cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5066833.v1
title: <i>In silico</i> estimation of basic activity-relevant parameters for a set of drug absorption promoters

description: Finding a balance between a desired drug’s potency and its physicochemical properties that are important for its molecule pharmacokinetic or pharmacodynamics profile is still a challenging issue in rational drug discovery. Quantitative assessment of the lipophilic characteristics of potential drug molecules is indispensable for efficient development of Absorption, Distribution, Metabolism, Excretion, Toxicity-tailored structure–activity models; therefore reliable procedures for deriving log <i>P</i> from molecular structure are desirable. In the current work a range of various software log <i>P</i> predictors for estimation of the numerical lipophilic values for a set of cholic acid derivatives were employed and subsequently cross-compared with the experimental parameters. Thus, the empirical lipophilicity (<i>R</i><sub><i>M</i></sub>) was compared with the corresponding log <i>P</i> characteristics calculated using alternative methods for deducing the lipophilic features. The mean values of the selected molecular descriptors that were averaged over the chosen calculation methods (consensus clog <i>P</i>) were subsequently correlated with the <i>R</i><sub><i>M</i></sub> parameter. As an additional experiment, the iterative variable elimination partial least squares (IVE-PLS) methodology for an ensemble of descriptors retrieved from Dragon 6.0 software was applied for a set of drug transporters. To investigate the variations within the ensemble of cholic acid derivatives principal component analysis (PCA) and self-organizing neural network (SOM) procedures were used to visualize the major differences in the performance of drug promoters with respect to their lipophilic profile.
DOI: 10.6084/m9.figshare.5065525
title: Genome-wide sequential, evolutionary, organizational and expression analyses of phenylpropanoid biosynthesis associated MYB domain transcription factors in <i>Arabidopsis</i>

description: The MYB gene family represents one of the largest groups of transcription factors in plants. Recent evidences have also demonstrated key role of MYB transcription factors in regulating the expression of major genes involved in the biosynthesis of phenylpropanoid compounds which confer biotic and abiotic stress tolerance in plant species. However, no comprehensive genome-wide analysis of the phenylpropanoid pathway-associated MYB transcription factors has been reported thus far. In this study, 11 <i>Arabidopsis</i> MYB proteins, such as MYB3, MYB4, MYB7, MYB11, MYB12, MYB32, MYB75, MYB90, MYB111, MYB113, and MYB114 were initially identified considering their reported regulatory function in phenylpropanoid biosynthesis pathway. Subsequent genome-wide analysis have identified the corresponding homologues from <i>Glycine max</i>, <i>Vigna radiata</i>, <i>Oryza sativa</i>, and <i>Zea mays,</i> while homologous of <i>Arabidopsis</i> MYB75, MYB90, MYB113, and MYB114 were not detected in rice and maize genomes. The identified MYB proteins were classified into three groups (I-III) based on phylogeny. Sequence and domain analysis revealed presence of two conserved DNA binding MYB domains in the selected MYB proteins. Promoter analysis indicated presence of <i>cis</i>-regulatory elements related to light signaling, development, and stress response. Expression analysis of selected <i>Arabidopsis MYB</i> genes revealed their function in plant development and abiotic stress response, consistent with gene ontology annotations. Together, these results provide a useful framework for further experimental studies for the functional characterization of the target MYB genes in the context of regulation of phenylpropanoid biosynthesis and plant stress response.
DOI: 10.6084/m9.figshare.5065531
title: Supplementary Material for: Genetic Predictors of ≥5% Weight Loss by Multidisciplinary Advice to Severely Obese Subjects

description: <b><i>Background:</i></b> Weight loss success is determined by genetic factors, which may differ according to treatment strategy. <b><i>Methods:</i></b> From a multidisciplinary obesity treatment program involving dietary advice, psychological counseling, and increased physical activity, 587 subjects (68% female; 46.1 ± 12.4 years; BMI 39.9 ± 6.3) were recruited. At baseline, a blood sample was drawn for DNA isolation. Genotypes were determined for 30 polymorphisms in 25 candidate genes. The association between genotypes and weight loss was assessed after 3 months (short-term) and after 12 months of treatment (long-term). Weight loss was categorized as ≥5% or &lt;5% of initial weight. <b><i>Results:</i></b> The G/G genotype of PLIN1 (rs2289487) and PLIN1 (rs2304795), the T/T genotype of PLIN1 (rs1052700), and the C/C genotype of MMP2 predicted ≥5% weight loss in the first 3 months. The C/G-G/G genotype of PPARγ (rs1801282) and the T/C genotype of TIMP4 (rs3755724) predicted ≥5% weight loss after 12 months. Subjects with the combination of PPARγ (rs1801282) C/G-G/G and TIMP4 (rs3755724) T/C lost even more weight. <b><i>Conclusion:</i></b> Polymorphisms in genes related to regulation of fat storage and structural adaptation of the adipocytes are predictors for weight loss success with different genes being relevant for short-term and long-term weight loss success.
DOI: 10.6084/m9.figshare.5065525.v1
title: Genome-wide sequential, evolutionary, organizational and expression analyses of phenylpropanoid biosynthesis associated MYB domain transcription factors in <i>Arabidopsis</i>

description: The MYB gene family represents one of the largest groups of transcription factors in plants. Recent evidences have also demonstrated key role of MYB transcription factors in regulating the expression of major genes involved in the biosynthesis of phenylpropanoid compounds which confer biotic and abiotic stress tolerance in plant species. However, no comprehensive genome-wide analysis of the phenylpropanoid pathway-associated MYB transcription factors has been reported thus far. In this study, 11 <i>Arabidopsis</i> MYB proteins, such as MYB3, MYB4, MYB7, MYB11, MYB12, MYB32, MYB75, MYB90, MYB111, MYB113, and MYB114 were initially identified considering their reported regulatory function in phenylpropanoid biosynthesis pathway. Subsequent genome-wide analysis have identified the corresponding homologues from <i>Glycine max</i>, <i>Vigna radiata</i>, <i>Oryza sativa</i>, and <i>Zea mays,</i> while homologous of <i>Arabidopsis</i> MYB75, MYB90, MYB113, and MYB114 were not detected in rice and maize genomes. The identified MYB proteins were classified into three groups (I-III) based on phylogeny. Sequence and domain analysis revealed presence of two conserved DNA binding MYB domains in the selected MYB proteins. Promoter analysis indicated presence of <i>cis</i>-regulatory elements related to light signaling, development, and stress response. Expression analysis of selected <i>Arabidopsis MYB</i> genes revealed their function in plant development and abiotic stress response, consistent with gene ontology annotations. Together, these results provide a useful framework for further experimental studies for the functional characterization of the target MYB genes in the context of regulation of phenylpropanoid biosynthesis and plant stress response.
DOI: 10.6084/m9.figshare.5065522
title: Supplementary Material for: Eppikajutsuto Protects against Food Allergy Induced by Ovalbumin in a Murine Model

description: <b><i>Background:</i></b> Currently, there are no efficient medications available for the prevention and treatment of food allergy (FA). Herbal medicines, including traditional Japanese Kampo medicines (TJKMs), are promising therapeutic drugs. <b><i>Methods:</i></b> We screened 18 TJKMs for treatment of FA symptoms in a mouse FA model induced by ovalbumin (OVA). BALB/c mice were sensitized intraperitoneally by an OVA/aluminum hydroxide gel mixture followed by 4 booster doses of oral OVA and FA symptom induction by 50 mg of OVA. TJKMs were orally administered for 28 days from the day of sensitization to the day before FA symptom induction. Evaluated FA symptoms included a decrease in body temperature and allergic diarrhea. Allergic sensitization was determined by plasma OVA-specific IgE levels. Cytokine mRNA levels in mesenteric lymph nodes, plasma mouse mast cell protease-1, and the number of mast cells in the small and large intestines were analyzed. Additionally, the therapeutic effect of the TJKM eppikajutsuto (EJT) on mast cell degranulation was determined in active anaphylaxis and passive cutaneous anaphylaxis models. <b><i>Results:</i></b> EJT effectively prevented FA symptoms. Although OVA-specific IgE levels and the intestinal mast cell numbers were not different between the EJT-treated and untreated FA mice, plasma mMcpt1 and IL-4 levels were lower in EJT-treated FA mice than untreated FA mice. EJT could alleviate symptoms in both active and passive anaphylaxis models. <b><i>Conclusion:</i></b> EJT prevented OVA-induced FA symptoms in a mouse model, suggesting that EJT might exert its therapeutic activity via IL-4 suppression and the inhibition of mucosal mast cell degranulation.
DOI: 10.17029/dfac1c87-8584-48da-808e-bd9354846bb0
title: Dataset for 'Does Leadership Matter for Healthcare Service Quality? Evidence from NHS England'.

description: Data collated from various public databases.
DOI: 10.6084/m9.figshare.5065507
title: Maullinia braseltonii sp. nov.

description: Raw data (alignments, images) accompaning the manuscript <i>Maullinia braseltonii</i> sp. nov., A cyst-forming parasite of the bull kelp <i>Durvillaea</i> spp. <br>
DOI: 10.6084/m9.figshare.5065507.v1
title: Maullinia braseltonii sp. nov.

description: Raw data (alignments, images) accompaning the manuscript <i>Maullinia braseltonii</i> sp. nov., A cyst-forming parasite of the bull kelp <i>Durvillaea</i> spp. <br>
DOI: 10.6084/m9.figshare.5065501
title: Research crowdfunding interview with Deakin

description: On the 11 April 2016, I conducted an interview with Mel Thomson at Deakin University. I was particularly interested in her experiences of running three successful research crowdfunding campaigns.<br>This data set contains the interview (MP3), a transcript of the interview (PDF) and two consent forms (JPG) for the interview and for the public release of the information.
DOI: 10.6084/m9.figshare.5065138
title: Use of a rostral appendage during social interactions in the Ecuadorian <i>Anolis proboscis</i>

description: The use of sexually selected characters in inter- and intra-sexual interactions has long been of interest to evolutionary biologists. Recently, a distinction between sexually selected traits as ornaments versus weapons has been advanced. We investigated the behaviour of an enigmatic lizard with a prominent sexually dimorphic trait in an effort to describe whether the trait was the product of sexual selection and further whether it functioned as a weapon or an ornament. The subject of our study was the Ecuadorian proboscis anole (<i>Anolis proboscis</i>), a slow-moving cryptic species endemic to the north-western slopes of the Andes in Ecuador. Males, but not females, of this species bear a rostral appendage that has been described as an exaggerated trait resulting from sexual selection. However, a thorough description of the use of the rostral appendage in social interactions is lacking. Here, we describe social interactions of this species during 11 male–female courtships and mating interactions, as well as three male–male agonistic interactions. We describe four types of displays by males, many involving the rostral appendage. We found that the rostral appendage is used as an ornament in social displays but not as a weapon in combat. We also show that, unlike other lizards with rostral appendages, male <i>A. proboscis</i> hatch with this structure already developed.
DOI: 10.6084/m9.figshare.5065501.v1
title: Research crowdfunding interview with Deakin

description: On the 11 April 2016, I conducted an interview with Mel Thomson at Deakin University. I was particularly interested in her experiences of running three successful research crowdfunding campaigns.<br>This data set contains the interview (MP3), a transcript of the interview (PDF) and two consent forms (JPG) for the interview and for the public release of the information.
DOI: 10.6084/m9.figshare.5065138.v2
title: Use of a rostral appendage during social interactions in the Ecuadorian <i>Anolis proboscis</i>

description: The use of sexually selected characters in inter- and intra-sexual interactions has long been of interest to evolutionary biologists. Recently, a distinction between sexually selected traits as ornaments versus weapons has been advanced. We investigated the behaviour of an enigmatic lizard with a prominent sexually dimorphic trait in an effort to describe whether the trait was the product of sexual selection and further whether it functioned as a weapon or an ornament. The subject of our study was the Ecuadorian proboscis anole (<i>Anolis proboscis</i>), a slow-moving cryptic species endemic to the north-western slopes of the Andes in Ecuador. Males, but not females, of this species bear a rostral appendage that has been described as an exaggerated trait resulting from sexual selection. However, a thorough description of the use of the rostral appendage in social interactions is lacking. Here, we describe social interactions of this species during 11 male–female courtships and mating interactions, as well as three male–male agonistic interactions. We describe four types of displays by males, many involving the rostral appendage. We found that the rostral appendage is used as an ornament in social displays but not as a weapon in combat. We also show that, unlike other lizards with rostral appendages, male <i>A. proboscis</i> hatch with this structure already developed.
DOI: 10.6084/m9.figshare.5065138.v1
title: Use of a rostral appendage during social interactions in the Ecuadorian <i>Anolis proboscis</i>

description: The use of sexually selected characters in inter- and intra-sexual interactions has long been of interest to evolutionary biologists. Recently, a distinction between sexually selected traits as ornaments versus weapons has been advanced. We investigated the behaviour of an enigmatic lizard with a prominent sexually dimorphic trait in an effort to describe whether the trait was the product of sexual selection and further whether it functioned as a weapon or an ornament. The subject of our study was the Ecuadorian proboscis anole (<i>Anolis proboscis</i>), a slow-moving cryptic species endemic to the north-western slopes of the Andes in Ecuador. Males, but not females, of this species bear a rostral appendage that has been described as an exaggerated trait resulting from sexual selection. However, a thorough description of the use of the rostral appendage in social interactions is lacking. Here, we describe social interactions of this species during 11 male–female courtships and mating interactions, as well as three male–male agonistic interactions. We describe four types of displays by males, many involving the rostral appendage. We found that the rostral appendage is used as an ornament in social displays but not as a weapon in combat. We also show that, unlike other lizards with rostral appendages, male <i>A. proboscis</i> hatch with this structure already developed.
DOI: 10.25592/uhhfdm.1485
title: Parameterfixierung im Deutschen und Spanischen (PAIDUS)

description: Audio recordings of five German and five Spanish speaking monolingual children. For the German children there are 175 recordings (interviewer/child interaction), on an average starting at 9 months and ending at 3 years; for the Spanish children there are 77 recordings, on average starting at 9 months and ending at 2;6 years. PAIDUS is a phonetically and orthographically transcribed corpus of German and Spanish child language, finalized in the project Prosodic constraints on phonological and morphological development in bilingual first language acquisition at the Research Center on Multilingualism, University of Hamburg. Lleó, Conxita. 2012. "Monolingual and Bilingual Phonoprosodic Corpora of Child German and Child Spanish." In Multilingual Corpora and Multilingual Corpus Analysis, edited by Thomas Schmidt and Kai Wörner, 14:pp. 107–22. Hamburg Studies in Multilingualism. John Benjamins. <strong>CLARIN Metadata summary for Parameterfixierung im Deutschen und Spanischen (PAIDUS) (CMDI-based)</strong> <strong>Title: </strong>Parameterfixierung im Deutschen und Spanischen (PAIDUS)<br> <strong>Description: </strong>Audio recordings of five German and five Spanish speaking monolingual children. For the German children there are 175 recordings (interviewer/child interaction), on an average starting at 9 months and ending at 3 years; for the Spanish children there are 77 recordings, on average starting at 9 months and ending at 2;6 years.<br> <strong>Publication date: </strong>2010-09-30<br> <strong>Data owner: </strong> Conxita Lleó, Institut für Romanistik / Von-Melle-Park 6 / D-20146 Hamburg, lleo@uni-hamburg.de<br> <strong>Contributors: </strong> Conxita Lleó, Institut für Romanistik / Von-Melle-Park 6 / D-20146 Hamburg, lleo@uni-hamburg.de (compiler)<br> <strong>Project: </strong> E3 "Prosodic Constraints on Phonological and Morphological development in Bilingual First Language Acquisition", German Research Foundation (DFG)<br> <strong>Keywords: </strong> child language acquisition, longitudinal data, monolingual data, EXMARaLDA<br> <strong>Languages: </strong> German (deu), Spanish (spa)<br> <strong>Size: </strong> 66 speakers (43 female, 23 male), 253 communications, 252 recordings, 8217 minutes, 253 transcriptions, 166976 words<br> <strong>Genre: </strong> discourse<br> <strong>Modality: </strong> spoken<br> <strong>References: </strong> Lleó, Conxita. 2012. "Monolingual and Bilingual Phonoprosodic Corpora of Child German and Child Spanish." In Multilingual Corpora and Multilingual Corpus Analysis, edited by Thomas Schmidt and Kai Wörner, 14:pp. 107–22. Hamburg Studies in Multilingualism. John Benjamins.
DOI: 10.17029/37aff168-d2df-4d99-a373-e533a9517597
title: Chronic unpredictable early-life stress (CUELS) protocol: early-life stress changes anxiety levels of adult zebrafish

description: Dataset for CUELS protocol.
DOI: 10.6084/m9.figshare.5063725
title: Dataset for: Functional Joint Model for Longitudinal and Time-to-Event Data: An Application to Alzheimer's Disease

description: Functional data are increasingly collected in public health and medical studies to better understand many complex diseases. Besides the functional data, other clinical measures are often collected repeatedly. Investigating the association between these longitudinal data and time to a survival event is of great interest to these studies. In this article, we develop a functional joint model (FJM) to account for functional predictors in both longitudinal and survival submodels in the joint modeling framework. The parameters of FJM are estimated in a maximum likelihood framework via EM algorithm. The proposed FJM provides a flexible framework to incorporate many features both in joint modeling of longitudinal and survival data and in functional data analysis. The FJM is evaluated by a simulation study and is applied to the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, a motivating clinical study testing whether serial brain imaging, clinical and neuropsychological assessments can be combined to measure the progression of Alzheimer's disease.
DOI: 10.6084/m9.figshare.5063722
title: Dataset for: Mixture models for undiagnosed prevalent disease and interval-censored incident disease: Applications to a cohort assembled from electronic health records

description: For cost-effectiveness and efficiency, many large-scale general-purpose cohort studies are being assembled within large health-care providers who use electronic health records. Two key features of such data are that incident disease is interval-censored between irregular visits and there can be pre-existing (prevalent) disease. Because prevalent disease is not always immediately diagnosed, some disease diagnosed at later visits are actually undiagnosed prevalent disease. We consider prevalent disease as a point mass at time zero for clinical applications where there is no interest in time of prevalent disease onset. We demonstrate that the naive Kaplan-Meier cumulative risk estimator underestimates risks at early time points and overestimates later risks. We propose a general family of mixture models for undiagnosed prevalent disease and interval-censored incident disease that we call prevalence-incidence models. Parameters for parametric prevalence-incidence models, such as the logistic regression and Weibull survival (logistic-Weibull) model, are estimated by direct likelihood maximization or by EM algorithm. Non-parametric methods are proposed to calculate cumulative risks for cases without covariates. We compare naive Kaplan-Meier, logistic-Weibull, and non-parametric estimates of cumulative risk in the cervical cancer screening program at Kaiser Permanente Northern California. Kaplan-Meier provided poor estimates while the logistic-Weibull model was a close fit to the non-parametric. Our findings support our use of logistic-Weibull models to develop the risk estimates that underlie current U.S. risk-based cervical cancer screening guidelines.
DOI: 10.6084/m9.figshare.5063725.v1
title: Dataset for: Functional Joint Model for Longitudinal and Time-to-Event Data: An Application to Alzheimer's Disease

description: Functional data are increasingly collected in public health and medical studies to better understand many complex diseases. Besides the functional data, other clinical measures are often collected repeatedly. Investigating the association between these longitudinal data and time to a survival event is of great interest to these studies. In this article, we develop a functional joint model (FJM) to account for functional predictors in both longitudinal and survival submodels in the joint modeling framework. The parameters of FJM are estimated in a maximum likelihood framework via EM algorithm. The proposed FJM provides a flexible framework to incorporate many features both in joint modeling of longitudinal and survival data and in functional data analysis. The FJM is evaluated by a simulation study and is applied to the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, a motivating clinical study testing whether serial brain imaging, clinical and neuropsychological assessments can be combined to measure the progression of Alzheimer's disease.