR) of 25 to ≤45 mL/min/1.73 m<sup>2</sup>. Screening serum potassium must be 4.3–5.1 mEq/L. The primary efficacy endpoint is the between-group difference (spironolactone plus patiromer versus spironolactone plus placebo) in the proportion of patients remaining on spironolactone at Week 12. <b><i>Results:</i></b> Baseline characteristics have been analyzed as of March 2018 for 146 (of a targeted 290) patients. Mean (SD) baseline age is 69.3 (10.9) years; 52.1% are male, 99.3% White, and 47.3% have diabetes. Mean (SD) baseline serum potassium is 4.68 (0.25) mEq/L, systolic AOBP is 144.3 (6.8) mm Hg, eGFR is 35.7 (7.7) mL/min/1.73 m<sup>2</sup>. <b><i>Conclusion:</i></b> AMBER will define the ability of patiromer to facilitate the use of spironolactone, an effective antihypertensive therapy for patients with RHTN and CKD.
DOI: 10.6084/m9.figshare.7039373
title: Supplementary Material for: Novel Compound Induces Erythropoietin Secretion through Liver Effects in Chronic Kidney Disease Patients and Healthy Volunteers

description: <b><i>Background:</i></b> TP0463518 is a novel hypoxia-inducible factor prolyl hydroxylase inhibitor developed to aid in the treatment of anemia associated with chronic kidney disease (CKD) and is expected to increase erythropoietin (EPO) derived from liver. Two phase I studies were conducted in healthy volunteers (HV) and CKD patients undergoing hemodialysis (i.e., HD patients) or those not undergoing dialysis (i.e., ND patients). <b><i>Methods:</i></b> Pharmacokinetics, pharmacodynamics, and safety profiles of TP0463518 were assessed. Forty HV received single oral doses of TP0463518 at 3, 6, 11, 20, and 36 mg or placebo. Twenty ND patients received single doses of TP0463518 at 1, 6, and 11 mg and 9 HD patients received TP0463518 at 1 and 11 mg doses. To identify the source organ of EPO, glycosylation patterns were determined using percentage migrated isoform (PMI) values. <b><i>Results:</i></b> Declining renal function slowed elimination of TP0463518 and increased the mean AUC<sub>0–∞</sub>. ∆E<sub>max</sub> of serum EPO in 11-mg groups of HV, ND patients, and HD patients were 24.37 ± 11.37, 201.57 ± 130.34, and 1,324.76 ± 1,189.24 mIU/mL respectively. A strong correlation was ­observed between logarithm conversions of ∆E<sub>max</sub> and AUC<sub>0–∞</sub> with correlation coefficients of 0.945. PMI values of blood after TP0463518 administration were elevated to similar or higher levels in comparison with those of umbilical cord blood, which mainly contains liver-derived EPO. <b><i>Conclusions:</i></b> TP0463518 induced dose-dependent EPO production, mainly derived from the liver in HV and CKD patients. These results suggest that TP0463518 is a new strategy for treating anemia in CKD, which can be used regardless of renal functions.
DOI: 10.6084/m9.figshare.7039376.v1
title: Prelimbic cortical targets of ventromedial thalamic projections include inhibitory interneurons and corticostriatal pyramidal neurons in the rat (supplementary data)

description: This dataset contains the raw and processed image files that were used to create figures presented in Sieveritz and Arbuthnott (2020) as well as supplementary data of 4 more animals to illustrate RGS14 expression in prelimbic intratelencephalic neurons, 2 more animals to illustrate RGS14 expression in prelimbic corticothalamic neurons, 3 more animals to illustrate 5HT3aR expression in prelimbic cortical layer 1 inhibitory interneurons and 4 more animals to illustrate neurotransmitter expression (VGluT1, VGluT2 and GAD67) in ventral motor thalamic axon terminals in uppermost prelimbic cortical layer 1. In addition, supplementary data from 6 animals to illustrate 5HT3aR expression in supplementary motor cortical (M2) layer 1 are provided. All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the Okinawa Institute of Science and Technology Graduate University and were approved by the Animal Care and Use Committee of the Okinawa Institute of Science and Technology Graduate University (protocols #2016-131-00 and #2018-212).
DOI: 10.6084/m9.figshare.7039370
title: <i>Neisseria meningitidis</i> disease-associated clones in Amazonas State, Brazil

description: <b>Background:</b> The aim of this study is to describe the molecular epidemiology of <i>Neisseria meningitidis</i> invasive disease before the introduction of serogroup C conjugate vaccine in Amazonas State in 2010. <b>Methods:</b> Meningococcal disease reported cases were investigated in Amazonas State during the period 2000–2010. <i>N. meningitidis</i> isolates (<i>n</i> = 196) recovered from patients were genotyped by multilocus sequence typing (MLST) and sequencing of <i>porB</i>, <i>porA</i>, <i>fetA</i>, <i>fHbp</i> and <i>penA</i>. Antimicrobial susceptibility was determined using E-test. <b>Results:</b> In the study period, 948 cases were reported; the incidence was 2.8 for the entire state and 4.8 per 100,000 in the capital of Manaus. Most meningococcal disease was caused by <i>N. meningitidis</i> belonging to ST-32 (72%; 141/196) or ST-103 (21%; 41/196) clonal complexes. Capsular switching (B→C) was suggested within clonal complex (cc) 32. There were 6 (3%; 6/196) strains with intermediate susceptibility to penicillin and a single strain was resistant to rifampicin. Since 2007, serogroup C strains belonging to the cc103 have predominated and case-fatality has increased. <b>Conclusion:</b> We demonstrate a high rate of meningococcal disease in Amazonas State, where, like other parts of Brazil, serogroup C replaced serogroup B during 2000s. These data serve as a baseline to measure impact of serogroup C conjugate vaccine introduction in 2010. This study emphasizes the need for enhanced surveillance to monitor changes in meningococcal disease trends following the introduction of meningococcal vaccines.
DOI: 10.6084/m9.figshare.7039370.v1
title: <i>Neisseria meningitidis</i> disease-associated clones in Amazonas State, Brazil

description: <b>Background:</b> The aim of this study is to describe the molecular epidemiology of <i>Neisseria meningitidis</i> invasive disease before the introduction of serogroup C conjugate vaccine in Amazonas State in 2010. <b>Methods:</b> Meningococcal disease reported cases were investigated in Amazonas State during the period 2000–2010. <i>N. meningitidis</i> isolates (<i>n</i> = 196) recovered from patients were genotyped by multilocus sequence typing (MLST) and sequencing of <i>porB</i>, <i>porA</i>, <i>fetA</i>, <i>fHbp</i> and <i>penA</i>. Antimicrobial susceptibility was determined using E-test. <b>Results:</b> In the study period, 948 cases were reported; the incidence was 2.8 for the entire state and 4.8 per 100,000 in the capital of Manaus. Most meningococcal disease was caused by <i>N. meningitidis</i> belonging to ST-32 (72%; 141/196) or ST-103 (21%; 41/196) clonal complexes. Capsular switching (B→C) was suggested within clonal complex (cc) 32. There were 6 (3%; 6/196) strains with intermediate susceptibility to penicillin and a single strain was resistant to rifampicin. Since 2007, serogroup C strains belonging to the cc103 have predominated and case-fatality has increased. <b>Conclusion:</b> We demonstrate a high rate of meningococcal disease in Amazonas State, where, like other parts of Brazil, serogroup C replaced serogroup B during 2000s. These data serve as a baseline to measure impact of serogroup C conjugate vaccine introduction in 2010. This study emphasizes the need for enhanced surveillance to monitor changes in meningococcal disease trends following the introduction of meningococcal vaccines.
DOI: 10.6084/m9.figshare.7039331
title: Table S1. Summary of 13 protein-coding gene sequences of Scotoplanes sp. and ten holothurian species.

description: Table S1. Takano, T., M. Ijichi, H. Itoh, H. Fukuda & S. Yoshizawa. Complete mitochondrial genome sequences of a deep-sea holothurian species of the genus<em> Scotoplanes</em> (Elasipodida: Elpidiidae).<em> Mitochondrial DNA Part B: Resources</em> 4: 112–113.
DOI: 10.6084/m9.figshare.7039331.v1
title: Table S1. Summary of 13 protein-coding gene sequences of Scotoplanes sp. and ten holothurian species.

description: Table S1. Takano, T., M. Ijichi, H. Itoh, H. Fukuda & S. Yoshizawa. Complete mitochondrial genome sequences of a deep-sea holothurian species of the genus<em> Scotoplanes</em> (Elasipodida: Elpidiidae).<em> Mitochondrial DNA Part B: Resources</em> 4: 112–113.
DOI: 10.6084/m9.figshare.7039298
title: Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

description: Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same <i>locus</i>. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon <i>Halobacterium salinarum</i>. In the present work we used differential RNA-seq (dRNA-seq) in <i>H. salinarum</i> NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for <i>kef1, acs3</i> and <i>orc4</i> genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene <i>gvpC1</i>. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone <i>dnaK</i> and the aerobic respiration related <i>cydA</i> in both <i>H. salinarum</i> and <i>Escherichia coli</i>. Also, intraRNA translation evidence in <i>H. salinarum, E. coli</i> and yeast of a universal elongation factor (<i>aEF-2, fusA</i> and <i>eEF</i>-2) suggests that this is an ancient phenomenon present in all domains of life.
DOI: 10.6084/m9.figshare.7039298.v2
title: Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

description: Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same <i>locus</i>. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon <i>Halobacterium salinarum</i>. In the present work we used differential RNA-seq (dRNA-seq) in <i>H. salinarum</i> NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for <i>kef1, acs3</i> and <i>orc4</i> genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene <i>gvpC1</i>. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone <i>dnaK</i> and the aerobic respiration related <i>cydA</i> in both <i>H. salinarum</i> and <i>Escherichia coli</i>. Also, intraRNA translation evidence in <i>H. salinarum, E. coli</i> and yeast of a universal elongation factor (<i>aEF-2, fusA</i> and <i>eEF</i>-2) suggests that this is an ancient phenomenon present in all domains of life.
DOI: 10.6084/m9.figshare.7039298.v1
title: Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

description: Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same <i>locus</i>. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon <i>Halobacterium salinarum</i>. In the present work we used differential RNA-seq (dRNA-seq) in <i>H. salinarum</i> NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for <i>kef1, acs3</i> and <i>orc4</i> genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas visicle protein gene <i>gvpC1</i>. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone <i>dnaK</i> and the aerobic respiration related <i>cydA</i> in both <i>H. salinarum</i> and <i>Escherichia coli</i>. Also, intraRNA translation evidence in <i>H. salinarum, E. coli</i> and yeast of a universal elongation factor (<i>aEF-2, fusA</i> and <i>eEF</i>-2) suggests that this is an ancient phenomenon present in all domains of life.
DOI: 10.6084/m9.figshare.7039286
title: REACHES

description: This database reflects an ongoing project of constructing an East Asian climate database REACHES based on Chinese historical documents. The main record source is Compendium of Meteorological Records of China in the Last 3000 Years which collects meteorology and climate related records from mainly official and local chronicles along with a small number of other documents. The first entries are the records of the early half of the last Qing dynasty (1644-1975). More data will be uploaded while records are properly digitized.
DOI: 10.6084/m9.figshare.7039286.v1
title: REACHES

description: This database reflects an ongoing project of constructing an East Asian climate database REACHES based on Chinese historical documents. The main record source is Compendium of Meteorological Records of China in the Last 3000 Years which collects meteorology and climate related records from mainly official and local chronicles along with a small number of other documents. The first entries are the records of the early half of the last Qing dynasty (1644-1975). More data will be uploaded while records are properly digitized.
DOI: 10.25374/mcri.7039280
title: Data Dictionary

description: This is a data dictionary example we will use in the MVP presentation. It can be deleted after 13/9/18.
DOI: 10.25374/mcri.7039280.v1
title: Data Dictionary

description: This is a data dictionary example we will use in the MVP presentation. It can be deleted after 13/9/18.