cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3808173.v1
title: Ecology and phylogenetic relationships of gall midges

description: Collection of COI, 12S, EF 1a gene sequences of gall midges
DOI: 10.6084/m9.figshare.3808167
title: Exploring the read-write genome: mobile DNA and mammalian adaptation

description: The read–write genome idea predicts that mobile DNA elements will act in evolution to generate adaptive changes in organismal DNA. This prediction was examined in the context of mammalian adaptations involving regulatory non-coding RNAs, viviparous reproduction, early embryonic and stem cell development, the nervous system, and innate immunity. The evidence shows that mobile elements have played specific and sometimes major roles in mammalian adaptive evolution by generating regulatory sites in the DNA and providing interaction motifs in non-coding RNA. Endogenous retroviruses and retrotransposons have been the predominant mobile elements in mammalian adaptive evolution, with the notable exception of bats, where DNA transposons are the major agents of RW genome inscriptions. A few examples of independent but convergent exaptation of mobile DNA elements for similar regulatory rewiring functions are noted.
DOI: 10.6084/m9.figshare.3808167.v1
title: Exploring the read-write genome: mobile DNA and mammalian adaptation

description: The read–write genome idea predicts that mobile DNA elements will act in evolution to generate adaptive changes in organismal DNA. This prediction was examined in the context of mammalian adaptations involving regulatory non-coding RNAs, viviparous reproduction, early embryonic and stem cell development, the nervous system, and innate immunity. The evidence shows that mobile elements have played specific and sometimes major roles in mammalian adaptive evolution by generating regulatory sites in the DNA and providing interaction motifs in non-coding RNA. Endogenous retroviruses and retrotransposons have been the predominant mobile elements in mammalian adaptive evolution, with the notable exception of bats, where DNA transposons are the major agents of RW genome inscriptions. A few examples of independent but convergent exaptation of mobile DNA elements for similar regulatory rewiring functions are noted.
DOI: 10.6084/m9.figshare.3808164
title: Aridification as a driver of biodiversity: A case study for the cycad genus Dioon (Zamiaceae)

description: This zip contains a NEXUS file including data of 35 specimens representing all the 14 Dioon species. Such data comprise the 6,048 bp length DNA sequence dataset consisting on seven cpDNA regions and the nrDNA spacer ITS2. Substitution models for each partition are assigned, and the Bayesian tree constructed in Mr. Bayes is included in Newick format.
DOI: 10.6084/m9.figshare.3808164.v1
title: Aridification as a driver of biodiversity: A case study for the cycad genus Dioon (Zamiaceae)

description: This zip contains a NEXUS file including data of 35 specimens representing all the 14 Dioon species. Such data comprise the 6,048 bp length DNA sequence dataset consisting on seven cpDNA regions and the nrDNA spacer ITS2. Substitution models for each partition are assigned, and the Bayesian tree constructed in Mr. Bayes is included in Newick format.<br>Also, there is a folder that includes the MIG-seq raw data obtained from an Illumina MiSeq Sequencer. They are two read files for each of the 90 individuals of the species Dioon sonorense used in the paper. File names starting with Ds01, Ds03, Ds07 and Ds08 correspond to Northern region populations. File names starting with Ds02 and Ds04 correspond to Southern region populations.
DOI: 10.6084/m9.figshare.3808161
title: Supplementary Material for: International Multi-Specialty Delphi Survey: Identification of Diagnostic Criteria for Hepatic and Renal Cyst Infection

description: <i>Background:</i> Cyst infection is one of the complications of autosomal dominant polycystic kidney disease and polycystic liver disease. The diagnosis is typically made on a mix of clinical, laboratory and imaging abnormalities but the importance of individual items is uncertain. We aimed to perform a Delphi survey amongst physicians to achieve consensus on diagnostic criteria. <i>Methods:</i> We retrieved diagnostic items from the literature and conducted physician and patient interviews. All items were combined to create the online questionnaire. Participants rated each item during 3 consecutive rounds. Items were rated for diagnostic helpfulness for hepatic and renal cyst infection on a 9-point scale with anchors, from extremely unimportant (n = 1) to extremely important (n = 9). We determined consensus with the disagreement index. The median rating of each item was calculated and categorized into inappropriate (≤3.4), uncertain (3.5-6.4) or appropriate (≥6.5). By combining all items that reached an appropriate consensus rating, we developed a diagnostic algorithm based on expert consensus. <i>Results:</i> We invited 58 physicians to participate in the survey. In total, 35 (60%) responded to round 1 of which 91% (n = 32) and 86% (n = 30) responded to round 2 and 3, respectively. The final panel included 23 nephrologists, 5 hepatologists, a nuclear medicine specialist and an infectious disease physician from 11 countries (male 67%, mean age 47 ± 11 years, median clinical experience 21 years). The panel rated the diagnostic helpfulness of 59 potential items. Ultimately, 22 hepatic and 26 renal items were rated appropriate, including positive blood cultures and fluorodeoxyglucose positron-emission CT imaging. Ultrasonography and absence of intracystic bleeding were amongst those deemed uncertain or inappropriate. Subsequently, by combining items rated appropriate, we developed a clinical tool to diagnose hepatic and renal cyst infection.<i>Conclusions:</i> We identified diagnostic items for hepatic and renal cyst infection and developed an expert-based diagnostic algorithm, which may aid physicians in the diagnostic work-up. A prospective study is necessary to validate this algorithm.
DOI: 10.6084/m9.figshare.3808161.v2
title: Supplementary Material for: International Multi-Specialty Delphi Survey: Identification of Diagnostic Criteria for Hepatic and Renal Cyst Infection

description: <i>Background:</i> Cyst infection is one of the complications of autosomal dominant polycystic kidney disease and polycystic liver disease. The diagnosis is typically made on a mix of clinical, laboratory and imaging abnormalities but the importance of individual items is uncertain. We aimed to perform a Delphi survey amongst physicians to achieve consensus on diagnostic criteria. <i>Methods:</i> We retrieved diagnostic items from the literature and conducted physician and patient interviews. All items were combined to create the online questionnaire. Participants rated each item during 3 consecutive rounds. Items were rated for diagnostic helpfulness for hepatic and renal cyst infection on a 9-point scale with anchors, from extremely unimportant (n = 1) to extremely important (n = 9). We determined consensus with the disagreement index. The median rating of each item was calculated and categorized into inappropriate (≤3.4), uncertain (3.5-6.4) or appropriate (≥6.5). By combining all items that reached an appropriate consensus rating, we developed a diagnostic algorithm based on expert consensus. <i>Results:</i> We invited 58 physicians to participate in the survey. In total, 35 (60%) responded to round 1 of which 91% (n = 32) and 86% (n = 30) responded to round 2 and 3, respectively. The final panel included 23 nephrologists, 5 hepatologists, a nuclear medicine specialist and an infectious disease physician from 11 countries (male 67%, mean age 47 ± 11 years, median clinical experience 21 years). The panel rated the diagnostic helpfulness of 59 potential items. Ultimately, 22 hepatic and 26 renal items were rated appropriate, including positive blood cultures and fluorodeoxyglucose positron-emission CT imaging. Ultrasonography and absence of intracystic bleeding were amongst those deemed uncertain or inappropriate. Subsequently, by combining items rated appropriate, we developed a clinical tool to diagnose hepatic and renal cyst infection.<i>Conclusions:</i> We identified diagnostic items for hepatic and renal cyst infection and developed an expert-based diagnostic algorithm, which may aid physicians in the diagnostic work-up. A prospective study is necessary to validate this algorithm.
DOI: 10.6084/m9.figshare.3808158
title: CABNpaper_data

description: Data from:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169349/
DOI: 10.6084/m9.figshare.3808158.v1
title: CABNpaper_data

description: Data from:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169349/
DOI: 10.6084/m9.figshare.3808152
title: Supplementary Material for: Analysis of Bacterial Activity in Sound and Cariogenic Biofilm: A Pilot in vivo Study

description: Dental caries is a multifactorial disease with many associated microbial taxa, but only a few are notably contributing to acidogenicity. The ribosome number and the corresponding 16S ribosomal RNA (rRNA) concentration are considered a molecular indicator for general metabolic activity of bacteria, as they are elevated with increased anabolic and catabolic activities. We hypothesize that the activity of aciduric/acidogenic bacterial taxa, reflected by a rise in ribosomal counts, could resolve differences between plaque biofilm from sound surfaces and caries lesions. The included subjects were allocated to two groups: caries-free (CF) or caries-active (CA). CF subjects presented one donor site, namely one sound surface (CFS, n = 10), whereas CA subjects presented two donor sites: a cavitated lesion with an ICDAS score of 5-6 (CAC, n = 13), and a sound reference surface (CAS, n = 13). Four aciduric/acidogenic bacterial taxa <i>(Streptococcus mutans, </i>lactobacilli<i>, Bifidobacterium dentium, </i>and<i> Scardovia wiggsiae)</i> and one asaccharolytic taxon (fusobacteria) as a contrast were selected. 16S rRNA and 16S rRNA genes were quantified by quantitative PCR. Based on these parameters, bacterial and ribosomal counts, as well as relative activities were calculated as the quotient of relative ribosomal abundance and relative genome abundance. Caries-associated bacteria showed the highest relative activity in caries lesions (e.g. lactobacilli CAC: 177.5 ± 46.0%) and lower activities on sound surfaces (e.g. lactobacilli CAS: 96.3 ± 31.5%), whereas asaccharolytic fusobacteria were most active on sound surfaces and less active in caries lesions (CFS: 275.7 ± 171.1%; CAS: 205.8 ± 114.3%; CAC: 51.1 ± 19.0%). Thus, the present study suggests different activity patterns for biofilms from CF and CA individuals.
DOI: 10.6084/m9.figshare.3808152.v3
title: Supplementary Material for: Analysis of Bacterial Activity in Sound and Cariogenic Biofilm: A Pilot in vivo Study

description: Dental caries is a multifactorial disease with many associated microbial taxa, but only a few are notably contributing to acidogenicity. The ribosome number and the corresponding 16S ribosomal RNA (rRNA) concentration are considered a molecular indicator for general metabolic activity of bacteria, as they are elevated with increased anabolic and catabolic activities. We hypothesize that the activity of aciduric/acidogenic bacterial taxa, reflected by a rise in ribosomal counts, could resolve differences between plaque biofilm from sound surfaces and caries lesions. The included subjects were allocated to two groups: caries-free (CF) or caries-active (CA). CF subjects presented one donor site, namely one sound surface (CFS, n = 10), whereas CA subjects presented two donor sites: a cavitated lesion with an ICDAS score of 5-6 (CAC, n = 13), and a sound reference surface (CAS, n = 13). Four aciduric/acidogenic bacterial taxa <i>(Streptococcus mutans, </i>lactobacilli<i>, Bifidobacterium dentium, </i>and<i> Scardovia wiggsiae)</i> and one asaccharolytic taxon (fusobacteria) as a contrast were selected. 16S rRNA and 16S rRNA genes were quantified by quantitative PCR. Based on these parameters, bacterial and ribosomal counts, as well as relative activities were calculated as the quotient of relative ribosomal abundance and relative genome abundance. Caries-associated bacteria showed the highest relative activity in caries lesions (e.g. lactobacilli CAC: 177.5 ± 46.0%) and lower activities on sound surfaces (e.g. lactobacilli CAS: 96.3 ± 31.5%), whereas asaccharolytic fusobacteria were most active on sound surfaces and less active in caries lesions (CFS: 275.7 ± 171.1%; CAS: 205.8 ± 114.3%; CAC: 51.1 ± 19.0%). Thus, the present study suggests different activity patterns for biofilms from CF and CA individuals.
DOI: 10.6084/m9.figshare.3808149
title: Supplementary Material for: Electroencephalography Is a Good Complement to Currently Established Dementia Biomarkers

description: <i>Background/Aims:</i> Dementia biomarkers that are accessible and easily applicable in nonspecialized clinical settings are urgently needed. Quantitative electroencephalography (qEEG) is a good candidate, and the statistical pattern recognition (SPR) method has recently provided promising results. We tested the diagnostic value of qEEG-SPR in comparison to cognition, structural imaging, and cerebrospinal fluid (CSF) biomarkers. <i>Methods:</i> A total of 511 individuals were recruited from the multicenter NORD EEG study [141 healthy controls, 64 subjective cognitive decline, 124 mild cognitive impairment, 135 Alzheimer's disease (AD), 15 dementia with Lewy bodies/Parkinson's disease with dementia (DLB/PDD), 32 other dementias]. The EEG data were recorded in a standardized way. Structural imaging data were visually rated using scales of atrophy in the medial temporal, frontal, and posterior cortex. <i>Results:</i> qEEG-SPR outperformed structural imaging, cognition, and CSF biomarkers in DLB/PDD diagnosis, outperformed structural imaging in AD diagnosis, and improved the differential diagnosis of AD. In addition, qEEG-SPR allowed differentiation of two clinically different AD subtypes. <i>Conclusion:</i> Adding qEEG to the diagnostic workup substantially increases the detection of AD pathology even in pre-dementia stages and improves differential diagnosis. EEG could serve as a good complement to currently established dementia biomarkers since it is cheap, noninvasive, and extensively applied outside academic centers.
DOI: 10.6084/m9.figshare.3808146
title: Supplementary Material for: Sedation for Bronchoscopy and Complications in Obese Patients

description: <i>Background:</i> Bronchoscopy is a safe and minimally invasive diagnostic tool, but no studies have reported prospectively on sedation and outcomes in patients with objectively defined obesity. <i>Objectives:</i> The purpose of the study is to determine if obese patients require more sedation or had more procedural complications during bronchoscopy under moderate sedation than non-obese patients. <i>Methods:</i> We evaluated complications and sedation requirements in non-obese versus obese patients, defined by multiple criteria including body mass index (BMI), neck circumference, abdominal height, and Mallampati scores. <i>Results:</i> Data were collected prospectively in 258 patients undergoing bronchoscopy under moderate sedation. By varying criteria, there were the following proportions of obese patients: 30% by BMI &gt;30, 39% by neck circumference &gt;40 cm, and 35% by abdominal height &gt;22 cm in males and &gt;20 cm in females. Sedative and analgesic dosing was not clinically significantly higher in obese patients than in non-obese patients. There was no difference in complications or procedural success based on obesity criteria. Hemoglobin oxygen desaturations occurred more often during bronchoscopy in patients with increasing Mallampati scores (p = 0.04), but this had no effect on bronchoscopy time or successful completion of the procedure. A subset of patients with previous polysomnogram-proven obstructive sleep apnea were more likely to have earlier termination of their procedure (15.8%) than patients with no diagnosed sleep apnea (2.3%; p = 0.002). <i>Conclusion:</i> In this prospective assessment of patients with obesity, we found neither clinically significant differences in sedation needs nor increases in complications in obese versus non-obese patients using a variety of indices of obesity.
DOI: 10.6084/m9.figshare.3808146.v1
title: Supplementary Material for: Sedation for Bronchoscopy and Complications in Obese Patients

description: <i>Background:</i> Bronchoscopy is a safe and minimally invasive diagnostic tool, but no studies have reported prospectively on sedation and outcomes in patients with objectively defined obesity. <i>Objectives:</i> The purpose of the study is to determine if obese patients require more sedation or had more procedural complications during bronchoscopy under moderate sedation than non-obese patients. <i>Methods:</i> We evaluated complications and sedation requirements in non-obese versus obese patients, defined by multiple criteria including body mass index (BMI), neck circumference, abdominal height, and Mallampati scores. <i>Results:</i> Data were collected prospectively in 258 patients undergoing bronchoscopy under moderate sedation. By varying criteria, there were the following proportions of obese patients: 30% by BMI &gt;30, 39% by neck circumference &gt;40 cm, and 35% by abdominal height &gt;22 cm in males and &gt;20 cm in females. Sedative and analgesic dosing was not clinically significantly higher in obese patients than in non-obese patients. There was no difference in complications or procedural success based on obesity criteria. Hemoglobin oxygen desaturations occurred more often during bronchoscopy in patients with increasing Mallampati scores (p = 0.04), but this had no effect on bronchoscopy time or successful completion of the procedure. A subset of patients with previous polysomnogram-proven obstructive sleep apnea were more likely to have earlier termination of their procedure (15.8%) than patients with no diagnosed sleep apnea (2.3%; p = 0.002). <i>Conclusion:</i> In this prospective assessment of patients with obesity, we found neither clinically significant differences in sedation needs nor increases in complications in obese versus non-obese patients using a variety of indices of obesity.
DOI: 10.6084/m9.figshare.3808143
title: The Brexit vote: a divided nation, a divided continent

description: The outcome of the British referendum on European Union (EU) membership sent shockwaves through Europe. While Britain is an outlier when it comes to the strength of Euroscepticism, the anti-immigration and anti-establishment sentiments that produced the referendum outcome are gaining strength across Europe. Analysing campaign and survey data, this article shows that the divide between winners and losers of globalization was a key driver of the vote. Favouring British EU exit, or ‘Brexit’, was particularly common among less-educated, poorer and older voters, and those who expressed concerns about immigration and multi-culturalism. While there is no evidence of a short-term contagion effect with similar membership referendums in other countries, the Brexit vote nonetheless poses a serious challenge to the political establishment across Europe.
DOI: 10.6084/m9.figshare.3808143.v1
title: The Brexit vote: a divided nation, a divided continent

description: The outcome of the British referendum on European Union (EU) membership sent shockwaves through Europe. While Britain is an outlier when it comes to the strength of Euroscepticism, the anti-immigration and anti-establishment sentiments that produced the referendum outcome are gaining strength across Europe. Analysing campaign and survey data, this article shows that the divide between winners and losers of globalization was a key driver of the vote. Favouring British EU exit, or ‘Brexit’, was particularly common among less-educated, poorer and older voters, and those who expressed concerns about immigration and multi-culturalism. While there is no evidence of a short-term contagion effect with similar membership referendums in other countries, the Brexit vote nonetheless poses a serious challenge to the political establishment across Europe.
DOI: 10.6084/m9.figshare.3808140
title: Supplementary Material for: Intellectual Disability in a Birth Cohort: Prevalence, Etiology, and Determinants at the Age of 4 Years

description: <i>Background:</i> Intellectual disability (ID), characterized by impairments in intellectual function and adaptive behavior, affects 1-3% of the population. Many studies investigated its etiology, but few are cohort studies in middle-income countries.<i>Aims:</i> To estimate prevalence, etiology, and factors related to ID among children prospectively followed since birth in a Southern Brazilian city (Pelotas). <i>Methods:</i> In 2004, maternity hospitals were visited daily and births were identified. Live-born infants (n = 4,231) whose family lived in the urban area have been followed for several years. At the age of 2 and 4 years, performances in development and intelligence tests were evaluated using the Battelle Developmental Inventory and Wechsler Intelligence Scale, respectively. Children considered as having developmental delay were invited to attend a genetic evaluation. <i>Results:</i> At 4 years of age, the prevalence of ID was 4.5%, and the etiology was classified into 5 groups: environmental (44.4%), genetic (20.5%), idiopathic (12.6%), neonatal sequelae (13.2%), other diseases (9.3%). Most children presented impairment in two or more areas of adaptive behavior. There was no difference in prenatal care attendance or maternal schooling among the groups. <i>Conclusion:</i> For about 40% of children, ID was attributed to nonbiological factors, suggesting that the rate may be reduced with appropriate interventions early in life.
DOI: 10.6084/m9.figshare.3808128
title: Effective practice resources in knowledge exchange for UK universities

description: This dataset provides an overview of sources of effective practice and reference materials relevant to Knowledge Exchange within UK universities. It has been prepared by Research Consulting as part of a project commissioned by the Higher Education Funding Council for England (HEFCE).For a graphical representation of this data, please see the link provided.<br>
DOI: 10.6084/m9.figshare.3808128.v2
title: Effective practice resources in knowledge exchange for UK universities

description: This dataset provides an overview of sources of effective practice and reference materials relevant to Knowledge Exchange within UK universities. It has been prepared by Research Consulting as part of a project commissioned by the Higher Education Funding Council for England (HEFCE).For a graphical representation of this data, please see the link provided.<br>
DOI: 10.6084/m9.figshare.3808128.v1
title: Effective practice resources in knowledge exchange for UK universities

description: This dataset provides an overview of sources of effective practice and reference materials relevant to Knowledge Exchange within UK universities. It has been prepared by Research Consulting as part of a project commissioned by the Higher Education Funding Council for England (HEFCE).For a graphical representation of this data, please see the link provided.<br>