cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1255028.v2
title: Cell line differences in replication timing of human glutamate receptor genes and other large genes associated with neural disease

description: There is considerable current interest in the function of epigenetic mechanisms in neuroplasticity with regard to learning and memory formation and to a range of neural diseases. Previously, we described replication timing on human chromosome 21q in the THP-1 human cell line (2n = 46, XY) and showed that several genes associated with neural diseases, such as the neuronal glutamate receptor subunit GluR-5 (<i>GRIK1</i>) and amyloid precursor protein (<i>APP</i>), were located in regions where replication timing transitioned from early to late S phase. Here, we compared replication timing of all known human glutamate receptor genes (26 genes in total) and <i>APP</i> in 6 different human cell lines including human neuron-related cell lines. Replication timings were obtained by integrating our previously reported data with new data generated here and information from the online database ReplicationDomain. We found that many of the glutamate receptor genes were clearly located in replication timing transition zones in neural precursor cells, but this relationship was less clear in embryonic stem cells before neural differentiation; in the latter, the genes were often located in later replication timing zones that displayed DNA hypermethylation. Analysis of selected large glutamate receptor genes (&gt;200 kb), and of <i>APP</i>, showed that their precise replication timing patterns differed among the cell lines. We propose that the transition zones of DNA replication timing are altered by epigenetic mechanisms, and that these changes may affect the neuroplasticity that is important to memory and learning, and may also have a role in the development of neural diseases.
DOI: 10.6084/m9.figshare.1255023
title: A comparison of DNA methylation specific droplet digital PCR (ddPCR) and real time qPCR with flow cytometry in characterizing human T cells in peripheral blood

description: Quantitating the copy number of demethylated CpG promoter sites of the CD3Z gene can be used to estimate the numbers and proportions of T cells in human blood and tissue. Quantitative methylation specific PCR (qPCR) is useful for studying T cells but requires extensive calibration and is imprecise at low copy numbers. Here we compared the performance of a new digital PCR platform (droplet digital PCR or ddPCR) to qPCR using bisulfite converted DNA from 157 blood specimens obtained from ambulatory care controls and patients with primary glioma. We compared both ddPCR and qPCR with conventional flow cytometry (FACS) evaluation of CD3 positive T cells. Repeated measures on the same blood sample revealed ddPCR to be less variable than qPCR. Both qPCR and ddPCR correlated significantly with FACS evaluation of peripheral blood CD3 counts and CD3/total leukocyte values. However, statistical measures of agreement showed that linear concordance was stronger for ddPCR than for qPCR and the absolute values were closer to FACS for ddPCR. Both qPCR and ddPCR could distinguish clinically significant differences in T cell proportions and performed similarly to FACS. Given the higher precision, greater accuracy, and technical simplicity of ddPCR, this approach appears to be a superior DNA methylation based method than conventional qPCR for the assessment of T cells.
DOI: 10.6084/m9.figshare.1255024.v1
title: Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation

description: Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis <i>P</i> &lt; 5 × 10<sup>−8</sup>. All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at <i>CPOX</i> near <i>GPR15.</i> In addition, we found 6 new loci at <i>PRSS23</i>, <i>AVPR1B</i>, <i>PSEN2</i>, <i>LINC00299</i>, <i>RPS6KA2,</i> and <i>KIAA0087.</i> Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or / and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the <i>CHRND</i> gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
DOI: 10.6084/m9.figshare.1255023.v1
title: A comparison of DNA methylation specific droplet digital PCR (ddPCR) and real time qPCR with flow cytometry in characterizing human T cells in peripheral blood

description: Quantitating the copy number of demethylated CpG promoter sites of the CD3Z gene can be used to estimate the numbers and proportions of T cells in human blood and tissue. Quantitative methylation specific PCR (qPCR) is useful for studying T cells but requires extensive calibration and is imprecise at low copy numbers. Here we compared the performance of a new digital PCR platform (droplet digital PCR or ddPCR) to qPCR using bisulfite converted DNA from 157 blood specimens obtained from ambulatory care controls and patients with primary glioma. We compared both ddPCR and qPCR with conventional flow cytometry (FACS) evaluation of CD3 positive T cells. Repeated measures on the same blood sample revealed ddPCR to be less variable than qPCR. Both qPCR and ddPCR correlated significantly with FACS evaluation of peripheral blood CD3 counts and CD3/total leukocyte values. However, statistical measures of agreement showed that linear concordance was stronger for ddPCR than for qPCR and the absolute values were closer to FACS for ddPCR. Both qPCR and ddPCR could distinguish clinically significant differences in T cell proportions and performed similarly to FACS. Given the higher precision, greater accuracy, and technical simplicity of ddPCR, this approach appears to be a superior DNA methylation based method than conventional qPCR for the assessment of T cells.
DOI: 10.6084/m9.figshare.1255024.v3
title: Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation

description: Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis <i>P</i> &lt; 5 × 10<sup>−8</sup>. All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at <i>CPOX</i> near <i>GPR15.</i> In addition, we found 6 new loci at <i>PRSS23</i>, <i>AVPR1B</i>, <i>PSEN2</i>, <i>LINC00299</i>, <i>RPS6KA2,</i> and <i>KIAA0087.</i> Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or / and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the <i>CHRND</i> gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
DOI: 10.6084/m9.figshare.1255017
title: LTSTM data October 2003

description: This is low temperature STM data from October 2003.
DOI: 10.6084/m9.figshare.1255017.v1
title: LTSTM data October 2003

description: This is low temperature STM data from October 2003.
DOI: 10.6084/m9.figshare.1255023.v3
title: A comparison of DNA methylation specific droplet digital PCR (ddPCR) and real time qPCR with flow cytometry in characterizing human T cells in peripheral blood

description: Quantitating the copy number of demethylated CpG promoter sites of the CD3Z gene can be used to estimate the numbers and proportions of T cells in human blood and tissue. Quantitative methylation specific PCR (qPCR) is useful for studying T cells but requires extensive calibration and is imprecise at low copy numbers. Here we compared the performance of a new digital PCR platform (droplet digital PCR or ddPCR) to qPCR using bisulfite converted DNA from 157 blood specimens obtained from ambulatory care controls and patients with primary glioma. We compared both ddPCR and qPCR with conventional flow cytometry (FACS) evaluation of CD3 positive T cells. Repeated measures on the same blood sample revealed ddPCR to be less variable than qPCR. Both qPCR and ddPCR correlated significantly with FACS evaluation of peripheral blood CD3 counts and CD3/total leukocyte values. However, statistical measures of agreement showed that linear concordance was stronger for ddPCR than for qPCR and the absolute values were closer to FACS for ddPCR. Both qPCR and ddPCR could distinguish clinically significant differences in T cell proportions and performed similarly to FACS. Given the higher precision, greater accuracy, and technical simplicity of ddPCR, this approach appears to be a superior DNA methylation based method than conventional qPCR for the assessment of T cells.
DOI: 10.6084/m9.figshare.1255005
title: A Yeast Cell Cycle Data

description: This is a yeast cell cycle data downloaded at http : ==gasch:genetics:wisc:edu
DOI: 10.6084/m9.figshare.1255023.v2
title: A comparison of DNA methylation specific droplet digital PCR (ddPCR) and real time qPCR with flow cytometry in characterizing human T cells in peripheral blood

description: Quantitating the copy number of demethylated CpG promoter sites of the CD3Z gene can be used to estimate the numbers and proportions of T cells in human blood and tissue. Quantitative methylation specific PCR (qPCR) is useful for studying T cells but requires extensive calibration and is imprecise at low copy numbers. Here we compared the performance of a new digital PCR platform (droplet digital PCR or ddPCR) to qPCR using bisulfite converted DNA from 157 blood specimens obtained from ambulatory care controls and patients with primary glioma. We compared both ddPCR and qPCR with conventional flow cytometry (FACS) evaluation of CD3 positive T cells. Repeated measures on the same blood sample revealed ddPCR to be less variable than qPCR. Both qPCR and ddPCR correlated significantly with FACS evaluation of peripheral blood CD3 counts and CD3/total leukocyte values. However, statistical measures of agreement showed that linear concordance was stronger for ddPCR than for qPCR and the absolute values were closer to FACS for ddPCR. Both qPCR and ddPCR could distinguish clinically significant differences in T cell proportions and performed similarly to FACS. Given the higher precision, greater accuracy, and technical simplicity of ddPCR, this approach appears to be a superior DNA methylation based method than conventional qPCR for the assessment of T cells.
DOI: 10.6084/m9.figshare.1255024.v2
title: Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation

description: Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis <i>P</i> &lt; 5 × 10<sup>−8</sup>. All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at <i>CPOX</i> near <i>GPR15.</i> In addition, we found 6 new loci at <i>PRSS23</i>, <i>AVPR1B</i>, <i>PSEN2</i>, <i>LINC00299</i>, <i>RPS6KA2,</i> and <i>KIAA0087.</i> Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or / and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the <i>CHRND</i> gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
DOI: 10.6084/m9.figshare.1254988
title: HTDE 2012 Workshop Interviews

description: Interview Presentations for HTDE 2012 Workshop.
DOI: 10.6084/m9.figshare.1254985
title: HTDE 2012 Workshop Talk Abstracts

description: Talk abstracts from HTDE 2012 Workshop.
DOI: 10.6084/m9.figshare.1254988.v1
title: HTDE 2012 Workshop Interviews

description: Interview Presentations for HTDE 2012 Workshop.
DOI: 10.6084/m9.figshare.1254993
title: HTDE 2012 Workshop Lectures

description: Lectures from the HTDE 2012 Workshop.
DOI: 10.6084/m9.figshare.1254993.v1
title: HTDE 2012 Workshop Lectures

description: Lectures from the HTDE 2012 Workshop.
DOI: 10.6084/m9.figshare.1254985.v2
title: HTDE 2012 Workshop Talk Abstracts

description: Talk abstracts from HTDE 2012 Workshop.
DOI: 10.6084/m9.figshare.1254985.v1
title: HTDE 2012 Talk Abstracts

description: Talk abstracts from HTDE 2012 Conference
DOI: 10.6084/m9.figshare.1254959
title: Radiolytic Treatment of the Next-Generation Caustic-Side Solvent Extraction (NGS) Solvent and its Effect on the NGS Process

description: It is shown in this work that the solvent used in the Next Generation Caustic-Side Solvent Extraction (NGS) process can withstand a radiation dose well in excess of the dose it would receive in multiple years of treating legacy salt waste at the US Department of Energy Savannah River Site. The solvent was subjected to a maximum of 50 kGy of gamma radiation while in dynamic contact with each of the aqueous phases of the current NGS process, namely SRS−15 (a highly caustic waste simulant), sodium hydroxide scrub solution (0.025 M), and boric acid strip solution (0.01 M). Bench-top testing of irradiated solvent confirmed that irradiation has inconsequential impact on the extraction, scrubbing, and stripping performance of the solvent up to 13 times the estimated 0.73 kGy/y annual absorbed dose. Stripping performance is the most sensitive step to radiation, deteriorating more due to buildup of p-sec-butylphenol (SBP) and possibly other proton-ionizable products than to degradation of the guanidine suppressor, as shown by chemical analyses.
DOI: 10.6084/m9.figshare.1254959.v2
title: Radiolytic Treatment of the Next-Generation Caustic-Side Solvent Extraction (NGS) Solvent and its Effect on the NGS Process

description: It is shown in this work that the solvent used in the Next Generation Caustic-Side Solvent Extraction (NGS) process can withstand a radiation dose well in excess of the dose it would receive in multiple years of treating legacy salt waste at the US Department of Energy Savannah River Site. The solvent was subjected to a maximum of 50 kGy of gamma radiation while in dynamic contact with each of the aqueous phases of the current NGS process, namely SRS−15 (a highly caustic waste simulant), sodium hydroxide scrub solution (0.025 M), and boric acid strip solution (0.01 M). Bench-top testing of irradiated solvent confirmed that irradiation has inconsequential impact on the extraction, scrubbing, and stripping performance of the solvent up to 13 times the estimated 0.73 kGy/y annual absorbed dose. Stripping performance is the most sensitive step to radiation, deteriorating more due to buildup of p-sec-butylphenol (SBP) and possibly other proton-ionizable products than to degradation of the guanidine suppressor, as shown by chemical analyses.
DOI: 10.6084/m9.figshare.1254959.v1
title: Radiolytic Treatment of the Next-Generation Caustic-Side Solvent Extraction (NGS) Solvent and its Effect on the NGS Process

description: It is shown in this work that the solvent used in the Next Generation Caustic-Side Solvent Extraction (NGS) process can withstand a radiation dose well in excess of the dose it would receive in multiple years of treating legacy salt waste at the US Department of Energy Savannah River Site. The solvent was subjected to a maximum of 50 kGy of gamma radiation while in dynamic contact with each of the aqueous phases of the current NGS process, namely SRS−15 (a highly caustic waste simulant), sodium hydroxide scrub solution (0.025 M), and boric acid strip solution (0.01 M). Bench-top testing of irradiated solvent confirmed that irradiation has inconsequential impact on the extraction, scrubbing, and stripping performance of the solvent up to 13 times the estimated 0.73 kGy/y annual absorbed dose. Stripping performance is the most sensitive step to radiation, deteriorating more due to buildup of p-sec-butylphenol (SBP) and possibly other proton-ionizable products than to degradation of the guanidine suppressor, as shown by chemical analyses.
DOI: 10.6084/m9.figshare.1254928
title: Synthesis, Crystal Structure, and Properties of Two 2D Lamella Coordination Polymers Generated from Unsymmetrically Carboxylate Bridging Ligand

description: Self-assembly between simple unsymmetrical ligands, such as h<sub>2</sub>epda (5-ethyl-pyridine-2,3-dcarboxylic acid) and H<sub>2</sub>hmph(homophthalic acid) and two transition metals produce two new 2D lamella coordination polymers [Cu(hedpa)<sub>2</sub>]<sub>n</sub><b>1</b> and [Co(hmph)(bpe)]<sub>n</sub><b>2</b> (bpe = 1,2-di(4-pyridyl)ethylene), respectively. The 2D lamella structure of <b>2</b> features hmph-bridged binuclear cobalt(II) chains joined by less flexible trans-bpe ligands, whereas the 2D layer of <b>1</b> manifests that unsymmetrical ligand h<sub>2</sub>epda directly bridges mononuclear copper(II) running along the <i>bc</i> plane. The thermogravimetric (TG) reveal that both compounds are stable. Magnetic measurements show that complex <b>2</b> exhibits global metamagnetic behaviors.
DOI: 10.6084/m9.figshare.1254928.v2
title: Synthesis, Crystal Structure, and Properties of Two 2D Lamella Coordination Polymers Generated from Unsymmetrically Carboxylate Bridging Ligand

description: Self-assembly between simple unsymmetrical ligands, such as h<sub>2</sub>epda (5-ethyl-pyridine-2,3-dcarboxylic acid) and H<sub>2</sub>hmph(homophthalic acid) and two transition metals produce two new 2D lamella coordination polymers [Cu(hedpa)<sub>2</sub>]<sub>n</sub><b>1</b> and [Co(hmph)(bpe)]<sub>n</sub><b>2</b> (bpe = 1,2-di(4-pyridyl)ethylene), respectively. The 2D lamella structure of <b>2</b> features hmph-bridged binuclear cobalt(II) chains joined by less flexible trans-bpe ligands, whereas the 2D layer of <b>1</b> manifests that unsymmetrical ligand h<sub>2</sub>epda directly bridges mononuclear copper(II) running along the <i>bc</i> plane. The thermogravimetric (TG) reveal that both compounds are stable. Magnetic measurements show that complex <b>2</b> exhibits global metamagnetic behaviors.
DOI: 10.6084/m9.figshare.1254928.v1
title: Synthesis, Crystal Structure, and Properties of Two 2D lamella Coordination Polymers Generated from Unsymmetrically Carboxylate Bridging Ligand

description: Self-assembly between simple unsymmetrical ligands, such as h<sub>2</sub>epda (5-ethyl-pyridine-2,3-dcarboxylic acid) and H<sub>2</sub>hmph(homophthalic acid) and two transition metals produce two new 2D lamella coordination polymers [Cu(hedpa)<sub>2</sub>]<sub>n</sub><b>1</b> and [Co(hmph)(bpe)]<sub>n</sub><b>2</b> (bpe = 1,2-di(4-pyridyl)ethylene), respectively. The 2D lamella structure of <b>2</b> features hmph-bridged binuclear cobalt(II) chains joined by less flexible trans-bpe ligands, whereas the 2D layer of <b>1</b> manifests that unsymmetrical ligand h<sub>2</sub>epda directly bridges mononuclear copper(II) running along the bc plane. The thermogravimetric (TG) reveal that both compounds are stable. Magnetic measurements show that complex <b>2</b> exhibits global metamagnetic behaviors.
DOI: 10.6084/m9.figshare.1254927.v2
title: Energy Density Functionals From the Strong-Interaction Limit of Density Functional Theory

description: Dissertation Thesis, VU University Amsterdam, 2014 Monography on: - electronic structure problem, focus DFT - strictly correlated electrons concept - functional approximations by interpolations on the local energy density - KS-SCE method with pilot applications - the derivative discontinuity of the SCE functional - SCE functional applied to the Hydrogen anion
DOI: 10.6084/m9.figshare.1254927.v3
title: Energy Density Functionals From the Strong-Interaction Limit of Density Functional Theory

description: Dissertation Thesis, VU University Amsterdam, 2014 Monography on: - electronic structure problem, focus DFT - strictly correlated electrons concept - functional approximations by interpolations on the local energy density - KS-SCE method with pilot applications - the derivative discontinuity of the SCE functional - SCE functional applied to the Hydrogen anion