cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5241067.v1
title: Erratum: Strategy for Detecting Susceptibility Genes with Weak or No Marginal Effect

description: Most human diseases result from complex interactions among multiple genes that yield weak or modest effects. Despite the growing awareness of the importance of gene-gene interactions, the paradigm of detectable effects of individual variants remains the cornerstone of genome association studies with tagSNPs. The interactive effect of two variants is only tested once the individual effect of one variant is detected. Both genes, however, may have at the same time a weak (or even no) marginal effect but an important effect through their interaction. In such a situation, current approaches may fail to detect variants having a crucial role in the causal chain. Here, we propose a new strategy: the 2-locus TDT. It allows the detection of the involvement of two genes without individual effect. Our strategy simultaneously uses information on biallelic candidate polymorphisms in two genes M and N. We first estimate the relative marginal penetrances of the genotype at each locus and of the joint (two-locus) genotype and then we test for the interactive effect of the two genes using a likelihood ratio test. We show that our approach has good power to detect the effect of two genes in situations for which a locus-by-locus strategy would have been unsuccessful. At a time where genome-wide association studies are fashionable, we think it is important to consider the strategy of studying good candidate pathways with our approach.
DOI: 10.6084/m9.figshare.5241073.v1
title: Erratum: The Novel mTOR Inhibitor RAD001 (Everolimus) Induces Antiproliferative Effects in Human Pancreatic Neuroendocrine Tumor Cells

description: <i>Background/Aim:</i> Tumors exhibiting constitutively activated PI(3)K/Akt/mTOR signaling are hypersensitive to mTOR inhibitors such as RAD001 (everolimus) which is presently being investigated in clinical phase II trials in various tumor entities, including neuroendocrine tumors (NETs). However, no preclinical data about the effects of RAD001 on NET cells have been published. In this study, we aimed to evaluate the effects of RAD001 on BON cells, a human pancreatic NET cell line that exhibits constitutively activated PI(3)K/Akt/mTOR signaling. <i>Methods:</i> BON cells were treated with different concentrations of RAD001 to analyze its effect on cell growth using proliferation assays. Apoptosis was examined by Western blot analysis of caspase-3/PARP cleavage and by FACS analysis of DNA fragmentation. <i>Results:</i> RAD001 potently inhibited BON cell growth in a dose-dependent manner which was dependent on the serum concentration in the medium. RAD001-induced growth inhibition involved G0/G1-phase arrest as well as induction of apoptosis. <i>Conclusion:</i> In summary, our data demonstrate antiproliferative and apoptotic effects of RAD001 in NET cells in vitro supporting its clinical use in current phase II trials in NET patients.
DOI: 10.6084/m9.figshare.5241046
title: Supplementary material 'Stat-tracks and mediotypes: powerful tools for modern ichnology based on 3D models'

description: Here we present the previously unpublished raw data used for some of the 'Stat-tracks and mediotypes: powerful tools for modern ichnology based on 3D models' paper. ReferenceBelvedere M., Bennett M.R., Marty D., Reynolds S., Budka M., Bakirov R. 2018. Stat-tracks and mediotypes: powerful tools for modern ichnology based on 3D models. <i>PeerJ</i>, 6, e4247
DOI: 10.6084/m9.figshare.5241058.v1
title: Erratum: Effect of Polymorphism of the β<sub>2</sub>-Adrenergic Receptor on Response to Regular Use of Albuterol in Asthma

description: <i>Background:</i> Regular use of inhaled β-adrenergic agonists may have adverse effects in some asthma patients. Polymorphisms of the β<sub>2</sub>-adrenergic receptor (β<sub>2</sub>-AR) can affect its regulation; however, results of smaller studies of the effects of such polymorphisms on response to β-agonist therapy have been inconsistent. <i>Methods:</i> We examined the possible effects of polymorphisms at codons 16 (β<sub>2</sub>-AR-16) and 27 (β<sub>2</sub>-AR-27) on response to albuterol by genotyping 190 asthmatics who had participated in a trial of regular versus as-needed albuterol use. <i>Results:</i> During the 16-week treatment period, patients homozygous for arginine (Arg/Arg) at β<sub>2</sub>-AR-16 who used albuterol regularly had a small decline in morning peak expiratory flow (AM PEF). This effect was magnified during a 4-week run-out period, when all patients returned to as-needed albuterol only. By the end of the study, Arg/Arg subjects who had used albuterol regularly had an AM PEF 30.5 ± 12.1 liters/min lower (p = 0.012) than Arg/Arg patients who had used albuterol as needed only. Subjects homozygous for glycine at β<sub>2</sub>-AR-16 showed no such decline. Evening PEF also declined in the Arg/Arg regular but not in as-need albuterol users. No significant differences between regular and as-needed treatment were associated with polymorphisms at β<sub>2</sub>-AR-27. <i>Conclusions:</i> Polymorphisms of the β<sub>2</sub>-AR may influence airway responses to regular inhaled β-agonist treatment.
DOI: 10.6084/m9.figshare.5241064.v1
title: Erratum: RETRACTION: Intraoperative Touch Imprint Cytological Analysis of Sentinel Lymph Nodes for the Presence of Metastases in Breast Cancer

description: Background: Imprint cytology may provide a fast and accurate method for intraoperative screening of sentinel lymph nodes, so a decision can be made regarding whether to perform axillary clearance during primary surgery. If the findings are negative, in many cases axillary dissection can be omitted. Patients and Methods: 128 sentinel nodes from a cohort of 87 patients that had been identified using technetium-99m nanocolloid as a radioactive tracer and Patent blue dye were disected for rapid Diff-Quick stained touch preparations. Intraoperative evaluation of sentinel node status by imprint cytology was correlated with histopathological results of permanent sections. Tumor-negative nodes in routine paraffin sections were further investigated with the employment of an anti-cytokeratin antibody. Results: 36 of all sentinel nodes harbored metastases in the paraffin sections, of which 32 were identified by imprint cytology (sensitivity 88.8%). 3 sentinel nodes were positive by imprint cytology and negative by histopathology of the paraffin sections. Comparison of the results of the touch preparations with the final histopathology (hematoxylin-eosin and anticytokeratin antibody stains) demonstrated a sensitivity of 83.3% and a negative predictive value of 92.5%. The specificity and positive predictive value were 100% each. Conclusions: Touch imprint cytology is potentially useful for intraoperative evaluation of sentinel lymph nodes in breast cancer patients.
DOI: 10.6084/m9.figshare.5241061.v1
title: Erratum: Clinicopathologic Features of Mucinous Gastric Carcinoma

description: <i>Background/Aims:</i> Mucinous gastric carcinoma (MGC) is a histopathologic subtype of gastric carcinoma with a poor prognosis. The purpose of this study was to compare the disease course of MGC with non-mucinous gastric carcinoma (NMGC) and study the clinicopathologic features that influence the prognosis of MGC patients. <i>Methods:</i> We reviewed the records of 2,383 patients with a confirmed histologic diagnosis of gastric carcinoma. There were 157 patients with MGC compared to 2,226 with NMGC. <i>Results:</i> A depth of invasion greater than T3 was more frequently found in MGC than in NMGC. The mean number of lymph nodes with metastases was 2.78 in MGC and 2.28 in NMGC (p &lt; 0.001). There were more MGC patients with TNM stages II through IV (UICC classification). The overall survival rate was lower for the MGC group (46.5%) than for the NMGC group (64.0%; p &lt; 0.05). Depth of invasion, lymph node metastases, and stage at diagnosis were significant factors affecting the outcome. <i>Conclusion:</i> The factors influencing the poorer prognosis (lower 5-year survival rate) of MGC are the advanced stage at the time of diagnosis, lymph node metastases, and a higher TNM status. Mucinous histologic type itself was not an independent predictive factor in survival.
DOI: 10.6084/m9.figshare.5240956
title: Modern pollen types, Ghana.

description: Modern pollen types from artificial pollen traps, observed in Ghana, tropical West Africa. This is my personal database of pollen types observed during my PhD 'Modern pollen-vegetation relationships in Ghana, tropical West Africa', at The Open University.Some scale bars missing from first 11 Holotypes; see excel sheet for pollen sizes. Many taxa have not been assigned botanical affinities. <br>Modern pollen was recovered from the following sites in Ghana:Kogyae Forest Reserve, Savannah (7°18'04"N, 1°09'53"W), Transition (7°18'07"N, 1°10'50"W) and Forest (7°15'41"N, 1°09'00"W) plots (slides with 'K' in code- see below)Bobiri Forest Reserve (6°42'15 "N 1°19'06 "W)<br> (slides with 'B' in code- see below) Ankasa Conservation Area (5°16'06"N 2°41'38"W) (Slides with 'A' in code- see below)Explanation of codes:'Pollen types were assigned codes, for example the 3rd grain (G3), photographed in Slide 28 (S28), Kogyae 2014 (K14), Transition vegetation plot (T), Trap 55 (T55) would be S28K14TT55G3. Types were numbered sequentially from 1 upwards, and Holotypes (sets of images which acted as a standard for that pollen type) were designated. Holotypes were designated when the grain being photographed met the standards outlined below: - images of only one grain - includes both polar and equatorial views - includes a scale bar - grain not damaged - images clear enough to see the diagnostic features of the grain such as pore shape and wall structure When a new grain was found which did not meet the criteria to be designated as a holotype, it was photographed and given only a code, not a Type number, until a grain of the same morphotype was observed which could then be photographed as the holotype for that type. Pollen taxa were counted using their Type numbers, and taxonomic information was assigned to Types when this information became available.'Where identifications are present, they are from:William D. Gosling, Charlotte S. Miller, Daniel A. Livingstone, Atlas of the tropical West African pollen flora, Review of Palaeobotany and Palynology, Volume 199, 2013, Pages 1-135, ISSN 0034-6667, http://dx.doi.org/10.1016/j.revpalbo.2013.01.003.Annie Vincens, Anne-Marie Lézine, Guillaume Buchet, Dorothée Lewden, Annick Le Thomas, African pollen database inventory of tree and shrub pollen types, Review of Palaeobotany and Palynology, Volume 145, Issue 1, 2007, Pages 135-141, ISSN 0034-6667, http://dx.doi.org/10.1016/j.revpalbo.2006.09.004.Riollet G, Bonnefille R. 1980. Pollens des savanes d’Afrique orientale. Paris: Éd. du Centre national de la recherche scientifique. Paris.van Campo M. 1974. Pollen et Spores d’Afrique tropicale. Talence: Association des Palynologues de Langue Francaise.Ybert J-P. 1979. Atlas de pollens de Côte d’Ivoire [Internet]. Paris: ORSTOM; [cited 2017 Feb 21]. Available from: http://www.documentation.ird.fr/hor/fdi:09859<br><br>
DOI: 10.6084/m9.figshare.5240956.v1
title: Modern pollen types, Ghana.

description: Modern pollen types from artificial pollen traps, observed in Ghana, tropical West Africa. This is my personal database of pollen types observed during my PhD thesis 'Modern pollen-vegetation relationships in Ghana, tropical West Africa'. Some scale bars missing from first 11 Holotypes; see excel sheet for pollen sizes. Many taxa have not been assigned botanical affinities. <br>Modern pollen was recovered from the following sites:Kogyae Forest Reserve, Savannah, Transition and Forest plots (slides with 'K' in code- see below)Bobiri Strict Nature Reserve (slides with 'B' in code- see below)Ankasa National Park (Slides with 'A' in code- see below)<br>Explanation of codes:'Pollen types were assigned codes, for example the 3rd grain (G3), photographed in Slide 28 (S28), Kogyae 2014 (K14), Transition vegetation plot (T), Trap 55 (T55) would be S28K14TT55G3. Types were numbered sequentially from 1 upwards, and Holotypes (sets of images which acted as a standard for that pollen type) were designated. Holotypes were designated when the grain being photographed met the standards outlined below: - images of only one grain - includes both polar and equatorial views - includes a scale bar - grain not damaged - images clear enough to see the diagnostic features of the grain such as pore shape and wall structure When a new grain was found which did not meet the criteria to be designated as a holotype, it was photographed and given only a code, not a Type number, until a grain of the same morphotype was observed which could then be photographed as the holotype for that type. Pollen taxa were counted using their Type numbers, and taxonomic information was assigned to Types when this information became available.'Where identifications are present, they are from:Gosling WD, Miller CS, Livingstone DA. 2013. Atlas of the tropical West African pollen flora. Review of Palaeobotany and Palynology<br>Annie Vincens, Anne-Marie Lézine, Guillaume Buchet, Dorothée Lewden, Annick Le Thomas, African pollen database inventory of tree and shrub pollen types, Review of Palaeobotany and Palynology, Volume 145, Issue 1, 2007, Pages 135-141, ISSN 0034-6667, http://dx.doi.org/10.1016/j.revpalbo.2006.09.004.Riollet G, Bonnefille R. 1980. Pollens des savanes d’Afrique orientale. Paris: Éd. du Centre national de la recherche scientifique. Paris.van Campo M. 1974. Pollen et Spores d’Afrique tropicale. Talence: Association des Palynologues de Langue Francaise.Ybert J-P. 1979. Atlas de pollens de Côte d’Ivoire [Internet]. Paris: ORSTOM; [cited 2017 Feb 21]. Available from: http://www.documentation.ird.fr/hor/fdi:09859<br><br>
DOI: 10.6084/m9.figshare.5240878
title: Supplementary Material for: Frontal Cortex and Hippocampal γ-Secretase Activating Protein Levels in Prodromal Alzheimer Disease

description: <b><i>Background:</i></b> β-Amyloid (Aβ) is the product of concerted cleavage of the amyloid precursor protein (APP) by β- and γ-secretases. However, the molecular mechanisms that regulate this process are not well understood. Recently, evidence was reported that γ-secretase activating protein (GSAP, 16 kDa), derived from a larger precursor protein (98 kDa), plays a role in Aβ metabolism through a mechanism involving its interaction with both γ-secretase and APP. However, a detailed evaluation of GSAP protein levels and their association with clinical and neuropathological variables are lacking during the clinical progression of Alzheimer disease (AD). <b><i>Methods:</i></b> We quantified levels of the GSAP precursor (98 kDa) and its active form (16 kDa) in the frontal cortex and hippocampus, areas displaying extensive Aβ and neurofibrillary tangle (NFT) pathology, in subjects who came to autopsy with a premortem clinical diagnosis of noncognitive impairment, mild cognitive impairment, mild to moderate AD, and severe AD using Western blotting. <b><i>Results:</i></b> Analysis found that 98-kDa GSAP levels were increased, while those of 16 kDa were reduced in the frontal cortex of severe-AD subjects. By contrast, GSAP levels remained stable in the hippocampus. Frontal cortex and hippocampal GSAP 98- and 16-kDa levels were not associated with Aβ, NFT, and neuropathological criteria across clinical groups. Interestingly, only neocortical 98-kDa GSAP values showed a significant correlation with the Mini-Mental State Examination and episodic memory scores. <b><i>Conclusions:</i></b> These data demonstrate that GSAP proteins are differentially dysregulated in severe AD, but only the full-length form was associated with cognitive test scores in AD.
DOI: 10.6084/m9.figshare.5240878.v1
title: Supplementary Material for: Frontal Cortex and Hippocampal γ-Secretase Activating Protein Levels in Prodromal Alzheimer Disease

description: <b><i>Background:</i></b> β-Amyloid (Aβ) is the product of concerted cleavage of the amyloid precursor protein (APP) by β- and γ-secretases. However, the molecular mechanisms that regulate this process are not well understood. Recently, evidence was reported that γ-secretase activating protein (GSAP, 16 kDa), derived from a larger precursor protein (98 kDa), plays a role in Aβ metabolism through a mechanism involving its interaction with both γ-secretase and APP. However, a detailed evaluation of GSAP protein levels and their association with clinical and neuropathological variables are lacking during the clinical progression of Alzheimer disease (AD). <b><i>Methods:</i></b> We quantified levels of the GSAP precursor (98 kDa) and its active form (16 kDa) in the frontal cortex and hippocampus, areas displaying extensive Aβ and neurofibrillary tangle (NFT) pathology, in subjects who came to autopsy with a premortem clinical diagnosis of noncognitive impairment, mild cognitive impairment, mild to moderate AD, and severe AD using Western blotting. <b><i>Results:</i></b> Analysis found that 98-kDa GSAP levels were increased, while those of 16 kDa were reduced in the frontal cortex of severe-AD subjects. By contrast, GSAP levels remained stable in the hippocampus. Frontal cortex and hippocampal GSAP 98- and 16-kDa levels were not associated with Aβ, NFT, and neuropathological criteria across clinical groups. Interestingly, only neocortical 98-kDa GSAP values showed a significant correlation with the Mini-Mental State Examination and episodic memory scores. <b><i>Conclusions:</i></b> These data demonstrate that GSAP proteins are differentially dysregulated in severe AD, but only the full-length form was associated with cognitive test scores in AD.
DOI: 10.6084/m9.figshare.5240863
title: Supplementary Material for: Cervical Alpha-Actinin-4 Is Upregulated in Women with Threatened Preterm Labor and Microbial Invasion of the Amniotic Cavity

description: <b><i>Objective:</i></b> To characterize the proteome profile of women with threatened preterm labor (PTL) below 34;0 weeks with and without microbial invasion of the amniotic cavity (MIAC) using mass spectrometry in the amniotic fluid (AF) and Western blot analysis in the cervical mucus and the vaginal fluid. <b><i>Subjects and Methods:</i></b> In the discovery phase, a case-control study including 8 women with MIAC and 7 without matched for gestational age at sampling was performed. Proteomic profile characterization was done using the LTQ VELOS Orbitrap mass spectrometer in the AF. In the validation phase, a selection of the proteins differentially expressed by mass spectrometry in the genital samples of a prospective cohort of 109 women was validated by Western blot analysis. <b><i>Results:</i></b> In the discovery phase, the mass spectrometry analysis identified a total of 444 proteins. Sixteen were chosen for validation, being involved in defense (calgranulin A, B, C, C-reactive protein), cytoskeletal remodeling (alpha-actinin-4 [ACTN-4], plastin-2, α2-antiplasmin, vitronectin), metabolism (cystatin-β, glucose 6 phosphate isomerase, glutathione S-transferase, prostaglandin D2 synthase, corticosteroid-binding globulin), and vascular (α1-antichymotrypsin, hemopexin, endosialin) pathways. In the validation phase, cervical ACTN-4 was the only significantly upregulated protein in women with MIAC with an odds ratio of 6.8 (<i>p</i> = 0.002). <b><i>Conclusions:</i></b> Cervical ACTN-4 was significantly upregulated in the group of women with PTL with MIAC.
DOI: 10.6084/m9.figshare.5240779
title: Angular dependent mobility

description: Mobility code and input files for the enantiopure and racemic crystal structures of 1-aza[6]helicene.
DOI: 10.6084/m9.figshare.5240779.v1
title: Angular dependent mobility

description: Mobility code and input files for the enantiopure and racemic crystal structures of 1-aza[6]helicene.
DOI: 10.6084/m9.figshare.5240761
title: Chromosomal and plasmid sequences from Bacillus thuringiensis

description: Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group.
DOI: 10.6084/m9.figshare.5240749
title: Experimental data

description: Experimental data presented in the paper
DOI: 10.6084/m9.figshare.5240749.v1
title: Experimental data

description: Experimental data presented in the paper
DOI: 10.6084/m9.figshare.5240761.v2
title: Chromosomal and plasmid sequences from Bacillus thuringiensis

description: Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group.
DOI: 10.6084/m9.figshare.5240761.v1
title: Chromosomal and plasmid sequences from Bacillus thuringiensis

description: Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group
DOI: 10.17632/sbxr7xxvnd.2
title: Pore sizes, porosity, and surface area of TPMS-based scaffold

description: This dataset enabled the researchers to design the tissue engineering scaffold computationally with a specific porosity and pore size by choosing the scaffold pattern (TPMS, or the customized implicit function), ω, and t. The TPMS-based scaffolds were generated from the marching cube algorithm (https://github.com/nodtem66/Scaffolder). The pore sizes (minimum Feret diameter and maximum Feret diameter), porosity (1 -scaffold volume / original volume), and surface area were acquired by the slice contour technique and geometric algorithm. The two parameters: angular frequency (ω) and iso-level (t), were introduce to customize the TPMS functions.
DOI: 10.6084/m9.figshare.5240650
title: Supplementary Material for: Sleep and Olfaction among Older Adults

description: <b><i>Background:</i></b> Sleep and olfaction are both critical physiological processes that tend to worsen with age. Decline in olfaction can be an early indicator of neurodegenerative diseases, whereas poor sleep quality is associated with reduced physical and mental health. Given associations with aging-related health declines, we explored whether variations in sleep were associated with olfactory function among older adults. <b><i>Methods:</i></b> We assessed the relationship between sleep characteristics and olfaction among 354 community-dwelling older adults. Olfaction was measured using a validated field and survey research tool. Sleep characteristics were measured using wrist actigraphy and with self-report of sleep problems. We fit structural equation models of latent constructs of olfaction based on olfactory task items and let this be a function of each sleep characteristic. <b><i>Results:</i></b> Actigraph sleep quality measures were associated with odor identification, but not with odor sensitivity. Longer duration sleepers had worse odor sensitivity compared to medium (58 h) sleepers, but sleep duration was not associated with odor identification. Reported sleep problems and reported usual duration were not associated with olfaction. <b><i>Conclusions:</i></b> Diminished sleep quality was associated with reduced capacity to identify odors. Determining whether this is a causal association will require further study and longitudinal data.
DOI: 10.6084/m9.figshare.5240614
title: Dataset S1. List of Red Sea and Mediterranean bivalve species used in the analyses. from Climate change and body size shift in Mediterranean bivalve assemblages: unexpected role of biological invasions

description: List of bivalve species reported from shelf depths in the Mediterranean Sea and the Red Sea, their alien status in the Mediterranean, body size, and taxonomic and functional affiliation.
DOI: 10.6084/m9.figshare.5240608
title: Dataset UK A&B Survey-cleaned.sav

description: <b>Survey data of 1,358 management practitioners in the UK regarding attitudes and barriers towards evidence-based practice in management. </b>