cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127418
title: Supplementary Material for: M235T Polymorphism in the <b><i>AGT</i></b> Gene and A/G<sup>I8-83</sup> Substitution in the <b><i>REN</i></b> Gene Correlate with End-Stage Renal Disease

description: <b><i>Background/Aims:</i></b> This study aimed at investigating if M235T polymorphism in the AGT gene and A/G<sup>I8-83</sup> polymorphism in the REN gene correlate with end-stage renal disease (ESRD). <b><i>Methods:</i></b> We analyzed 173 ESRD patients and 329 individuals with normal kidney function for differences in the genotype distribution of AGT-M235T and REN-A/G<sup>I8-83</sup> polymorphisms between the two groups. The data for cases and controls were compared using the χ<sup>2</sup> test. <b><i>Results:</i></b> We found significantly higher levels of serum creatinine and CRP in cases in comparison to controls (p &lt; 0.0001). Data comparison showed a significant association of AGT M235T substitution with ESRD in the dominant model (p = 0.008) and in the comparison of the heterozygous substitution with the homozygous common genotype (p = 0.005). Similarly, REN A/G<sup>I8-83</sup> polymorphism showed a significant difference in the distribution of genotypes between cases and controls (p &lt; 0.038) such that a heterozygous substitution was significantly more common in the ESRD cases in comparison to the homozygous common genotype (p = 0.023). <b><i>Conclusion:</i></b> We conclude that heterozygous substitutions at the AGT M235T and REN A/G<sup>I8-83</sup> loci correlate significantly with ESRD in a north Indian population.
DOI: 10.6084/m9.figshare.5127421
title: Supplementary Material for: Sterol Regulatory Element Binding Transcription Factor-1 Gene Variation and Medication Load Influence White Matter Structure in Schizophrenia

description: <b><i>Background:</i></b> Diffusion tensor imaging (DTI) studies have shown a widespread disruption of white matter (WM) microstructure in schizophrenia. Furthermore, higher fractional anisotropy (FA) has been consistently correlated with the severity of psychotic symptoms. Antipsychotic drugs (APDs) affect lipid homeostasis. Gene polymorphisms in sterol regulatory element binding transcription factor (SREBF)-1 and SREBF-2 have been associated with schizophrenia. <b><i>Methods:</i></b> In a sample of 65 patients affected by chronic schizophrenia, we investigated the effect of ongoing APD medication, SREBF-1 rs11868035<b> </b>polymorphism and SREBF-2 rs1052717 polymorphism on the WM microstructure, using tract-based spatial statistics with threshold-free cluster enhancement. <b><i>Results:</i></b> We reported increased FA associated with the risk rs11868035<b> </b>G/G genotype in several WM tracts, mainly located in the left hemisphere, and opposite effects of the APD medication load, with reduced FA and generally increased diffusivity. These opposite effects overlapped in the forceps minor, cingulum, uncinate fasciculus, the superior and inferior longitudinal fasciculi, the corticospinal tract, inferior fronto-occipital fasciculus and the anterior thalamic radiation. <b><i>Conclusion:</i></b> We suggest that changes of WM structure could be an as yet poorly explored biomarker of the effects of APDs, to be further investigated in prospective studies correlating long-term clinical effects with changes of DTI measures in specific WM tracts contributing to the functional integrity of the brain.
DOI: 10.6084/m9.figshare.5127424
title: Supplementary Material for: Clinical and Molecular Characterization of a Patient with 15q21.2q22.2 Deletion Syndrome

description: We report on a 16-year-old girl with a complex phenotype, including intellectual disability, facial dysmorphisms, and obesity. During her infancy, she presented with weak sucking, global developmental delay, and later with excessive eating with central obesity. The girl was clinically diagnosed with probable Prader-Willi syndrome. Chromosomal analysis showed a de novo deletion 46,XX,del(15)(q21q22). However, the use of the Affymetrix CytoScan HD Array defined the exact breakpoints of the deleted 15q21q22 region. The imbalance, about 10.5 Mb in size, is to date the second largest deletion ever described in this chromosomal region. In addition, our patient carries a microdeletion in the 1q44 region and a gain in 9p24. The array result was arr[hg19] 9p24.1(6,619,823-6,749,335)×3, 1q44(248,688,586-248,795,277)×1, 15q21.2 q22.2(50,848,301-61,298,006)×1. Although our patient presents additional chromosomal alterations, we provide a correlation between the clinical findings and the phenotype of the 15q21 deletion syndrome.
DOI: 10.6084/m9.figshare.5127415
title: Supplementary Material for: Novel Repeated DNAs in the Antarctic Polyplacophoran <b><i>Nuttallochiton</i></b> <b><i>mirandus </i></b>(Thiele, 1906)

description: Within the scope of a project on the characterization of satellite DNAs in polar mollusks, the Antarctic chiton <i>Nuttallochiton</i><i>mirandus</i> (Thiele, 1906) was analyzed. Two novel families of tandemly repeated DNAs, namely NmH and NmP, are described in their structure and chromosomal localization, and, furthermore, their presence was analyzed in related species. Data reported here display a particular variability in the structural organization of DNA satellites within this species. Processes driving satellite evolution, which are likely responsible for the intriguing variability of the identified satellite DNAs, are discussed.
DOI: 10.6084/m9.figshare.5127418.v1
title: Supplementary Material for: M235T Polymorphism in the <b><i>AGT</i></b> Gene and A/G<sup>I8-83</sup> Substitution in the <b><i>REN</i></b> Gene Correlate with End-Stage Renal Disease

description: <b><i>Background/Aims:</i></b> This study aimed at investigating if M235T polymorphism in the AGT gene and A/G<sup>I8-83</sup> polymorphism in the REN gene correlate with end-stage renal disease (ESRD). <b><i>Methods:</i></b> We analyzed 173 ESRD patients and 329 individuals with normal kidney function for differences in the genotype distribution of AGT-M235T and REN-A/G<sup>I8-83</sup> polymorphisms between the two groups. The data for cases and controls were compared using the χ<sup>2</sup> test. <b><i>Results:</i></b> We found significantly higher levels of serum creatinine and CRP in cases in comparison to controls (p &lt; 0.0001). Data comparison showed a significant association of AGT M235T substitution with ESRD in the dominant model (p = 0.008) and in the comparison of the heterozygous substitution with the homozygous common genotype (p = 0.005). Similarly, REN A/G<sup>I8-83</sup> polymorphism showed a significant difference in the distribution of genotypes between cases and controls (p &lt; 0.038) such that a heterozygous substitution was significantly more common in the ESRD cases in comparison to the homozygous common genotype (p = 0.023). <b><i>Conclusion:</i></b> We conclude that heterozygous substitutions at the AGT M235T and REN A/G<sup>I8-83</sup> loci correlate significantly with ESRD in a north Indian population.
DOI: 10.6084/m9.figshare.5127424.v1
title: Supplementary Material for: Clinical and Molecular Characterization of a Patient with 15q21.2q22.2 Deletion Syndrome

description: We report on a 16-year-old girl with a complex phenotype, including intellectual disability, facial dysmorphisms, and obesity. During her infancy, she presented with weak sucking, global developmental delay, and later with excessive eating with central obesity. The girl was clinically diagnosed with probable Prader-Willi syndrome. Chromosomal analysis showed a de novo deletion 46,XX,del(15)(q21q22). However, the use of the Affymetrix CytoScan HD Array defined the exact breakpoints of the deleted 15q21q22 region. The imbalance, about 10.5 Mb in size, is to date the second largest deletion ever described in this chromosomal region. In addition, our patient carries a microdeletion in the 1q44 region and a gain in 9p24. The array result was arr[hg19] 9p24.1(6,619,823-6,749,335)×3, 1q44(248,688,586-248,795,277)×1, 15q21.2 q22.2(50,848,301-61,298,006)×1. Although our patient presents additional chromosomal alterations, we provide a correlation between the clinical findings and the phenotype of the 15q21 deletion syndrome.
DOI: 10.6084/m9.figshare.5127430.v1
title: Supplementary Material for: Correlation of EEG Slowing with Cognitive Domains in Nondemented Patients with Parkinson's Disease

description: <b><i>Background:</i></b> Cognitive deficits in Parkinson's disease (PD) are heterogeneous and can be classified into cognitive domains. Quantitative EEG is related to and predictive of cognitive status in PD. In this cross-sectional study, the relationship of cognitive domains and EEG slowing in PD patients without dementia is investigated. <b><i>Methods:</i></b> A total of 48 patients with idiopathic PD were neuropsychologically tested. Cognitive domain scores were calculated combining Z-scores of test variables. Slowing of EEG was measured with median EEG frequency. Linear regression was used for correlational analyses and to control for confounding factors. <b><i>Results:</i></b> EEG median frequency was significantly correlated to cognitive performance in most domains (episodic long-term memory, rho = 0.54; overall cognitive score, rho = 0.47; fluency, rho = 0.39; attention, rho = 0.37; executive function, rho = 0.34), but not to visuospatial functions and working memory. <b><i>Conclusion:</i></b> Global EEG slowing is a marker for overall cognitive impairment in PD and correlates with impairment in the domains attention, executive function, verbal fluency, and episodic long-term memory, but not with working memory and visuospatial functions. These disparate effects warrant further investigations.
DOI: 10.6084/m9.figshare.5127409
title: Supplementary Material for: The Anti-Inflammatory Effects of the Small Molecule Pifithrin-µ on BV2 Microglia

description: Neonatal encephalopathy (NE) is a leading cause of childhood death and disability in term infants. Treatment options for perinatal brain injury are limited and developing therapies that target multiple pathways within the pathophysiology of NE are of great interest. Pifithrin-µ (PFT-µ) is a drug with striking neuroprotective abilities in a preclinical model of hypoxia-ischemia (HI)-induced NE wherein cell death is a substantial cause of injury. Work from neurons and tumor cells reports that PFT-µ is able to inhibit p53 binding to the mitochondria, heat shock protein (HSP)-70 substrate binding and activation of the NF-kB pathway. The purpose of this study is to understand whether the neuroprotective effects of PFT-µ also include direct effects on microglia. We utilized the microglial cell line, BV2, and we studied the dose-dependent effect of PFT-µ on M1-like and M2-like phenotype using qRT-PCR and Western blotting, including the requirement for the presence of p53 or HSP-70 in these effects. We also assessed phagocytosis and the effects of PFT-µ on genes within metabolic pathways related to phenotype. We noted that PFT-µ robustly reduced the M1-like (lipopolysaccharide, LPS-induced) BV2 response, spared the LPS-induced phagocytic ability of BV2 and had no effect on the genes related to metabolism and that effects on phenotype were partially dependent on the presence of HSP-70 but not p53. This study demonstrates that the neuroprotective effects of PFT-µ in HI-induced NE may include an anti-inflammatory effect on microglia and adds to the evidence that this drug might be of clinical interest for the treatment of NE.
DOI: 10.6084/m9.figshare.5127412
title: Supplementary Material for: Metformin Use in Kidney Transplant Recipients in the United States: An Observational Study

description: <b><i>Background/Aims:</i></b> Although metformin is contraindicated in patients with increased serum creatinine levels (≥1.5 mg/dl in men, ≥1.4 mg/dl in women) in the United States, its use has not been systematically examined in kidney transplant recipients. We aimed to determine the frequency of metformin use and its associations among kidney transplant recipients, and to assess allograft and patient survival associated with metformin use. <b><i>Methods:</i></b> In this retrospective cohort study, we linked Scientific Registry of Transplant Recipients data for all incident kidney transplants 2001-2012 and national pharmacy claims (n = 46,914). We compared recipients having one or more pharmacy claims for a metformin-containing product (n = 4,609) and recipients having one or more claims for a non-metformin glucose-lowering agent (n = 42,305). <b><i>Results:</i></b> On average, metformin claims were filled later after transplant and were associated with higher estimated glomerular filtration rates before the first claim. Median serum creatinine (mg/dl) levels before the first claim were lower in recipients with metformin claims than in those with non-metformin claims (1.3 [interquartile range 1.0-1.7] vs. 1.6 [1.2-2.5], respectively; p &lt; 0.0001). Metformin was associated with lower adjusted hazards for living donor (0.55, 95% confidence interval 0.38-0.80; p = 0.002) and deceased donor (0.55, 0.44-0.70; p &lt; 0.0001) allograft survival at 3 years posttransplant, and with lower mortality. <b><i>Conclusions:</i></b> Despite metformin being contraindicated in renal dysfunction, many kidney transplant recipients receive it, and it is not associated with worse patient or allograft survival.
DOI: 10.6084/m9.figshare.5127421.v1
title: Supplementary Material for: Sterol Regulatory Element Binding Transcription Factor-1 Gene Variation and Medication Load Influence White Matter Structure in Schizophrenia

description: <b><i>Background:</i></b> Diffusion tensor imaging (DTI) studies have shown a widespread disruption of white matter (WM) microstructure in schizophrenia. Furthermore, higher fractional anisotropy (FA) has been consistently correlated with the severity of psychotic symptoms. Antipsychotic drugs (APDs) affect lipid homeostasis. Gene polymorphisms in sterol regulatory element binding transcription factor (SREBF)-1 and SREBF-2 have been associated with schizophrenia. <b><i>Methods:</i></b> In a sample of 65 patients affected by chronic schizophrenia, we investigated the effect of ongoing APD medication, SREBF-1 rs11868035<b> </b>polymorphism and SREBF-2 rs1052717 polymorphism on the WM microstructure, using tract-based spatial statistics with threshold-free cluster enhancement. <b><i>Results:</i></b> We reported increased FA associated with the risk rs11868035<b> </b>G/G genotype in several WM tracts, mainly located in the left hemisphere, and opposite effects of the APD medication load, with reduced FA and generally increased diffusivity. These opposite effects overlapped in the forceps minor, cingulum, uncinate fasciculus, the superior and inferior longitudinal fasciculi, the corticospinal tract, inferior fronto-occipital fasciculus and the anterior thalamic radiation. <b><i>Conclusion:</i></b> We suggest that changes of WM structure could be an as yet poorly explored biomarker of the effects of APDs, to be further investigated in prospective studies correlating long-term clinical effects with changes of DTI measures in specific WM tracts contributing to the functional integrity of the brain.
DOI: 10.6084/m9.figshare.5127406
title: Supplementary Material for: Accuracy of Reporting the Hyperdense Middle Cerebral Artery Sign as a Function of Clinical Experience

description: <b><i>Background/Aim:</i></b> The hyperdense middle cerebral artery sign (HMCAS) is a useful clinical sign in the management of acute stroke and may alter time-critical decisions within an emergency setting. Though gold standards have been published, these are rarely used in clinical practice and scans tend to be reported subjectively. It is therefore possible that the level of experience of the doctor reporting the scan may impact on the accuracy of the reporting and hence patient management. This study was designed to evaluate the accuracy in detecting HMCAS across doctors with varying levels of experience. <b><i>Methods:</i></b> Forty doctors were recruited into four categories of experience. Each subject received a brief computer-based tutorial on how to identify an HMCAS and was then asked to report on the presence or absence of an HMCAS in 19 pre-prepared CT scans using a standardised viewing template. <b><i>Results:</i></b> The mean (±SE) percentage correct scores increased with experience from 76.8 ± 3.69 among interns and residents to 90.1 ± 2.23 (neurologists and radiologists; p &lt; 0.01). Sensitivity and specificity as well as positive and negative predictive values all increased with experience. In addition, more experienced clinicians were better able to distinguish scans which met the radiological criteria for HMCAS from those which only just failed to do so. <b><i>Conclusions:</i></b> Experienced neurologists and radiologists consistently and accurately reported the presence or absence of HMCAS, whereas less experienced clinicians tended to over-report the presence of HMCAS. This may have implications for the acute management of thromboembolic stroke.
DOI: 10.6084/m9.figshare.5127412.v1
title: Supplementary Material for: Metformin Use in Kidney Transplant Recipients in the United States: An Observational Study

description: <b><i>Background/Aims:</i></b> Although metformin is contraindicated in patients with increased serum creatinine levels (≥1.5 mg/dl in men, ≥1.4 mg/dl in women) in the United States, its use has not been systematically examined in kidney transplant recipients. We aimed to determine the frequency of metformin use and its associations among kidney transplant recipients, and to assess allograft and patient survival associated with metformin use. <b><i>Methods:</i></b> In this retrospective cohort study, we linked Scientific Registry of Transplant Recipients data for all incident kidney transplants 2001-2012 and national pharmacy claims (n = 46,914). We compared recipients having one or more pharmacy claims for a metformin-containing product (n = 4,609) and recipients having one or more claims for a non-metformin glucose-lowering agent (n = 42,305). <b><i>Results:</i></b> On average, metformin claims were filled later after transplant and were associated with higher estimated glomerular filtration rates before the first claim. Median serum creatinine (mg/dl) levels before the first claim were lower in recipients with metformin claims than in those with non-metformin claims (1.3 [interquartile range 1.0-1.7] vs. 1.6 [1.2-2.5], respectively; p &lt; 0.0001). Metformin was associated with lower adjusted hazards for living donor (0.55, 95% confidence interval 0.38-0.80; p = 0.002) and deceased donor (0.55, 0.44-0.70; p &lt; 0.0001) allograft survival at 3 years posttransplant, and with lower mortality. <b><i>Conclusions:</i></b> Despite metformin being contraindicated in renal dysfunction, many kidney transplant recipients receive it, and it is not associated with worse patient or allograft survival.
DOI: 10.6084/m9.figshare.5127415.v1
title: Supplementary Material for: Novel Repeated DNAs in the Antarctic Polyplacophoran <b><i>Nuttallochiton</i></b> <b><i>mirandus </i></b>(Thiele, 1906)

description: Within the scope of a project on the characterization of satellite DNAs in polar mollusks, the Antarctic chiton <i>Nuttallochiton</i><i>mirandus</i> (Thiele, 1906) was analyzed. Two novel families of tandemly repeated DNAs, namely NmH and NmP, are described in their structure and chromosomal localization, and, furthermore, their presence was analyzed in related species. Data reported here display a particular variability in the structural organization of DNA satellites within this species. Processes driving satellite evolution, which are likely responsible for the intriguing variability of the identified satellite DNAs, are discussed.
DOI: 10.6084/m9.figshare.5127403
title: Supplementary Material for: Rare Disease Registries Classification and Characterization: A Data Mining Approach

description: <b><i>Background:</i></b> The European Commission and Patients Organizations identify rare disease registries (RDRs) as strategic instruments to develop research and improve knowledge in the field of rare diseases. Interoperability between RDRs is needed for research activities, validation of therapeutic treatments, and public health actions. Sharing and comparing information requires a uniform and standardized way of data collection, so levels of interconnection between RDRs with similar aims and/or nature of data should be identified. The objective of this study is to define a classification and characterization of RDRs in order to identify different profiles and informative needs. <b><i>Methods:</i></b> Exploratory statistical analyses (cluster analysis and random forest) were applied to data derived from the EPIRARE project (‘Building Consensus and Synergies for the EU Rare Disease Patient Registration') survey on the activities and needs of RDRs. <b><i>Results:</i></b> The cluster analysis identified 3 main typologies of RDRs: public health, clinical and genetic research, and treatment registries. The analysis of the most informative variables, identified by the random forest method, led to the characterization of 3 types of RDRs and the definition of different profiles and informative needs. <b><i>Conclusions:</i></b> These results represent a useful source of information to facilitate the harmonization and interconnection of RDRs in accordance with the different profiles identified. It could help sharing the information between RDRs with similar profiles and, whenever possible, interconnections between registries with different profiles.
DOI: 10.6084/m9.figshare.5127409.v1
title: Supplementary Material for: The Anti-Inflammatory Effects of the Small Molecule Pifithrin-µ on BV2 Microglia

description: Neonatal encephalopathy (NE) is a leading cause of childhood death and disability in term infants. Treatment options for perinatal brain injury are limited and developing therapies that target multiple pathways within the pathophysiology of NE are of great interest. Pifithrin-µ (PFT-µ) is a drug with striking neuroprotective abilities in a preclinical model of hypoxia-ischemia (HI)-induced NE wherein cell death is a substantial cause of injury. Work from neurons and tumor cells reports that PFT-µ is able to inhibit p53 binding to the mitochondria, heat shock protein (HSP)-70 substrate binding and activation of the NF-kB pathway. The purpose of this study is to understand whether the neuroprotective effects of PFT-µ also include direct effects on microglia. We utilized the microglial cell line, BV2, and we studied the dose-dependent effect of PFT-µ on M1-like and M2-like phenotype using qRT-PCR and Western blotting, including the requirement for the presence of p53 or HSP-70 in these effects. We also assessed phagocytosis and the effects of PFT-µ on genes within metabolic pathways related to phenotype. We noted that PFT-µ robustly reduced the M1-like (lipopolysaccharide, LPS-induced) BV2 response, spared the LPS-induced phagocytic ability of BV2 and had no effect on the genes related to metabolism and that effects on phenotype were partially dependent on the presence of HSP-70 but not p53. This study demonstrates that the neuroprotective effects of PFT-µ in HI-induced NE may include an anti-inflammatory effect on microglia and adds to the evidence that this drug might be of clinical interest for the treatment of NE.