cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28590501.v1
title: Dental macro- and mesowear in two vole species under spatial and temporal dynamics of feeding conditions: implications for paleodiet reconstruction

description: One indirect method of animal diet reconstruction is the dental wear analysis. Species of the generic group <i>«Microtus»</i> exhibit dietary plasticity, and the structure of their cheek teeth allows for a subtle response to changes in diet composition. Their remains are abundant and well-preserved in palaeontological localities. This study analysed the dental macro- and mesowear in <i>Microtus arvalis</i> sensu lato and the <i>Alexandromys oeconomus</i>. The investigation was conducted over two years, from April to September, on two plots with different compositions of plant communities, using an intravital impressions method. Both species showed similar seasonal dental wear signals, indicating a transition from low-abrasive food in spring to more abrasive food in summer, followed by a return to low-abrasive diets in autumn. <i>A. oeconomus</i> displayed less worn but more abrasive mesowear compared to <i>M. arvalis</i> s.l. These differences may be attributed to morphological variations in the molars of the species and their feeding selectivity. Slight variations in dental wear among the animals from the two study plots likely reflect differences in their diets. Thus, using dental mesowear of the generic group <i>«Microtus»</i> species in palaeoenvironmental studies can provide a broad picture of animal habitats and foraging conditions in the past.
DOI: 10.11588/duerer.online.69774a185d4aa
title: Bildnis des Albrecht Dürer, https://d-nb.info/gnd/1194887619
DOI: 10.6084/m9.figshare.31149076
title: <b>Italian Style Coffee consumption and </b><b>Metabolically Dysfunctional-Associated Steatotic Liver Disease (MASLD):</b><b> </b><b>A Cohort Population Study in Southern Italy</b>

description: Metabolic dysfunction-associated steatotic liver disease (MASLD) is currently the most prevalent chronic liver disease globally, and its incidence is rising consistently along with the prevalence of type 2 diabetes mellitus and overweight/obesity. Coffee has a unique chemical composition consisting of numerous compounds that contribute to metabolic and liver health. Nevertheless, it is not yet clear what dose of coffee should be safely consumed to positively impact MASLD. The current study aimed to examine the association between the consumption of Italian-style coffee in terms of cups per day, and the protection against MASLD within a cohort from southern Italy. The results indicated that the risk of developing MASLD decreased as daily coffee consumption increased when compared to consuming less than one cup per day (1 cup: 0.497 95% CI 0.254; 0.973; 2 cups: 0.443 95% CI 0.230; 0.853; 3 cups: 0.430 95% CI 0.216; 0.857), with the greatest benefit at 4-6 cups (OR: 0.385; 95% CI 0.175; 0.845). These findings suggest that moderate coffee consumption, specifically Italian-style coffee, may offer potential benefits due to its unique chemical composition and preparation method. This type of coffee may provide specific protective effects on liver and metabolic health. Given its cultural significance and positive metabolic attributes, Italian-style coffee has the potential to be recognized as a functional food for the prevention of MASLD.
DOI: 10.6084/m9.figshare.31149076.v1
title: <b>Italian Style Coffee consumption and </b><b>Metabolically Dysfunctional-Associated Steatotic Liver Disease (MASLD):</b><b> </b><b>A Cohort Population Study in Southern Italy</b>

description: Metabolic dysfunction-associated steatotic liver disease (MASLD) is currently the most prevalent chronic liver disease globally, and its incidence is rising consistently along with the prevalence of type 2 diabetes mellitus and overweight/obesity. Coffee has a unique chemical composition consisting of numerous compounds that contribute to metabolic and liver health. Nevertheless, it is not yet clear what dose of coffee should be safely consumed to positively impact MASLD. The current study aimed to examine the association between the consumption of Italian-style coffee in terms of cups per day, and the protection against MASLD within a cohort from southern Italy. The results indicated that the risk of developing MASLD decreased as daily coffee consumption increased when compared to consuming less than one cup per day (1 cup: 0.497 95% CI 0.254; 0.973; 2 cups: 0.443 95% CI 0.230; 0.853; 3 cups: 0.430 95% CI 0.216; 0.857), with the greatest benefit at 4-6 cups (OR: 0.385; 95% CI 0.175; 0.845). These findings suggest that moderate coffee consumption, specifically Italian-style coffee, may offer potential benefits due to its unique chemical composition and preparation method. This type of coffee may provide specific protective effects on liver and metabolic health. Given its cultural significance and positive metabolic attributes, Italian-style coffee has the potential to be recognized as a functional food for the prevention of MASLD.
DOI: 10.5281/zenodo.18374534
title: Data for Mated female dispersal and solitary gallery initiation in Ips typographus: evidence from a range expansion gradient

description: Supplementary datasets for the article: Mated female dispersal and solitary gallery initiation in Ips typographus: evidence from a range expansion gradient.

This repository contains the supplementary data associated with the article. It includes two video files illustrating the behaviour of Ips typographus females turning inside and outside their galleries, as well as the raw data tables used for all statistical analyses presented in the study.
DOI: 10.5281/zenodo.18374535
title: Data for Mated female dispersal and solitary gallery initiation in Ips typographus: evidence from a range expansion gradient

description: Supplementary datasets for the article: Mated female dispersal and solitary gallery initiation in Ips typographus: evidence from a range expansion gradient.

This repository contains the supplementary data associated with the article. It includes two video files illustrating the behaviour of Ips typographus females turning inside and outside their galleries, as well as the raw data tables used for all statistical analyses presented in the study.
DOI: 10.5281/zenodo.18374273
title: Profiling Participants of Community Question‐Answering Sites: An Empirical Study of Stack Exchange

description: ABSTRACT

Background. Gray literature (GL) can provide valuable insights into software engineering (SE) practitioners’ opinions, behavior, and practices. Since SE professionals widely use community question- answering sites (CQAs), their usage has grown in SE research. De- spite the popularity of GL in SE studies, our research community still needs to grasp how to thoroughly characterize the CQAs par- ticipants that produce the content considered in their research. Objective. This paper aims to discuss the profiling of participants who contribute to CQAs to ensure the validity of their contributions to GL-based research. Method. To achieve this goal, we discuss our experience mining the profile of participants in the Stack Ex- change Project Management (SEPM) CQA. We have used this site in previous GL studies and argue that its size and popularity make it an interesting testbed for this study. We selected all the SEPM participants’ profiles with links to their LinkedIn pages and voting privileges on the SEPM site. We analyzed 929 profiles quantitatively and qualitatively, identifying their work experiences and how they interact within the forum. Results. We outline the participant’s characteristics by identifying 1) their roles and experience level and 2) the impact of their contributions in the forum. Conclusion. Par- ticipant profiling is essential in GL research. This paper discusses it from the perspective of SE CQAs and provides insights into how participants in these communities can be profiled.
DOI: 10.5281/zenodo.18374274
title: Profiling Participants of Community Question‐Answering Sites: An Empirical Study of Stack Exchange

description: ABSTRACT

Background. Gray literature (GL) can provide valuable insights into software engineering (SE) practitioners’ opinions, behavior, and practices. Since SE professionals widely use community question- answering sites (CQAs), their usage has grown in SE research. De- spite the popularity of GL in SE studies, our research community still needs to grasp how to thoroughly characterize the CQAs par- ticipants that produce the content considered in their research. Objective. This paper aims to discuss the profiling of participants who contribute to CQAs to ensure the validity of their contributions to GL-based research. Method. To achieve this goal, we discuss our experience mining the profile of participants in the Stack Ex- change Project Management (SEPM) CQA. We have used this site in previous GL studies and argue that its size and popularity make it an interesting testbed for this study. We selected all the SEPM participants’ profiles with links to their LinkedIn pages and voting privileges on the SEPM site. We analyzed 929 profiles quantitatively and qualitatively, identifying their work experiences and how they interact within the forum. Results. We outline the participant’s characteristics by identifying 1) their roles and experience level and 2) the impact of their contributions in the forum. Conclusion. Par- ticipant profiling is essential in GL research. This paper discusses it from the perspective of SE CQAs and provides insights into how participants in these communities can be profiled.
DOI: 10.6084/m9.figshare.28743185
title: Comparing LASSO and IPF-LASSO for multi-modal data: variable selection with Type I error control

description: Variable selection in high-dimensional regression models is challenging. Thus, developing stable and reliable methods for variable selection is essential. Omics data, a common source of high-dimensional data, brings the added complexity of integrating diverse genomic layers into the analysis. The IPF-LASSO model has previously addressed this by applying distinct penalty parameters for each data modality. However, incorporating heterogeneous data layers into variable selection with Type I error control remains an open problem. To address this, we applied stability selection to control the number of false positives in both IPF-LASSO and standard LASSO models. Our study aimed to compare the two methods, investigating whether introducing different penalty parameters per data modality enhances statistical power while controlling false positives. Two high-dimensional data structures were investigated in simulations, one with independent data and the other with correlated data. We also applied the models to breast cancer treatment data, where IPF-LASSO identified relevant clinical variables.
DOI: 10.6084/m9.figshare.28743185.v1
title: Comparing LASSO and IPF-LASSO for multi-modal data: variable selection with Type I error control

description: Variable selection in high-dimensional regression models is challenging. Thus, developing stable and reliable methods for variable selection is essential. Omics data, a common source of high-dimensional data, brings the added complexity of integrating diverse genomic layers into the analysis. The IPF-LASSO model has previously addressed this by applying distinct penalty parameters for each data modality. However, incorporating heterogeneous data layers into variable selection with Type I error control remains an open problem. To address this, we applied stability selection to control the number of false positives in both IPF-LASSO and standard LASSO models. Our study aimed to compare the two methods, investigating whether introducing different penalty parameters per data modality enhances statistical power while controlling false positives. Two high-dimensional data structures were investigated in simulations, one with independent data and the other with correlated data. We also applied the models to breast cancer treatment data, where IPF-LASSO identified relevant clinical variables.
DOI: 10.6084/m9.figshare.28532897
title: On an integer-valued stochastic intensity model for time series of counts

description: We propose a broad class of count time series models, the mixed Poisson integer-valued stochastic intensity (INSI) models. The proposed parameter- driven specification in which the log-intensity follows a drifted autoregression encompasses a wide range of conditional distributions of counts. We study its probabilistic structure and design Markov chain Monte Carlo estimation algorithms for two cases; the Poisson and the negative binomial distributions. The methodology is applied to simulated data as well as to various data sets. Model comparison is conducted using marginal likelihoods and forecast evaluation using point and density forecasts. The INSI specifications were also compared against the Poisson and negative binomial integer-valued GARCH (INGARCH) models, within the Bayesian framework, where the former dominated the latter.
DOI: 10.6084/m9.figshare.28532897.v1
title: On an integer-valued stochastic intensity model for time series of counts

description: We propose a broad class of count time series models, the mixed Poisson integer-valued stochastic intensity (INSI) models. The proposed parameter- driven specification in which the log-intensity follows a drifted autoregression encompasses a wide range of conditional distributions of counts. We study its probabilistic structure and design Markov chain Monte Carlo estimation algorithms for two cases; the Poisson and the negative binomial distributions. The methodology is applied to simulated data as well as to various data sets. Model comparison is conducted using marginal likelihoods and forecast evaluation using point and density forecasts. The INSI specifications were also compared against the Poisson and negative binomial integer-valued GARCH (INGARCH) models, within the Bayesian framework, where the former dominated the latter.
DOI: 10.6084/m9.figshare.28537274
title: On the non-central Dirichlet distribution

description: Our goal is to provide a valid point of reference for the theoretical study and the practical use of the Non-central Dirichlet distribution. An Achilles' heel of such model is the limited mathematical manageability of its joint density function, which is the main obstacle to the conduct of a further exploration of it. This paper is thus intended to enrich the little range of the already existing findings referring to this distribution by offering new insights into its analysis. An operating procedure to employ the Non-central Dirichlet as a model to be fitted to data consisting of vectors of proportions subject to the unit-sum constraint is illustrated. Simulation studies are performed to confirm the validity of the derived moments formula and to investigate the finite-sample performance of the asymptotic properties of the Maximum-Likelihood estimators and the Likelihood-Ratio tests used to accomplish the abovementioned applied matters.
DOI: 10.6084/m9.figshare.28537274.v1
title: On the non-central Dirichlet distribution

description: Our goal is to provide a valid point of reference for the theoretical study and the practical use of the Non-central Dirichlet distribution. An Achilles' heel of such model is the limited mathematical manageability of its joint density function, which is the main obstacle to the conduct of a further exploration of it. This paper is thus intended to enrich the little range of the already existing findings referring to this distribution by offering new insights into its analysis. An operating procedure to employ the Non-central Dirichlet as a model to be fitted to data consisting of vectors of proportions subject to the unit-sum constraint is illustrated. Simulation studies are performed to confirm the validity of the derived moments formula and to investigate the finite-sample performance of the asymptotic properties of the Maximum-Likelihood estimators and the Likelihood-Ratio tests used to accomplish the abovementioned applied matters.
DOI: 10.60817/v2fd-cq35
title: MEG dataset of continuous speech with five-level noise vocoding
DOI: 10.34894/hypucw
title: Ziegler folio transcriptions (deprecated)

description: Transcriptions of the folio's as described &lt;a href="http://www.iisg.nl/migration/ziegler/archivalien.php"&gt; here&lt;/a&gt;.
DOI: 10.5281/zenodo.18338616
title: Genome annotation of Arctia plantaginis (ArcPla_EST)

description: The wood tiger moth, Arctia plantaginis, is an important model organism for the study of polymorphism in warning colour. One major colour locus has been identified but studying its association with other traits as well as signatures of selection has been limited by the lack of a contiguous reference genome. A previous assembly consisted of more than 1000 scaffolds. We present the first chromosome level genome assembly based on PacBio-HiFi data and linkage map information. The final assembly spans 589 Mb consisting of 31 telomere-to-telomere chromosomes with a N50 scaffold length of 21.2 MB. The BUSCO analysis (n = 5,760) indicated a high completeness of 98.1 % with 97.5 % present as single copy and 0.6 % as duplicated. 17,456 genes were identified and 42.18 % of the genome was classified as repetitive. This new assembly provides an important resource for future research using genomic tools for studying the genetic basis and evolutionary mechanisms underlying colour polymorphisms in this species.

We used Liftoff v1.6.3 (1) to lift over the previous annotation from the W-reference (2)  to the new genome assembly, with the option to detect additional gene copies. A total of 17,456 genes (excluding additional copies) were successfully lifted over from the previous reference (97.4 %) to the new assembly. Overall, 27.0 % of the genome is within genes and 4.7 % within coding regions. The average length of single-copy genes was 8,946 bp, with an average of 6.5 coding sequences (CDS) per gene. Average CDS length was 238.5 bp.

The repeat annotation was generated using  RepeatModeler2 v.2.0.6 26 (3). 

 

1) Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639-1643 (2021).

2) Yen, E. C. et al. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 9 (2020).

3) Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. P Natl Acad Sci USA 117, 9451-9457 (2020).
DOI: 10.5281/zenodo.18338617
title: Genome annotation of Arctia plantaginis (ArcPla_EST)

description: The wood tiger moth, Arctia plantaginis, is an important model organism for the study of polymorphism in warning colour. One major colour locus has been identified but studying its association with other traits as well as signatures of selection has been limited by the lack of a contiguous reference genome. A previous assembly consisted of more than 1000 scaffolds. We present the first chromosome level genome assembly based on PacBio-HiFi data and linkage map information. The final assembly spans 589 Mb consisting of 31 telomere-to-telomere chromosomes with a N50 scaffold length of 21.2 MB. The BUSCO analysis (n = 5,760) indicated a high completeness of 98.1 % with 97.5 % present as single copy and 0.6 % as duplicated. 17,456 genes were identified and 42.18 % of the genome was classified as repetitive. This new assembly provides an important resource for future research using genomic tools for studying the genetic basis and evolutionary mechanisms underlying colour polymorphisms in this species.

We used Liftoff v1.6.3 (1) to lift over the previous annotation from the W-reference (2)  to the new genome assembly, with the option to detect additional gene copies. A total of 17,456 genes (excluding additional copies) were successfully lifted over from the previous reference (97.4 %) to the new assembly. Overall, 27.0 % of the genome is within genes and 4.7 % within coding regions. The average length of single-copy genes was 8,946 bp, with an average of 6.5 coding sequences (CDS) per gene. Average CDS length was 238.5 bp.

The repeat annotation was generated using  RepeatModeler2 v.2.0.6 26 (3). 

 

1) Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639-1643 (2021).

2) Yen, E. C. et al. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 9 (2020).

3) Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. P Natl Acad Sci USA 117, 9451-9457 (2020).
DOI: 10.21950/jspyqs
title: Federico-Tena World Population Historical Database : French Equatorial Africa - Congo

description: Project developed by Giovanni Federico (New York University Abu Dhabi) and Antonio Tena Junguito (Universidad Carlos III de Madrid). Dataset: French Equatorial Africa - Congo
description: Microsoft Excel
description: Web site: <strong>https://www.uc3m.es/investigacion/federico-tena-population</strong>



<strong>SEE MAP</strong>
DOI: 10.5281/zenodo.13141950
title: July 15, 2024 (v1)DatasetOpen Physical oceanography and meteorological data from the W1M3A observatory, Ligurian Sea (North Western Mediterranean) Aug 2024 - Aug 2025

description: Time series data of physical oceanography (salinity, temperature) and meteorology (atmospheric pressure, wind speed and direction, air temperature and humidity, shortwave radiation, longwave radiation, photosynthetically active radiation and rain) collected from August 2024 to August 2025  by observatory W1M3A at 1h interval. The file contains tabular data (tab delimited) with the following columns: Day; Month; Year; UTC Hour; Minute ; Longitude [deg]; Latitude [deg]; Atmospheric Pressure [hPa]; Wind speed [m/s]; Wind direction [deg]; Air Temperature [°C]; Relative air humidity [%]; Short wave Radiation [W/m2]; Long wave radiation [W/m2]; Photosynthetically active radiation [um/m2/s] and Rainfall [mm/h]; Sea temperature @ 6 m [°C]; Sea temperature @ 20 m [°C]; Sea temperature @ 36 m [°C];  Salinity @ 6 m [psu]; Salinity @ 20 m [psu],  Salinity @ 36 m [psu].
description: Data collection was partially funded by MUR within the Project PURE WIND under the call JPI Oceans 2022, by Horizon Erurope within the project AMRIT and by Horizon 2020 within the project MINKE
DOI: 10.5281/zenodo.13141951
title: July 15, 2024 (v1)DatasetOpen Physical oceanography and meteorological data from the W1M3A observatory, Ligurian Sea (North Western Mediterranean) Aug 2024 - Aug 2025

description: Time series data of physical oceanography (salinity, temperature) and meteorology (atmospheric pressure, wind speed and direction, air temperature and humidity, shortwave radiation, longwave radiation, photosynthetically active radiation and rain) collected from August 2024 to August 2025  by observatory W1M3A at 1h interval. The file contains tabular data (tab delimited) with the following columns: Day; Month; Year; UTC Hour; Minute ; Longitude [deg]; Latitude [deg]; Atmospheric Pressure [hPa]; Wind speed [m/s]; Wind direction [deg]; Air Temperature [°C]; Relative air humidity [%]; Short wave Radiation [W/m2]; Long wave radiation [W/m2]; Photosynthetically active radiation [um/m2/s] and Rainfall [mm/h]; Sea temperature @ 6 m [°C]; Sea temperature @ 20 m [°C]; Sea temperature @ 36 m [°C];  Salinity @ 6 m [psu]; Salinity @ 20 m [psu],  Salinity @ 36 m [psu].
description: Data collection was partially funded by MUR within the Project PURE WIND under the call JPI Oceans 2022, by Horizon Erurope within the project AMRIT and by Horizon 2020 within the project MINKE
DOI: 10.5281/zenodo.18375145
title: Eyetracking data for 58 participants assessing their engagement and attentional levels to AI Portrayals in Cinema
DOI: 10.5281/zenodo.18375032
title: Addressing supply side constraints for digital work creation: A Concurrent Embedded Mixed Method Study in Kenya

description: Data that was utilized to carry out research the above stated research