cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8342507
title: Supplementary Material for: The Impact of Focality and Centricity on Vulvar Intraepithelial Neoplasia on Disease Progression in HIV+ Patients: A 10-Year Retrospective Study

description: <b><i>Background:</i></b> The impact of lesion focality and centricity in relation to patient outcome and disease recurrence of vulvar intraepithelial neoplasia (VIN) is an understudied area of research, especially in immunocompromised women. The prevalence and incidence of VIN have increased steadily since the 1980s because of the co-existence of human papillomavirus (HPV) and human immunodeficiency virus (HIV). In this study, we retrospectively examined the records of VIN patients to determine the effect of lesion focality and centricity with respect to the interval to disease recurrence. <b><i>Materials and Methods:</i></b> All women diagnosed with VIN and managed between January 2002 and December 2011 were included (<i>n</i> = 90) and followed up until December 2017. Symptoms at the time of presentation, including HIV positivity (<i>n</i> = 75), were collated, including the influences of multifocality and multicentricity on time to disease recurrence. <b><i>Results:</i></b> Multicentricity caused a more rapid recurrence of disease than unicentricity (<i>p</i> = 0.006), whereas multifocality increased the risk of recurrence more than unifocality (<i>p</i> &lt; 0.0001). Viral load in the HIV+ patients was not associated with time to disease recurrence, but the reduced number of CD4+ lymphocytes present in HIV+ patients was. Treatment modalities had no effect on disease recurrence. <b><i>Conclusion:</i></b> Both focality and centricity have effects on interval to recurrence and final patient outcome, with multifocal disease having a poorer prognosis. Centricity and focality should be recorded at the time of diagnosis and act as a warning for disease recurrence. HIV+ VIN patients with multifocal disease and/or known immunosuppression (low CD4+ lymphocyte counts) should be regarded as “high-risk” patients and treated accordingly.
DOI: 10.6084/m9.figshare.8342525
title: Supplementary Material for: Phenobarbital, Midazolam Pharmacokinetics, Effectiveness, and Drug-Drug Interaction in Asphyxiated Neonates Undergoing Therapeutic Hypothermia

description: <b><i>Background:</i></b> Phenobarbital and midazolam are commonly used drugs in (near-)term neonates treated with therapeutic hypothermia for hypoxic-ischaemic encephalopathy, for sedation, and/or as anti-epileptic drug. Phenobarbital is an inducer of cytochrome P450 (CYP) 3A, while midazolam is a CYP3A substrate. Therefore, co-treatment with phenobarbital might impact midazolam clearance. <b><i>Objectives:</i></b> To assess pharmacokinetics and clinical anti-epileptic effectiveness of phenobarbital and midazolam in asphyxiated neonates and to develop dosing guidelines. <b><i>Methods:</i></b> Data were collected in the prospective multicentre PharmaCool study. In the present study, neonates treated with therapeutic hypothermia and receiving midazolam and/or phenobarbital were included. Plasma concentrations of phenobarbital and midazolam including its metabolites were determined in blood samples drawn on days 2–5 after birth. Pharmacokinetic analyses were performed using non-linear mixed effects modelling; clinical effectiveness was defined as no use of additional anti-epileptic drugs. <b><i>Results:</i></b> Data were available from 113 (phenobarbital) and 118 (midazolam) neonates; 68 were treated with both medications. Only clearance of 1-hydroxy midazolam was influenced by hypothermia. Phenobarbital co-administration increased midazolam clearance by a factor 2.3 (95% CI 1.9–2.9, <i>p</i> &lt; 0.05). Anticonvulsant effectiveness was 65.5% for phenobarbital and 37.1% for add-on midazolam. <b><i>Conclusions:</i></b> Therapeutic hypothermia does not influence clearance of phenobarbital or midazolam in (near-)term neonates with hypoxic-ischaemic encephalopathy. A phenobarbital dose of 30 mg/kg is advised to reach therapeutic concentrations. Phenobarbital co-administration significantly increased midazolam clearance. Should phenobarbital be substituted by non-CYP3A inducers as first-line anticonvulsant, a 50% lower midazolam maintenance dose might be appropriate to avoid excessive exposure during the first days after birth.
DOI: 10.6084/m9.figshare.8342525.v1
title: Supplementary Material for: Phenobarbital, Midazolam Pharmacokinetics, Effectiveness, and Drug-Drug Interaction in Asphyxiated Neonates Undergoing Therapeutic Hypothermia

description: <b><i>Background:</i></b> Phenobarbital and midazolam are commonly used drugs in (near-)term neonates treated with therapeutic hypothermia for hypoxic-ischaemic encephalopathy, for sedation, and/or as anti-epileptic drug. Phenobarbital is an inducer of cytochrome P450 (CYP) 3A, while midazolam is a CYP3A substrate. Therefore, co-treatment with phenobarbital might impact midazolam clearance. <b><i>Objectives:</i></b> To assess pharmacokinetics and clinical anti-epileptic effectiveness of phenobarbital and midazolam in asphyxiated neonates and to develop dosing guidelines. <b><i>Methods:</i></b> Data were collected in the prospective multicentre PharmaCool study. In the present study, neonates treated with therapeutic hypothermia and receiving midazolam and/or phenobarbital were included. Plasma concentrations of phenobarbital and midazolam including its metabolites were determined in blood samples drawn on days 2–5 after birth. Pharmacokinetic analyses were performed using non-linear mixed effects modelling; clinical effectiveness was defined as no use of additional anti-epileptic drugs. <b><i>Results:</i></b> Data were available from 113 (phenobarbital) and 118 (midazolam) neonates; 68 were treated with both medications. Only clearance of 1-hydroxy midazolam was influenced by hypothermia. Phenobarbital co-administration increased midazolam clearance by a factor 2.3 (95% CI 1.9–2.9, <i>p</i> &lt; 0.05). Anticonvulsant effectiveness was 65.5% for phenobarbital and 37.1% for add-on midazolam. <b><i>Conclusions:</i></b> Therapeutic hypothermia does not influence clearance of phenobarbital or midazolam in (near-)term neonates with hypoxic-ischaemic encephalopathy. A phenobarbital dose of 30 mg/kg is advised to reach therapeutic concentrations. Phenobarbital co-administration significantly increased midazolam clearance. Should phenobarbital be substituted by non-CYP3A inducers as first-line anticonvulsant, a 50% lower midazolam maintenance dose might be appropriate to avoid excessive exposure during the first days after birth.
DOI: 10.6084/m9.figshare.8342504
title: Dataset 1

description: This is the data of analitical validation of commercial cortisol and testosterone ELISA kits ( DRG, GmbH, Germany) included data of parallelism test, accuracy and precision (intra-inter assay variation) in serum of aceh cattle of the two of ELISA kits.
DOI: 10.6084/m9.figshare.8342468
title: Dynamic fractal structure in sedimentary rocks: the role of geological processes

description: The data of the paper entitled "Dynamic fractal structure in sedimentary rocks: the role of geological processes"
DOI: 10.6084/m9.figshare.8342504.v2
title: Dataset 1

description: This is the data of analitical validation of commercial cortisol and testosterone ELISA kits ( DRG, GmbH, Germany) included data of parallelism test, accuracy and precision (intra-inter assay variation) in serum of aceh cattle of the two of ELISA kits.
DOI: 10.6084/m9.figshare.8342462
title: Supplementary Material for: Inhibition of Heat Shock Factor 1 Enhances Repressive Molecular Mechanisms on the <b><i>POMC</i></b> Promoter

description: <b><i>Background:</i></b> Cushing’s disease (CD) is caused by adrenocorticotropic hormone (ACTH)-secreting pituitary tumours. They express high levels of heat shock protein 90 and heat shock factor 1 (HSF1) in comparison to the normal tissue counterpart, indicating activated cellular stress. <b><i>Aims:</i></b> Our objectives were: (1) to correlate HSF1 expression with clinical features and hormonal/radiological findings of CD, and (2) to investigate the effects of HSF1 inhibition as a target for CD treatment. <b><i>Patients/Methods:</i></b> We examined the expression of total and pSer<sup>326</sup>HSF1 (marker for its transcriptional activation) by Western blot on eight human CD tumours and compared to the HSF1 status of normal pituitary. We screened a cohort of 45 patients with CD for HSF1 by immunohistochemistry and correlated the HSF1 immunoreactivity score with the available clinical data. We evaluated the effects of HSF1 silencing with RNA interference and the HSF1 inhibitor KRIBB11 in AtT-20 cells and four primary cultures of human corticotroph tumours. <b><i>Results:</i></b> We show that HSF1 protein is highly expressed and transcriptionally active in CD tumours in comparison to normal pituitary. The immunoreactivity score for HSF1 did not correlate with the typical clinical features of the disease. HSF1 inhibition reduced proopiomelanocortin (<i>Pomc</i>) transcription in AtT-20 cells. The HSF1 inhibitor KRIBB11 suppressed ACTH synthesis from 75% of human CD tumours in primary cell culture. This inhibitory action on <i>Pomc</i> transcription was mediated by increased glucocorticoid receptor and suppressed Nurr77/Nurr1 and AP-1 transcriptional activities. <b><i>Conclusions:</i></b> These data show that HSF1 regulates <i>POMC</i> transcription. Pharmacological targeting of HSF1 may be a promising treatment option for the control of excess ACTH secretion in CD.
DOI: 10.6084/m9.figshare.8342468.v1
title: Dynamic fractal structure in sedimentary rocks: the role of geological processes

description: The data of the paper entitled "Dynamic fractal structure in sedimentary rocks: the role of geological processes"
DOI: 10.6084/m9.figshare.8342462.v1
title: Supplementary Material for: Inhibition of Heat Shock Factor 1 Enhances Repressive Molecular Mechanisms on the <b><i>POMC</i></b> Promoter

description: <b><i>Background:</i></b> Cushing’s disease (CD) is caused by adrenocorticotropic hormone (ACTH)-secreting pituitary tumours. They express high levels of heat shock protein 90 and heat shock factor 1 (HSF1) in comparison to the normal tissue counterpart, indicating activated cellular stress. <b><i>Aims:</i></b> Our objectives were: (1) to correlate HSF1 expression with clinical features and hormonal/radiological findings of CD, and (2) to investigate the effects of HSF1 inhibition as a target for CD treatment. <b><i>Patients/Methods:</i></b> We examined the expression of total and pSer<sup>326</sup>HSF1 (marker for its transcriptional activation) by Western blot on eight human CD tumours and compared to the HSF1 status of normal pituitary. We screened a cohort of 45 patients with CD for HSF1 by immunohistochemistry and correlated the HSF1 immunoreactivity score with the available clinical data. We evaluated the effects of HSF1 silencing with RNA interference and the HSF1 inhibitor KRIBB11 in AtT-20 cells and four primary cultures of human corticotroph tumours. <b><i>Results:</i></b> We show that HSF1 protein is highly expressed and transcriptionally active in CD tumours in comparison to normal pituitary. The immunoreactivity score for HSF1 did not correlate with the typical clinical features of the disease. HSF1 inhibition reduced proopiomelanocortin (<i>Pomc</i>) transcription in AtT-20 cells. The HSF1 inhibitor KRIBB11 suppressed ACTH synthesis from 75% of human CD tumours in primary cell culture. This inhibitory action on <i>Pomc</i> transcription was mediated by increased glucocorticoid receptor and suppressed Nurr77/Nurr1 and AP-1 transcriptional activities. <b><i>Conclusions:</i></b> These data show that HSF1 regulates <i>POMC</i> transcription. Pharmacological targeting of HSF1 may be a promising treatment option for the control of excess ACTH secretion in CD.
DOI: 10.6084/m9.figshare.8342504.v1
title: Dataset 1

description: This is the data of analitical validation of commercial cortisol and testosterone ELISA kits ( DRG, GmbH, Germany) included data of parallelism test, accuracy and precision (intra-inter assay variation) of the two of ELISA kits.
DOI: 10.6084/m9.figshare.8342459.v1
title: Patients’ experience of a workplace dialogue in physiotherapy practice in primary care: an interview study

description: <b>Purpose:</b> To describe how patients with acute/subacute back pain and/or neck pain experienced a workplace intervention, conducted as a structured workplace dialogue (convergence dialogue meeting, CDM) within physiotherapy practice in primary care. <b>Materials and methods:</b> Semi-structured interviews were performed with 10 patients who took part in the CDM. Qualitative content analysis was applied to the data. <b>Results:</b> Three categories emerged from the analysis: physiotherapist (PT) as a facilitator, the employer as a key stakeholder and lack of transparency and concrete changes. <b>Conclusion:</b> This study describes patients’ experiences of a workplace dialogue in physiotherapy practice. Even though few patients experienced concrete changes at the workplace, they were supportive for the intervention as well as how the PTs conducted the CDM. The patients expressed trust in the PTs who were seen as someone who could facilitate changes at the workplace, being proficient and supportive. The CDM could be a method to facilitate communication between stakeholders and support work ability.
DOI: 10.6084/m9.figshare.8342411
title: world-population-centroids.zip

description: Population centroids of the world 1992 - 20132019-09-04 <br> The repository contain 3 <b>folders</b>: <br> * Scripts (R-scripts to generate centroids based on Aboufadel and Austin method and Barmore method. Also, included is R-script to generate the area/distance plot found in the paper. <br> * AboufadelAustin (Output data from Aboufadel and Austin method) <br> * Barmore (Output data from Barmore method) <br> <br> <b>File formats</b> <br> Following files belong to ESRI vector data storage format (shape files). <br> .shp — shape format; the feature geometry itself .shx — shape index format; a positional index of the feature geometry to allow seeking forwards and backwards quickly .dbf — attribute format; columnar attributes for each shape, in dBase IV format .prj — projection description .sbn and .sbx — a spatial indexof the features .shp.xml — geospatial metadata in XML format .cpg — used to specify the code page for .dbf or identifying the character encoding to be used <br> Tabular data file format Comma separated values file (CSV) <br> In each of the .shp, .shx, and .dbf files, the shapes in each file correspond to each other in sequence (i.e., the first record in the .shp file corresponds to the first record in the .shx and .dbf files, etc.). https://en.wikipedia.org/wiki/Shapefile <br> <br> <b>Files in AboufadelAustin and Barmore folders</b> <br> The centroid datasets created were separated by algorithm (Aboufadel or Barmore), year (1992-2013), and GADM (Database of Global Administrative Areas) level (0, 1 and 2). <br> In total 132 different datasets were created each including a quality flag for each centroid point. Since each dataset is small in terms of storage they are grouped by algorithm and GADM level making the resulting data files 6 in total (3 shapefiles and 3 CSV-files). <br> Centroids that did not fall within the corresponding administrative area were flagged, as were administrative areas that did not have a corresponding centre. In each shapefile (adm0, adm1, adm2) the field OUT_FLAG is used to store the flag value. In addition, there are three corresponding CSV-files, which in tabular form report on unplaced centroids. The user can then decide how to proceed with the handling of unplaced centroids based on the specific user needs and application at hand. <br> As an example, in the aboufadel folder there are 3 shapefiles for year 1992 providing centroids for administrative levels 0, 1 and 2. In addition, there are 3 textfiles (.CSV) reporting on unplaced centroids for each administrative level. <br> <b>In the file name</b>; DMSP_xxxx corresponds to the year of nighttime lights data, e.g. DMSP_1992 _gadm28_ is the Database of Global Administrative Areas version 2.8, _admx_ is administrative level number, 0, 1 or 2. e.g, _adm0_, _name is the corresponding method, e.g. Barmore, and _gcs_that a geographic coordinate system is used. <br> <br> <br> Ola Hall, Department of Human Geography, Lund University (Ola.hall@keg.lu.se)
DOI: 10.6084/m9.figshare.8342405
title: project1.xls

description: This data from a cross-sectional study conducted in the four main cities of Eastern Province, Saudi Arabia, (AL-Khobar, Dammam, Qatif, and Safwa) between May 2016 and July 2016. A nonprobability method was used to select the sample population. The questionnaire was distributed online through social media (e.g., WhatsApp, Twitter, Facebook, LinkedIn, email). <br>Approval was obtained from the research committee of the Ministry of Health (MoH) in Eastern Province, SA, to perform the study in the MoH PHCs.<br>Written consent was obtained on the first page of the survey. The survey did not contain any identifying information and was labeled by serial number only. The online survey was conducted securely via SurveyMonkey without collecting responder IP addresses.
DOI: 10.6084/m9.figshare.8342402
title: Supplementary Material for: HIV Drug Efavirenz Inhibits CYP21A2 Activity with Possible Clinical Implications

description: <b><i>Background:</i></b> The HIV drugs lopinavir and ritonavir have recently been reported to cause transient adrenal insufficiency in preterm newborns. We, therefore, considered HIV drugs as a cause of transiently elevated 17-hydroxyprogesterone (17OHP) levels in a neonatal screening test for congenital adrenal hyperplasia in a preterm girl exposed to zidovudine, efavirenz, tenofovir, and emtricitabine. <b><i>Objective:</i></b> So far, HIV drugs have not been tested for their effect on steroidogenesis and the steroidogenic enzyme activity of CYP21A2 specifically in an in vitro system. <b><i>Methods:</i></b> We tested the effect of efavirenz, tenofovir, emtricitabine, and zidovudine on steroidogenesis of human adrenal H295R cells. Cells were treated with the drugs at different concentrations including concentrations in therapeutic use. The effect on CYP21A2 activity was assessed by testing the conversion of radiolabeled 17OHP to 11-deoxycortisol. Cell viability was tested by an MTT assay. In addition, recombinant human CYP21A2 protein was used to assess direct drug effects on CYP21A2 activity. <b><i>Results:</i></b> We observed significantly decreased CYP21A2 activity in both in vitro testing systems after treatment with efavirenz at therapeutic concentrations. Moreover, efavirenz affected cell viability. By contrast, the other test drugs did not affect steroidogenesis. Follow-up of our patient revealed elevated 17OHP and androgen levels during the first weeks of life, but values normalized spontaneously. Genetic testing for <i>CYP21A2</i> mutations was negative. Thus, it remains unsettled whether the transient 17OHP elevation in this baby was due to a drug effect. <b><i>Conclusion:</i></b> The HIV drug efavirenz inhibits CYP21A2 activity in vitro through direct interaction with enzyme catalysis at therapeutic concentrations. This may have clinical implications for HIV treatment in children and adults. However, so far, clinical data are scarce, and further studies are needed to be able to draw clinical conclusions.
DOI: 10.6084/m9.figshare.8342402.v1
title: Supplementary Material for: HIV Drug Efavirenz Inhibits CYP21A2 Activity with Possible Clinical Implications

description: <b><i>Background:</i></b> The HIV drugs lopinavir and ritonavir have recently been reported to cause transient adrenal insufficiency in preterm newborns. We, therefore, considered HIV drugs as a cause of transiently elevated 17-hydroxyprogesterone (17OHP) levels in a neonatal screening test for congenital adrenal hyperplasia in a preterm girl exposed to zidovudine, efavirenz, tenofovir, and emtricitabine. <b><i>Objective:</i></b> So far, HIV drugs have not been tested for their effect on steroidogenesis and the steroidogenic enzyme activity of CYP21A2 specifically in an in vitro system. <b><i>Methods:</i></b> We tested the effect of efavirenz, tenofovir, emtricitabine, and zidovudine on steroidogenesis of human adrenal H295R cells. Cells were treated with the drugs at different concentrations including concentrations in therapeutic use. The effect on CYP21A2 activity was assessed by testing the conversion of radiolabeled 17OHP to 11-deoxycortisol. Cell viability was tested by an MTT assay. In addition, recombinant human CYP21A2 protein was used to assess direct drug effects on CYP21A2 activity. <b><i>Results:</i></b> We observed significantly decreased CYP21A2 activity in both in vitro testing systems after treatment with efavirenz at therapeutic concentrations. Moreover, efavirenz affected cell viability. By contrast, the other test drugs did not affect steroidogenesis. Follow-up of our patient revealed elevated 17OHP and androgen levels during the first weeks of life, but values normalized spontaneously. Genetic testing for <i>CYP21A2</i> mutations was negative. Thus, it remains unsettled whether the transient 17OHP elevation in this baby was due to a drug effect. <b><i>Conclusion:</i></b> The HIV drug efavirenz inhibits CYP21A2 activity in vitro through direct interaction with enzyme catalysis at therapeutic concentrations. This may have clinical implications for HIV treatment in children and adults. However, so far, clinical data are scarce, and further studies are needed to be able to draw clinical conclusions.
DOI: 10.6084/m9.figshare.8342378
title: Sample Sheet

description: Sample sheet<br>
DOI: 10.6084/m9.figshare.8342378.v1
title: Sample Sheet

description: Sample sheet<br>
DOI: 10.6084/m9.figshare.8342411.v1
title: world-population-centroids.zip

description: Population centroids of the world 1992 - 2013
DOI: 10.6084/m9.figshare.8342324
title: Additional file 16: of Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation

description: Table S14. T1_FDP versus T0 Top annotated down-regulated contigs. LogFC = Log fold change, logCPM = log counts per million, F = F statistic, FDR = false discovery rate. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8342321
title: Additional file 8: of Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes

description: Table S8. List of resistance genes used for building model for prediction of class B MBLs and list of previously characterized genes used for clustering. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8342324.v1
title: Additional file 16: of Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation

description: Table S14. T1_FDP versus T0 Top annotated down-regulated contigs. LogFC = Log fold change, logCPM = log counts per million, F = F statistic, FDR = false discovery rate. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8342318
title: Additional file 15: of Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation

description: Table S13. T1_FDP versus T0 Top annotated up-regulated contigs. LogFC = Log fold change, logCPM = log counts per million, F = F statistic, FDR = false discovery rate. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8342312
title: Additional file 14: of Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation

description: Table S12. T1_Fed versus T0 Top annotated down-regulated contigs. LogFC = Log fold change, logCPM = log counts per million, F = F statistic, FDR = false discovery rate. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8342315
title: Additional file 7: of Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes

description: Table S7. List of resistance genes in the Resqu database. (XLSX 24 kb)