cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121475.v1
title: Supplementary Material for: Analysis of Thioester-Containing Proteins during the Innate Immune Response of Drosophila melanogaster

description: Thioester-containing proteins (TEPs) are conserved proteins among insects that are thought to be involved in innate immunity. In <i>Drosophila</i>, the <i>Tep</i> family is composed of 6 genes named <i>Tep1–Tep6</i>. In this study, we investigated the phylogeny, expression pattern and roles of these genes in the host defense of <i>Drosophila</i>. Protostomian<i> Tep </i>genes are clustered in 3 distinct branches, 1 of which is specific to mosquitoes. Most <i>D. melanogaster Tep</i> genes are expressed in hemocytes, can be induced in the fat body, and are expressed in specific regions of the hypodermis. This expression pattern is consistent with a role in innate immunity. However, we find that TEP1, TEP2, and TEP4 are not strictly required in the body cavity to fight several bacterial and fungal infections. One possibility is that <i>Drosophila</i> TEPs act redundantly or that their absence can be compensated by other components of the immune response. TEPs may thus provide a subtle selective advantage during evolution. Alternatively, they may be required in host defense against specific as yet unidentified natural pathogens of <i>Drosophila</i>.
DOI: 10.6084/m9.figshare.14447673.v1
title: Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa.gz

description: DNA sequence used for OSC Training Workshop<br>
DOI: 10.6084/m9.figshare.20071916.v1
title: Supplementary Material for: Sex-disaggregated analysis of biology, treatment tolerability and outcome of Multiple Myeloma in a German cohort

description: Introduction: Multiple Myeloma (MM) is a plasma cell disease that affects more men than women. Although there is an obvious imbalance in incidence, knowledge on differences in biology and outcome between the sexes is surprisingly rare. Methods: We performed a unicentric retrospective analysis of patients with MM treated at a tertiary cancer center between 2003 and 2018. Results: We present sex-disaggregated analysis of the characteristics and outcome of MM in a cohort of 655 patients (median age at diagnosis 62 years; 363 men with a median age at diagnosis 62 years and 292 women with a median age at diagnosis 63 years, p=0.086). Most patients (n=561, 86%) received myeloma-specific treatment. Median overall survival was 76 months (95% CI 63 – 89) (72 months in men [95% CI 54 – 90] and 83 months in women [95% CI 66 – 100], p=ns). Apart from a higher incidence of moderate and severe anaemia in women (p&lt;0.001) there were no statistically significant differences in the biology of the underlying MM. Similarly, in the group of patients who received high-dose therapy with autologous stem cell transplantation (ASCT, n=313), no statistically significant differences apart from more frequent anaemia in women were detected regarding the biology of the disease. However, there was a trend towards a higher plasma cell infiltration of the bone marrow and towards more frequent high-risk features in women. In contrast, relevant comorbidities were significantly more common in men (for example coronary heart disease in 13% of men vs. 2% of women, p&lt;0.001). Toxicities after ASCT were not significantly different between the sexes with the exception of severe mucositis, which occurred in 22% of men vs. 40% of women (p=0.001). Conclusion: In conclusion, this first sex-disaggregated analysis of MM patients in Germany supports previous findings that survival is comparable amongst sexes, but women experience more toxicity of high-dose therapy. The higher incidence of clinically relevant anaemia in women warrants further investigation to exclude underlying treatable causes.
DOI: 10.17028/rd.lboro.26090809.v1
title: Supplementary information files for "An overheating criterion for bedrooms in temperate climates: Derivation and application"

description: Supplementary files for article "An overheating criterion for bedrooms in temperate climates: Derivation and application"Adequate sleep is crucial to human health and well-being and elevated night-time temperatures can degrade sleep quality. European countries with temperate climates use temperature thresholds between 25°C and 28°C to identify homes that are overheated. The current UK bedroom threshold of 26°C, is based on one small study, which is now over 45 years old. An extensive literature review indicated that with modern summertime bedding and bedwear, which enables body coverage to be easily adjusted, thermal comfort can be achieved for night-time bedroom temperatures up to approximately 29°C. Temperatures measured in 591 bedrooms during England’s hottest ever summer, 2018, are re-analysed. The prevalences of night-time overheating generated by alternative criteria are compared with the prevalences generated by the established adaptive overheating criterion. Comparisons are made for homes with different dwelling and household characteristics. Finally, a new overheating criterion is proposed based on the mean night-time bedroom temperature, with thresholds between 26°C and 29°C depending on the application of the criterion. The allowable exceedance of the chosen threshold is limited to seven nights between May and September. Adopting thresholds of 27°C for vulnerable households and 28°C for others, 23% (5.5 million) of the main bedrooms in English homes were deemed to be overheated in the hot summer of 2018, far fewer than the 69% obtained using the current UK bedroom criterion. Irrespective of the threshold chosen, there were clear, consistent and significant differences in overheating prevalence depending on dwelling and household characteristics. The proposed new overheating criterion is applicable to unconditioned bedrooms in temperate regions. It seeks to strike a balance between the risk that hot bedrooms will be air-conditioned and the risk of temperatures detrimental to a “good nights’ sleep”. Practical Application A new overheating criterion is proposed to identify overheated bedrooms. It adopts the familiar format of a temperature threshold and an allowable exceedance. It is applicable in temperate climates when people are asleep in unconditioned bedrooms. The criterion is intended to aid the interpretation of night-time temperatures predicted by dynamic thermal models and temperature measurements in existing bedrooms. It is applicable to individuals of different heat sensitivity, the design of new homes or the refurbishment of existing homes. With further testing and refinement, it offers a credible replacement to the existing UK bedroom criterion given in CIBSE Guide A, TM59 and in other guides. It can thus underpin the new overheating regulations, Part O, for the design of new dwellings in England.© The Authors, CC BY 4.0
DOI: 10.6084/m9.figshare.25211768.v1
title: Supplementary Material for: Colonic diverticulosis at colonoscopy in Africa: a systematic review and meta-analysis of pooled estimates

description: Background: There is need to ascertain any epidemiologic shift of diverticulosis among Africans with traditionally high fiber diet consumption patterns and rare diverticulosis prevalence. 
Methods: We systematically searched PubMed, Scopus, Cochrane Library, African Journal Online (AJOL) and Google Scholar. Eligibility criteria included full text observational and experimental human colonoscopy studies on asymptomatic and symptomatic African population from 1985-2022. Case reports, conference abstracts, dissertations, systematic reviews, and studies lacking colonoscopy findings were excluded. NIH quality assessment tool for observational cohort and cross-sectional studies was used to assess risk of bias. Meta-analysis was performed using the random-effect model. Heterogeneity was assessed using inconsistency (I2) statistics. 
Results: Thirty studies were included. Pooled prevalence rate of colonic diverticulosis was 9.1% (95%CI 7.1-11.2; I2=96.3%) with highest regional prevalence rate in West African studies at 11.3% (95%CI 7.6-14.9; I2=96.2%). Proportion of individuals with diverticulosis ≥50 years and male sex were 86.9 % (95%CI 80.5-92.1) and 65.2% (95%CI 55.0-74.8), respectively. Left colon had the highest diverticulosis frequency [37% (148/400)]. 
Bleeding/inflammation complications were sparingly detected [OR 0.2 (95%CI 0.03-0.75;p&lt;0.0001)].
Conclusion: Colonic diverticulosis was most common in males aged &gt;50. Left was colon predominantly affected. Regional variation in detection of diverticulosis was reported across Africa.
DOI: 10.6084/m9.figshare.26351830.v1
title: InfeRNAl and HMMer3 databases used to find introns

description: InfeRNAl and HMMer3 databases used to find introns and delineate exon borders (used by the "find_introns.py" script from GitHub repository). Based on RFAM 14.9 and GISSD (last downloadable version 5.03.2014) and PHROGS database v4 (converted to HMMer3 format using "create_hmms.py" script from pharokka v1.7.3; https://github.com/gbouras13/pharokka/blob/master/scripts/create_hmms.py)
DOI: 10.6084/m9.figshare.24081894.v1
title: Long-term trends of local bird populations based on monitoring schemes: are they suitable for justifying management measures?

description: R workspace files containing list-type objects with the count data of the birds species analysed in <i>unmarked</i> format for each study site, La Muela and Carrascoy, respectively. Count data are composed the point sites in each study area in rows and the surveys in columns (corresponding to 2 visits per year).
DOI: 10.6084/m9.figshare.28191596.v1
title: Data related to Jeong*, Zheng* et al.

description: This data set was generated by recording the electrical activity of inhibitory and excitatory neurons simultaneously and by selectively stimulating neurons in mice during a spatial navigation task.See VR_NoveltySpreadsheet for metadata
DOI: 10.6084/m9.figshare.6235070.v1
title: Rapid maxillary expansion in mouth breathers: a short-term skeletal and soft-tissue effect on the nose

description: Abstract Introduction Rapid maxillary expansion can change the form and function of the nose. The skeletal and soft tissue changes can influence the esthetics and the stability of the results obtained by the procedure. Objective The aim of this retrospective study was to evaluate the short-term effects of rapid maxillary expansion on the skeletal and soft tissue structures of the nose, in mouth-breathing patients, using a reliable and reproducible, but simple methodology, with the aid of computed tomography. Methods A total of 55 mouth-breathing patients with maxillary hypoplasia were assessed and were divided into an experimental group treated with rapid maxillary expansion(39 patients, 23 of which were male and 16 female, with an average age of 9.7 years and a standard deviation of 2.28, ranging from 6.5 to 14.7 years) and a control group (16 patients, 9 of which were male and 7 female, with an average age of 8.8 years, standard deviation of 2.17, ranging from 5.11 to 13.7 years). The patients of the experimental group were submitted to multislice computed tomography examinations at two different points in time: (T1) pre-rapid maxillary expansion and (T2) three months after the procedure. The control group underwent to the same exams at the same intervals of time. Four skeletal and soft tissue variables were assessed, comparing the results of T1 and T2. Results There was in the experimental group a significant increases in all the skeletal and soft tissue variables (p &lt; 0.05) but no significant alteration was found in the control group. When comparing the experimental group and the control group, the most important change occurred in the width of the pyriform aperture (p &lt; 0.001). Conclusion Rapid maxillary expansion is capable of altering the shape and function of the nose, promoting alterations in skeletal and soft tissue structures. This kind of study may, in the future, permit the proper planning of esthetic procedures at the tip and base of the nose and also the performance of objective measurements in early or late surgical outcomes.
DOI: 10.6084/m9.figshare.12826391.v1
title: Supplementary Material for: Combined Multimodal Cerebral Monitoring and Focused Hemodynamic Assessment in the First 72 h in Extremely Low Gestational Age Infants

description: <b><i>Background:</i></b> Characteristic changes in cerebral saturation (CrSO<sub>2</sub>), amplitude-integrated electroencephalography (aEEG), and echocardiography (ECHO) may be associated with intraventricular hemorrhage (IVH); however, the feasibility of their combined application is not known. <b><i>Objective:</i></b> The aim of this work was to investigate the feasibility and safety of combined multimodal cerebral and hemodynamic monitoring in extremely low gestational age (ELGA) infants in the first 72 h after birth. <b><i>Methods:</i></b> In this prospective ­observational study of 50 infants born between 23 + 0 and 27 + 6 weeks gestation, we measured CrSO<sub>2</sub> and aEEG, starting &lt;8 h until 72 h of age. Sequential echocardiography and head ultrasound were performed at 4–8, 12–18, 24–30, and 48–60 h of age. The primary outcome was feasibility of multimodal monitoring, defined as &gt;75% of the subjects satisfying at least 3/4 criteria: (a) CrSO<sub>2</sub> and (b) aEEG monitoring each for &gt;75% of the time, and (c) at least 2 out of 4 ECHO and (d) head ultrasounds (at least one by age 24 h). Adverse reactions to sensors, desaturation, and bradycardia during ultrasound studies were recorded. <b><i>Results:</i></b> Fifty infants were enrolled over 14 months. Multimodal monitoring was feasible in 49 (98%) infants. Forty-one (82%) infants fulfilled all 4 criteria. Mild erythema below CrSO<sub>2</sub> sensors lasting 3–8 h without skin breakdown was noted in 8/50 subjects (16%). Desaturation was noted during 17/197 (8.6%) of the ultrasound studies. In total, 26/50 (52%) infants developed IVH (grade I/II, <i>n</i> = 22; grade III/IV, <i>n</i> = 4). <b><i>Conclusion:</i></b> Multimodal monitoring is feasible, safe, and well tolerated in ELGA infants in the first 72 h after birth.
DOI: 10.6084/m9.figshare.27698115.v1
title: Hyperparameter Grid Data

description: Results of large hyperparameter searches on 5 KGs (CoDexSmall, DBepdai50, Kinships, OpenEA, and UMLS) with 3 KGs (ComplEx, UMLS, and TransE). Experiments for ComplEx are given in quadruplicate.
DOI: 10.6084/m9.figshare.7330526.v1
title: Human Convalescent Serum Sample after CHIKV and DENV seroconversion.

description: Human Convalescent Serum Sample collected after CHIKV and DENV seroconversion.
DOI: 10.6084/m9.figshare.7868573.v1
title: Workshop Zoeken naar Onderzoeksdata_VOGIN-IP 2019

description: Slides en opdrachten van de workshop 'Zoeken naar onderzoeksdata', gegeven op de VOGIN-IP lezing van 2019.
DOI: 10.6084/m9.figshare.11983836.v5
title: High-Dimensional Copula Variational Approximation Through Transformation

description: Variational methods are attractive for computing Bayesian inference when exact inference is impractical. They approximate a target distribution—either the posterior or an augmented posterior—using a simpler distribution that is selected to balance accuracy with computational feasibility. Here, we approximate an element-wise parametric transformation of the target distribution as multivariate Gaussian or skew-normal. Approximations of this kind are implicit copula models for the original parameters, with a Gaussian or skew-normal copula function and flexible parametric margins. A key observation is that their adoption can improve the accuracy of variational inference in high dimensions at limited or no additional computational cost. We consider the Yeo–Johnson and inverse G&H transformations, along with sparse factor structures for the scale matrix of the Gaussian or skew-normal. We also show how to implement efficient reparameterization gradient methods for these copula-based approximations. The efficacy of the approach is illustrated by computing posterior inference for three different models using six real datasets. In each case, we show that our proposed copula model distributions are more accurate variational approximations than Gaussian or skew-normal distributions, but at only a minor or no increase in computational cost. Supplementary materials comprising an online appendix, MATLAB code to implement the method, and the datasets employed, are available online.
DOI: 10.6084/m9.figshare.27221061.v1
title: Single-nucleus chromatin landscape dataset of mouse PDX models of medulloblastoma

description: In this study, a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) was employed to generate comprehensive chromatin accessibility maps. The data were obtained from 80,273 cells derived from four distinct medulloblastoma xenografts: subcutaneous (SUB) and orthotopic (ORTH) xenograft models of the G3 and SHH subtypes of medulloblastoma.<br>
DOI: 10.6084/m9.figshare.25638120.v1
title: Raw data for microhardness test.docx

description: Raw data for microhardness test
DOI: 10.6084/m9.figshare.28845788.v1
title: ITS from bark beetle gallery

description: ITS Raw sequcencing data is updated.
DOI: 10.17608/k6.auckland.23549817.v1
title: Photo-Identification Catalogue of Long-finned Pilot Whales off Eastern Aotearoa/New Zealand

description: This catalogue is a collection of uniquely identified long-finned pilot whale dorsal fin photos from the east coast of Aotearoa/New Zealand between 2003-2019. Where possible there is a right and left side image of each dorsal fin. <br> The photograph codes are as follows:<br> NZ = New Zealand Gme = <em>Globicephala melas</em> (species name)<br> XXX = unique number for each whale<br> R/L = right / left (side of the whale)<br> <br> <br> All work was undertaken by researchers from the Far Out Research Collective (https://www.farout.org.nz/) in collaboration with the University of Auckland-Waipapa Taumata Rau. The research was conducted under a Department of Conservation permit with approval from mana whenua (Indigenous people from the study areas). The catalogue is curated by Catherine Meyer, University of Auckland (cmey106@aucklanduni.ac.nz) and Jochen Zaeschmar. Please contact Catherine if you have any queries.
DOI: 10.17632/3bpz84nj6z.1
title: Experimental handaxe data

description: Metric and flaking data for 80 flint handaxes produced for an experiment tracking reduction trajectories from flake blanks, to rough-outs, to final forms, prepared for publication. Metric data was produced via AGMT3-D (https://sourceforge.net/projects/artifact-geomorph-toolbox-3d/) with the exception of CEAM angle which used MATLAB code developed by Muller et al. (https://www.nature.com/articles/s41598-024-57450-y.pdf), and circumference and crushed circumference were manually estimated with a tape measurer.
DOI: 10.6084/m9.figshare.25927438.v1
title: Investigating Tool Usage in Ontology Engineering: a Survey

description: Aiming at getting evidence about the use of tools to support OE, we conducted a survey with 74 ontology engineers. We investigated which tools have been used, their main characteristics, benefits and difficulties perceived when using them, and properties considered important in OE tools. The results indicate that tools have been widely adopted, but some issues, such as integration problems and scope limitations, still need to be addressed. This paper presents the survey, its results, and discusses the main findings.
DOI: 10.6084/m9.figshare.19902595.v2
title: Smale et al 2022 raw stipe assemblage dataset

description: Stipe associated assemblage data of the kelps Laminaria ochroleuca and Laminaria hyperborea from Plymouth Sound UK
DOI: 10.6084/m9.figshare.25108460.v1
title: Data for Zvereva et al. (2024): “Does spatial variation in insect herbivory match variations in plant quality? A meta-analysis”

description: Variation in herbivore pressure at different temporal and spatial scales has often been predicted from patterns in plant traits considered as antiherbivore defences. Here, we tested whether spatial variation in field insect herbivory is associated with the variation in plant quality for herbivores by conducting a meta-analysis of 223 correlation coefficients between herbivory levels and the expression of selected plant traits. We found no overall correlation between herbivory and either concentrations of plant secondary metabolites or values of physical leaf traits. This result was due to both the large number of low correlations and the opposing directions of high correlations in individual studies. Field herbivory demonstrated a significant association only with nitrogen: herbivore pressure increased with an increase in nitrogen concentration in plant tissues. Thus, our meta-analysis does not support either theoretical prediction, i.e. that plants possess high antiherbivore defences in localities with high herbivore pressure or that herbivory is low in localities where plant defences are high. We conclude that information about putative plant defences is insufficient to predict plant losses to insects in field conditions and that the only bottom-up factor driving spatial variation in insect herbivory is plant nutritive value, i.e. foliar nitrogen concentration.
DOI: 10.6084/m9.figshare.5129617.v1
title: Supplementary Material for: Rat Osteosarcoma Cells as a Therapeutic Target Model for Osteoregeneration via Sclerostin Knockdown

description: There are various conceptually different strategies to improve bone regeneration and to treat osteoporosis, each with distinct inherent advantages and disadvantages. The use of RNA interference strategies to suppress the biological action of catabolic factors or antagonists of osteogenic proteins is promising, and such strategies can be applied locally. They are comparably inexpensive and do not suffer from stability problems as protein-based approaches. In this study, we focus on sclerostin, encoded by the SOST gene, a key regulator of bone formation and remodeling. Sclerostin is expressed by mature osteocytes but also by late osteogenically differentiated cells. Thus, it is difficult and requires long-term cultures to investigate the effects of SOST silencing on the expression of osteogenic markers using primary cells. We, therefore, selected a rat osteosarcoma cell line, UMR-106, that has been shown to express SOST and secrete sclerostin in a comparable fashion as late osteoblasts and osteocytes. We investigated the effects of differentiating supplements on SOST expression and sclerostin secretion in UMR-106 cells and found that addition of 100 ng/ml of bone morphogenetic protein (BMP)-2 strongly induced sclerostin secretion, whereas dexamethasone inhibited secretion. Effects of silencing SOST in UMR-106 cells cultured in various differentiation media including BMP-2 and/or dexamethasone were determined next with the aim to find promising test conditions for a readout system for the evaluation of future small interfering RNA release formulations for local induction of bone formation. We found a direct correlation between attenuated SOST expression and an increase in the osteogenic potential of UMR-106 cells. The combination of SOST silencing and BMP-2 could synergistically improve osteogenic factors. A lowered proliferation rate in silenced groups may indicate a faster switch to differentiation.