cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4103136
title: Electrophysiological profiles of cell-types in medial entorhinal cortex

description: This dataset shows electrophysiological profiles of different whole-cell patch-clamp recorded cell-types in the medial entorhinal cortex that receive monosynaptic input form the medial septum and diagonal band of broca.<br>DataSheets.pdf contains an overview of the electrophysiolgical characteristica, the .txt files contain raw data traces measured in mV. The first line contains headers, the first column is time. The tab-delimited columns refer to current injections of -200, -100, -50, -30, -20, -10, 10, 20, 30, 50, 100, 200, 300, 400, 500 pA. The data are sampled at 100 kHz. <br>For details refer to the original publication.
DOI: 10.6084/m9.figshare.4103136.v1
title: Electrophysiological profiles of cell-types in medial entorhinal cortex

description: This dataset shows electrophysiological profiles of different whole-cell patch-clamp recorded cell-types in the medial entorhinal cortex that receive monosynaptic input form the medial septum and diagonal band of broca.<br>DataSheets.pdf contains an overview of the electrophysiolgical characteristica, the .txt files contain raw data traces measured in mV. The first line contains headers, the first column is time. The tab-delimited columns refer to current injections of -200, -100, -50, -30, -20, -10, 10, 20, 30, 50, 100, 200, 300, 400, 500 pA. The data are sampled at 100 kHz. <br>For details refer to the original publication.
DOI: 10.7910/dvn/v1rjpf/1wnfus
title: cbb20170520_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4101765
title: Redactions extracted from ASIO surveillance records in National Archives of Australia Series A6119

description: This is a collection of 239,571 redactions (blacked out words and phrases) extracted from surveillance files created by the Australian Security Intelligence Organisation (ASIO) and held in Series A6119 at the National Archives of Australia. The digitised records were harvested from the NAA's online database as a collection of individual page images. These images were then processed to find and extract redactions. The script used to extract the redactions is in the linked GitHub repository. After running the script, I manually removed non-redactions (these are available in a separate fileset for comparison). There was about a 20% error rate. The redactions are saved as jpgs and are mostly very small images. The filenames of the images provide important contextual information. For example: 1009279-p10-1-74-54.jpg -- has the following attributes File barcode: 1009279 Page: 10 Redaction number: 1 Width: 74px Height: 54px You can search the NAA database to find the original file using the barcode, or construct a link like: https://owebrowse.herokuapp.com/items/1009279/pages/10/ to view the page from which the redaction was extracted in my own experimental interface.
DOI: 10.6084/m9.figshare.4101765.v1
title: Redactions extracted from ASIO surveillance records in National Archives of Australia Series A6119

description: This is a collection of 239,571 redactions (blacked out words and phrases) extracted from surveillance files created by the Australian Security Intelligence Organisation (ASIO) and held in Series A6119 at the National Archives of Australia. The digitised records were harvested from the NAA's online database as a collection of individual page images. These images were then processed to find and extract redactions. The script used to extract the redactions is in the linked GitHub repository. After running the script, I manually removed non-redactions (these are available in a separate fileset for comparison). There was about a 20% error rate. The redactions are saved as jpgs and are mostly very small images. The filenames of the images provide important contextual information. For example: 1009279-p10-1-74-54.jpg -- has the following attributes File barcode: 1009279 Page: 10 Redaction number: 1 Width: 74px Height: 54px You can search the NAA database to find the original file using the barcode, or construct a link like: https://owebrowse.herokuapp.com/items/1009279/pages/10/ to view the page from which the redaction was extracted in my own experimental interface.
DOI: 10.7910/dvn/v1rjpf/5uvbxg
title: cbb20170310_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4099743
title: R Code from Phenological shifts of native and invasive species under climate change: insights from the <i>Boechera Lythrum</i> model

description: Sample R code to re-create temperature and moisture curves shown in Fig 1, as well as the phenological models parameterized for Boechera stricta and Lythrum salicaria, and code to re-produce graphs in Fig 2
DOI: 10.6084/m9.figshare.4099743.v1
title: R Code from Phenological shifts of native and invasive species under climate change: insights from the <i>Boechera Lythrum</i> model

description: Sample R code to re-create temperature and moisture curves shown in Fig 1, as well as the phenological models parameterized for Boechera stricta and Lythrum salicaria, and code to re-produce graphs in Fig 2
DOI: 10.7910/dvn/v1rjpf/yvvlc8
title: cbb20170519_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/d4geuf
title: cbb20170629_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4097781
title: Individual Differences in the Rubber Hand Illusion are related to Sensory Suggestibility

description: Scores at the RHI task and Sensory Suggestibility Scale.<br>
DOI: 10.7910/dvn/v1rjpf/rforbv
title: cbb20170109_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4097781.v1
title: Individual Differences in the Rubber Hand Illusion are related to Sensory Suggestibility

description: Scores at the RHI task and Sensory Suggestibility Scale.<br>
DOI: 10.7910/dvn/v1rjpf/anw0ss
title: cbb20170427_03.txt.gz

description: :unav
DOI: 10.17608/k6.auckland.4097772
title: Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms.

description: Bioluminescence (relative light units [RLU] per well) of <i>M. tuberculosis </i>BSG001 (a stable bioluminescent derivative of H37Rv) growing as pellicles (floating biofilms), 7 days after exposure to different concentrations (Mg/L) of various common and experimental anti-tuberculosis treatments.
DOI: 10.7910/dvn/v1rjpf/zfnubd
title: cbb20171008_03.txt.gz

description: :unav
DOI: 10.17608/k6.auckland.4097772.v1
title: Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms.

description: Bioluminescence (relative light units [RLU] per well) of <i>M. tuberculosis </i>BSG001 (a stable bioluminescent derivative of H37Rv) growing as pellicles (floating biofilms), 7 days after exposure to different concentrations (Mg/L) of various common and experimental anti-tuberculosis treatments.
DOI: 10.7910/dvn/v1rjpf/mimtxq
title: cbb20171015_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fkixqk
title: cbb20170826_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zp96rz
title: cbb20170729_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/5nxtqb
title: cbb20170512_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4094436
title: Supplementary Data

description: Supplementary Data for the article "Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia"
DOI: 10.6084/m9.figshare.4095312
title: Neonatal microbiota can be classified into two distinct settler types with different development over time

description: Dataset containing raw data of intestinal microbiota composition of 77 newborn children and their mothers, and its development over time
DOI: 10.6084/m9.figshare.4095312.v1
title: Neonatal microbiota can be classified into two distinct settler types with different development over time

description: Dataset containing raw data of intestinal microbiota composition of 77 newborn children and their mothers, and its development over time
DOI: 10.7910/dvn/v1rjpf/xbij6o
title: cbb20170527_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4094424
title: PowerPoint Slides for: Patiromer Decreases Serum Potassium and Phosphate Levels in Patients on Hemodialysis

description: <b><i>Background:</i></b> Persistent hyperkalemia (serum potassium (K) ≥5.5 mEq/l) is a common condition in hemodialysis (HD) patients, is associated with increased mortality, and treatment options are limited. The effect of patiromer, a gastrointestinal K binder, on serum K was examined in HD patients. <b><i>Methods:</i></b> Six hyperkalemic HD patients (5 anuric) were admitted to clinical research units for 15 days (1 pretreatment week and 1 patiromer treatment week) and they received a controlled diet with identical meals on corresponding days of pretreatment and treatment weeks. Phosphate (P) binders were discontinued on admission. Patiromer, 12.6 g daily (divided 4.2 g TID with meals), was started on the Monday morning following the last pretreatment week blood sampling. Serum and 24-hour stool samples were collected daily. <b><i>Results:</i></b> Mean ± SE serum K decreased (maximum change per corresponding day, 0.6 ± 0.2 mEq/l, p = 0.009) and fecal K increased 58% on patiromer compared with the pretreatment week. During the pretreatment week, 69.0, 47.6, and 11.9% of patients' serum K values were ≥5.5, ≥6.0, and ≥6.5 mEq/l, respectively. This was reduced to 38.1% (p = 0.009), 11.9% (p &lt; 0.001), and 2.4% (p = 0.2) on patiromer. Following P binder discontinuation, the long interdialytic interval mean ± SE serum P numerically increased from 5.8 ± 0.4 to 7.0 ± 0.5 mg/dl (p = 0.06). On patiromer, P decreased from 7.0 ± 0.5 to 6.2 ± 0.5 mg/dl (p = 0.04). While on patiromer, fecal P numerically increased by 112 ± 72 mg/day (17%; p = 0.1792; range -148 to 344 mg/day). No patient discontinued patiromer because of adverse events (AEs); none had serious AEs. <b><i>Conclusions:</i></b> In 6 hyperkalemic HD patients, patiromer decreased serum K and P levels and increased fecal K.
DOI: 10.6084/m9.figshare.4094436.v2
title: Supplementary Data

description: Supplementary Data for the article "Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia"
DOI: 10.6084/m9.figshare.4094436.v1
title: TableS5_v2_MGEN-D-16-00060.xlsx

description: Distribution of the pan-genome genes according to Roary version 3.2.4.
DOI: 10.7910/dvn/v1rjpf/my6sav
title: cbb20171016_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4094424.v1
title: PowerPoint Slides for: Patiromer Decreases Serum Potassium and Phosphate Levels in Patients on Hemodialysis

description: <b><i>Background:</i></b> Persistent hyperkalemia (serum potassium (K) ≥5.5 mEq/l) is a common condition in hemodialysis (HD) patients, is associated with increased mortality, and treatment options are limited. The effect of patiromer, a gastrointestinal K binder, on serum K was examined in HD patients. <b><i>Methods:</i></b> Six hyperkalemic HD patients (5 anuric) were admitted to clinical research units for 15 days (1 pretreatment week and 1 patiromer treatment week) and they received a controlled diet with identical meals on corresponding days of pretreatment and treatment weeks. Phosphate (P) binders were discontinued on admission. Patiromer, 12.6 g daily (divided 4.2 g TID with meals), was started on the Monday morning following the last pretreatment week blood sampling. Serum and 24-hour stool samples were collected daily. <b><i>Results:</i></b> Mean ± SE serum K decreased (maximum change per corresponding day, 0.6 ± 0.2 mEq/l, p = 0.009) and fecal K increased 58% on patiromer compared with the pretreatment week. During the pretreatment week, 69.0, 47.6, and 11.9% of patients' serum K values were ≥5.5, ≥6.0, and ≥6.5 mEq/l, respectively. This was reduced to 38.1% (p = 0.009), 11.9% (p &lt; 0.001), and 2.4% (p = 0.2) on patiromer. Following P binder discontinuation, the long interdialytic interval mean ± SE serum P numerically increased from 5.8 ± 0.4 to 7.0 ± 0.5 mg/dl (p = 0.06). On patiromer, P decreased from 7.0 ± 0.5 to 6.2 ± 0.5 mg/dl (p = 0.04). While on patiromer, fecal P numerically increased by 112 ± 72 mg/day (17%; p = 0.1792; range -148 to 344 mg/day). No patient discontinued patiromer because of adverse events (AEs); none had serious AEs. <b><i>Conclusions:</i></b> In 6 hyperkalemic HD patients, patiromer decreased serum K and P levels and increased fecal K.
DOI: 10.7910/dvn/v1rjpf/eixfly
title: cbb20170112_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dqwwn8
title: cbb20170203_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/aqnlug
title: cbb20170810_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/t6icmq
title: cbb20171025_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4093170
title: Evaluation of molecular brain changes associated with environmental stress in rodent models compared to human major depressive disorder: A proteomic systems approach

description: <b>Objectives:</b> Rodent models of major depressive disorder (MDD) are indispensable when screening for novel treatments, but assessing their translational relevance with human brain pathology has proved difficult. <b>Methods:</b> Using a novel systems approach, proteomics data obtained from post-mortem MDD anterior prefrontal cortex tissue (<i>n</i> = 12) and matched controls (<i>n</i> = 23) were compared with equivalent data from three commonly used preclinical models exposed to environmental stressors (chronic mild stress, prenatal stress and social defeat). Functional pathophysiological features associated with depression-like behaviour were identified in these models through enrichment of protein–protein interaction networks. A cross-species comparison evaluated which model(s) represent human MDD pathology most closely. <b>Results:</b> Seven functional domains associated with MDD and represented across at least two models such as “carbohydrate metabolism and cellular respiration” were identified. Through statistical evaluation using kernel-based machine learning techniques, the social defeat model was found to represent MDD brain changes most closely for four of the seven domains. <b>Conclusions:</b> This is the first study to apply a method for directly evaluating the relevance of the molecular pathology of multiple animal models to human MDD on the functional level. The methodology and findings outlined here could help to overcome translational obstacles of preclinical psychiatric research.
DOI: 10.7910/dvn/v1rjpf/jxjlgh
title: cbb20170409_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4093170.v2
title: Evaluation of molecular brain changes associated with environmental stress in rodent models compared to human major depressive disorder: A proteomic systems approach

description: <b>Objectives:</b> Rodent models of major depressive disorder (MDD) are indispensable when screening for novel treatments, but assessing their translational relevance with human brain pathology has proved difficult. <b>Methods:</b> Using a novel systems approach, proteomics data obtained from post-mortem MDD anterior prefrontal cortex tissue (<i>n</i> = 12) and matched controls (<i>n</i> = 23) were compared with equivalent data from three commonly used preclinical models exposed to environmental stressors (chronic mild stress, prenatal stress and social defeat). Functional pathophysiological features associated with depression-like behaviour were identified in these models through enrichment of protein–protein interaction networks. A cross-species comparison evaluated which model(s) represent human MDD pathology most closely. <b>Results:</b> Seven functional domains associated with MDD and represented across at least two models such as “carbohydrate metabolism and cellular respiration” were identified. Through statistical evaluation using kernel-based machine learning techniques, the social defeat model was found to represent MDD brain changes most closely for four of the seven domains. <b>Conclusions:</b> This is the first study to apply a method for directly evaluating the relevance of the molecular pathology of multiple animal models to human MDD on the functional level. The methodology and findings outlined here could help to overcome translational obstacles of preclinical psychiatric research.
DOI: 10.7910/dvn/v1rjpf/q9rdqi
title: cbb20171022_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4093170.v1
title: Evaluation of molecular brain changes associated with environmental stress in rodent models compared to human major depressive disorder: a proteomic systems approach

description: <b>Objectives</b>: Rodent models of major depressive disorder (MDD) are indispensable when screening for novel treatments, but assessing their translational relevance with human brain pathology has proved difficult. <b>Methods:</b> Using a novel systems approach, proteomics data obtained from post-mortem MDD anterior prefrontal cortex tissue (n =12) and matched controls (n = 23) were compared with equivalent data from three commonly used preclinical models exposed to environmental stressors (chronic mild stress, prenatal stress, social defeat). Functional pathophysiological features associated with depression-like behaviour were identified in these models through enrichment of protein-protein interaction networks. A cross-species comparison evaluated which model(s) represent human MDD pathology most closely. <b>Results</b>: Seven functional domains associated with MDD and represented across at least two models such as “carbohydrate metabolism and cellular respiration” were identified. Through statistical evaluation using kernel-based machine learning techniques, the social defeat model was found to represent MDD brain changes most closely for four of the seven domains. <b>Conclusions</b>: This is the first study to apply a method for directly evaluating the relevance of the molecular pathology of multiple animal models to human MDD on the functional level. The methodology and findings outlined here could help to overcome translational obstacles of preclinical psychiatric research.
DOI: 10.6084/m9.figshare.4091505
title: PowerPoint Slides for: Cardiac Hepcidin Expression Associates with Injury Independent of Iron

description: <b><i>Background:</i></b> Hepcidin regulates systemic iron homeostasis by downregulating the iron exporter ferroportin. Circulating hepcidin is mainly derived from the liver but hepcidin is also produced in the heart. We studied the differential and local regulation of hepcidin gene expression in response to myocardial infarction (MI) and/or chronic kidney disease (CKD). We hypothesized that cardiac hepcidin gene expression is induced by and regulated to severity of cardiac injury, either through direct (MI) or remote (CKD) stimuli, as well as through increased local iron content. <b><i>Methods:</i></b> Nine weeks after subtotal nephrectomy (SNX) or sham surgery (CON), rats were subjected to coronary ligation (CL) or sham surgery to realize 4 groups: CON, SNX, CL and SNX + CL. In week 16, the gene expression of hepcidin, iron and damage markers in cardiac and liver tissues was assessed by quantitative polymerase chain reaction and ferritin protein expression was studied by immunohistochemistry. <b><i>Results:</i></b> Cardiac hepcidin messenger RNA (mRNA) expression was increased 2-fold in CL (p = 0.03) and 3-fold in SNX (p = 0.01). Cardiac ferritin staining was not different among groups. Cardiac hepcidin mRNA expression correlated with mRNA expression levels of brain natriuretic peptide (β = 0.734, p &lt; 0.001) and connective tissue growth factor (β = 0.431, p = 0.02). In contrast, liver hepcidin expression was unaffected by SNX and CL alone, while it had decreased 50% in SNX + CL (p &lt; 0.05). Hepatic ferritin immunostaining was not different among groups. <b><i>Conclusions:</i></b> Our data indicate differences in hepcidin regulation in liver and heart and suggest a role for injury rather than iron as the driving force for cardiac hepcidin expression in renocardiac failure.
DOI: 10.6084/m9.figshare.4091505.v1
title: PowerPoint Slides for: Cardiac Hepcidin Expression Associates with Injury Independent of Iron

description: <b><i>Background:</i></b> Hepcidin regulates systemic iron homeostasis by downregulating the iron exporter ferroportin. Circulating hepcidin is mainly derived from the liver but hepcidin is also produced in the heart. We studied the differential and local regulation of hepcidin gene expression in response to myocardial infarction (MI) and/or chronic kidney disease (CKD). We hypothesized that cardiac hepcidin gene expression is induced by and regulated to severity of cardiac injury, either through direct (MI) or remote (CKD) stimuli, as well as through increased local iron content. <b><i>Methods:</i></b> Nine weeks after subtotal nephrectomy (SNX) or sham surgery (CON), rats were subjected to coronary ligation (CL) or sham surgery to realize 4 groups: CON, SNX, CL and SNX + CL. In week 16, the gene expression of hepcidin, iron and damage markers in cardiac and liver tissues was assessed by quantitative polymerase chain reaction and ferritin protein expression was studied by immunohistochemistry. <b><i>Results:</i></b> Cardiac hepcidin messenger RNA (mRNA) expression was increased 2-fold in CL (p = 0.03) and 3-fold in SNX (p = 0.01). Cardiac ferritin staining was not different among groups. Cardiac hepcidin mRNA expression correlated with mRNA expression levels of brain natriuretic peptide (β = 0.734, p &lt; 0.001) and connective tissue growth factor (β = 0.431, p = 0.02). In contrast, liver hepcidin expression was unaffected by SNX and CL alone, while it had decreased 50% in SNX + CL (p &lt; 0.05). Hepatic ferritin immunostaining was not different among groups. <b><i>Conclusions:</i></b> Our data indicate differences in hepcidin regulation in liver and heart and suggest a role for injury rather than iron as the driving force for cardiac hepcidin expression in renocardiac failure.
DOI: 10.7910/dvn/v1rjpf/ajqnut
title: cbb20170806_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4091502
title: Probing the interaction of thionine with human serum albumin by multispectroscopic studies and its <i>in vitro</i> cytotoxic activity toward MCF-7 breast cancer cells

description: The studies on protein–dye interactions are important in biological process and it is regarded as vital step in rational drug design. The interaction of thionine (TH) with human serum albumin (HSA) was analyzed using isothermal titration calorimetry (ITC), spectroscopic, and molecular docking technique. The emission spectral titration of HSA with TH revealed the formation of HSA–TH complex <i>via</i> static quenching process. The results obtained from absorption, synchronous emission, circular dichroism, and three-dimensional (3D) emission spectral studies demonstrated that TH induces changes in the microenvironment and secondary structure of HSA. Results from ITC experiments suggested that the binding of TH dye was favored by negative enthalpy and a favorable entropy contribution. Site marker competitive binding experiments revealed that the binding site of TH was located in subdomain IIA (Sudlow site I) of HSA. Molecular docking study further substantiates that TH binds to the hydrophobic cavity of subdomain IIA (Sudlow site I) of HSA. Further, we have studied the cytotoxic activity of TH and TH–HSA complex on breast cancer cell lines (MCF-7) by MTT assay and LDH assay. These studies revealed that TH–HSA complex showed the higher level of cytotoxicity in cancer cells than TH dye-treated MCF-7 cells and the significant adverse effect did not found in the normal HBL-100 cells. Fluorescence microscopy analyses of nuclear fragmentation studies validate the significant reduction of viability of TH–HSA-treated human MCF-7 breast cancer cells through activation of apoptotic-mediated pathways.
DOI: 10.7910/dvn/v1rjpf/dqgnie
title: cbb20170904_03.txt.gz

description: :unav