cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/pj7gmk86cf.1
title: The Mla system of the diderm Firmicute Veillonella parvula reveals an ancestral envelope-spanning core for phospholipid trafficking

description: Despite extensive characterisation of envelope biogenesis systems in diderm (Gram-negative) bacteria, glycerophospholipid (GPL) trafficking remains poorly understood, and has only been studied in a handful of model species. In classical model diderms (Proteobacteria), the Mla system has been proposed to facilitate retrograde GPL trafficking and is composed of six proteins, MlaA-F. GPLs are extracted from the outer leaflet of the outer membrane (OM) by the lipoprotein MlaA which associates with porin trimers, then shipped through the periplasmic space by the periplasmic chaperone MlaC, which delivers GPLs to the inner membrane (IM) complex formed by MlaBDEF. Here, we investigate GPL trafficking in Veillonella parvula, a diderm member of the Firmicutes which encodes an Mla system devoid of MlaA and MlaC. V. parvula ∆mla mutants display phenotypes characteristic of disrupted lipid asymmetry such as hypervesiculation and detergent hypersensitivity. Lipid content analysis from outer membrane vesicles (OMVs) reveals an enrichment for the major lipid component phosphatidylethanolamine (PE). Interestingly, suppressor analysis identifies mutations in tamB that rescue detergent hypersensitivity of ∆mla strains, supporting the involvement of these two systems in antagonistic GPL trafficking functions across diverse bacterial lineages. A combination of structural modeling and subcellular localisation assays shows that MlaDVp is longer than in classical diderm models and forms a transenvelope bridge, encoding both an IM-localised MCE domain and an OM ß-barrel. These results strongly suggest that V. parvula possesses a minimal Mla system for GPL trafficking replacing the need for chaperones and OM lipoproteins by directly connecting the two membranes. Finally, phylogenomic analysis indicates that this MlaEFD self-contained architecture is widely distributed in diderm bacteria and most likely represents the ancestral functional core of the Mla system, which subsequently increased in complexity in Proteobacteria and closely related phyla following the emergence of MlaABC. Our work broadens the diversity of current models of GPL trafficking in diderm bacteria, challenging the paradigm set by classical models and shedding light on the evolution of a crucial system in the biogenesis and maintenance of the bacterial outer membrane.
DOI: 10.17632/s97wxc2jhs.1
title: News and Noise in Crime Politics: The Role of Announcements and Risk Attitudes

description: This repository contains all material needed to replicate the results of the paper "News and Noise in Crime Politics: The Role of Announcements and Risk Attitudes" published in Economic Modelling. For further details, please carefully read the included readme file.
DOI: 10.17632/w3vrrydbv2.1
title: IND-MCS - Solution Repository

description: This repository presents the entire set of solutions obtained by the IND-MCS tool for the RTS-WIND and BSS-WIND systems.
DOI: 10.17632/8644ssny7z.1
title: Questionnaire assessing teacher's competencies in designing and implementing online courses

description: This questions identities teacher's competencies in online course design, digital communication, basic and advanced computer skills, and use of learning management systems
DOI: 10.17632/s6vtgzpt2b.1
title: SELECTION BASED ON SEXUAL ORIENTATION: SOME WORRYING QUESTIONS

description: Abstract: Significant attention has been paid in recent years to the problems of discrimination and exclusion based on sexual orientation. The topic of this article is discrimination based on sexual orientation, especially as it occurs in the workplace and other social contexts. The study's key findings and the troubling concerns raised by them are summarized below. Both the personal and societal effects of selection based on sexual orientation are taken into account in this analysis of the ethical, legal, and social ramifications of this practice. We investigate this subject from several angles by reviewing relevant literature, conducting case studies, and conducting interviews. The first part of this paper explores the ethical problems of making hiring decisions based on an applicant's sexual orientation. It examines the possibility for spreading preconceptions and prejudices, as well as the infringement of an individual's right to privacy and personal identification. The research also looks at how such actions might further stigmatize and isolate the LGBTQ+ community. The second part discusses the laws surrounding hiring practices that take sexual orientation into account. As part of this process, we will examine the current state of anti-discrimination legislation and evaluate how well it protects its citizens. Given the difficulties in recognizing discriminatory activities, the research also investigates possible obstacles in adopting and enforcing legislative safeguards. In the third portion, we look at how sexual orientation might influence the hiring process. The effects on equality, efficiency, and morale in the workplace are analyzed. The research aims to learn how to spot and prevent potentially unfriendly circumstances that might stunt individual development and stymie societal advancement. Finally, this abstract identifies important issues that need more investigation. How can businesses make personal freedom a priority without sacrificing diversity and inclusion? Can selection processes be made more free of implicit biases and prejudices? What can we do to make our community more welcoming and safe for those who identify as LGBTQ+? In conclusion, this research tries to provide answers to pressing problems about sexual orientation discrimination in hiring. This study adds to our knowledge of the topic at hand by exploring relevant ethical, legal, and societal ramifications. It is anticipated that the results of this research will spark conversations and lead to measures that foster better tolerance and respect for people of all sexual orientations.
DOI: 10.17632/9jp4jdzy7k.1
title: Vogelherd ZooMS data

description: ZooMS analysis on highly fragmented bones obtained from water-screening sediment of the backdirt. VH 1, 2 and 3 used the Ambic protocol, VH4 and 5 used the Acid insoluble protocol.
DOI: 10.17632/8b46tsv3h5.1
title: The Effect of Job Insecurity on Job Satisfaction by Wage/Promotion Opportunities and Motivation in Gig Economy and Asymmetric Analysis

description: The aim of the study is to determine the moderating effect of wage and promotion opportunities and the mediating effect of motivation on the effect of job insecurity on job satisfaction. Survey data was collected from a sample of 411 gig workers.
DOI: 10.17632/h464gsf77t.1
title: development preterm infant 

description: The primary hypothesis of this research was to ascertain whether specific neonatal and maternal factors significantly influence the neurodevelopmental outcomes in preterm infants. It was hypothesized that variables such as gestational age, birth weight, and specific neonatal complications would have a notable impact on the developmental trajectories of these infants, as measured through the Bayley Scales of Infant and Toddler Development.
The dataset is a rich compilation of data gathered from a retrospective cohort study conducted on preterm infants admitted to the NICU at Ghaem Hospital, Mashhad, between 2016 and 2020. It encompasses a wide range of variables that provide a comprehensive view of both maternal and neonatal factors.

Notable findings from the data indicate significant associations between several neonatal and maternal factors and developmental outcomes in preterm infants. Variables such as Intrauterine Growth Restriction (IUGR), pneumothorax, and Bronchopulmonary Dysplasia (BPD) were found to be significantly associated with impairments in various developmental domains. Furthermore, the data revealed that longer durations of hospitalization and oxygen therapy were linked with negative developmental outcomes in different domains.To interpret the data, researchers can analyze the associations between the various recorded variables and the developmental outcomes measured through the Bayley Scales. The dataset includes detailed categorizations within developmental domains, offering insights into the severity and type of developmental delays experienced by the infants.
The data can be utilized to conduct further research into the complex interplay of biological and environmental factors influencing preterm infant development. It can serve as a foundational resource for developing targeted early intervention strategies, thereby aiding in optimizing developmental outcomes for this vulnerable population.

Researchers aiming to use this data should approach it with a comprehensive analytical strategy, considering the multifaceted nature of the variables involved. It would be beneficial to employ statistical analyses such as logistic regression to identify potential associations and influences between the variables.
By providing a detailed overview of both neonatal and maternal factors, the dataset promises to be a significant asset in fostering further research in the field of neonatal healthcare, potentially paving the way for advancements in preventative and interventional strategies to enhance the quality of life for preterm infants.
DOI: 10.17632/h464gsf77t.2
title: development preterm infant

description: The primary hypothesis of this research was to ascertain whether specific neonatal and maternal factors significantly influence the neurodevelopmental outcomes in preterm infants. It was hypothesized that variables such as gestational age, birth weight, and specific neonatal complications would have a notable impact on the developmental trajectories of these infants, as measured through the Bayley Scales of Infant and Toddler Development. The dataset is a rich compilation of data gathered from a retrospective cohort study conducted on preterm infants admitted to the NICU at Ghaem Hospital, Mashhad, between 2016 and 2020. It encompasses a wide range of variables that provide a comprehensive view of both maternal and neonatal factors. Notable findings from the data indicate significant associations between several neonatal and maternal factors and developmental outcomes in preterm infants. Variables such as Intrauterine Growth Restriction (IUGR), pneumothorax, and Bronchopulmonary Dysplasia (BPD) were found to be significantly associated with impairments in various developmental domains. Furthermore, the data revealed that longer durations of hospitalization and oxygen therapy were linked with negative developmental outcomes in different domains.To interpret the data, researchers can analyze the associations between the various recorded variables and the developmental outcomes measured through the Bayley Scales. The dataset includes detailed categorizations within developmental domains, offering insights into the severity and type of developmental delays experienced by the infants. The data can be utilized to conduct further research into the complex interplay of biological and environmental factors influencing preterm infant development. It can serve as a foundational resource for developing targeted early intervention strategies, thereby aiding in optimizing developmental outcomes for this vulnerable population. Researchers aiming to use this data should approach it with a comprehensive analytical strategy, considering the multifaceted nature of the variables involved. It would be beneficial to employ statistical analyses such as logistic regression to identify potential associations and influences between the variables. By providing a detailed overview of both neonatal and maternal factors, the dataset promises to be a significant asset in fostering further research in the field of neonatal healthcare, potentially paving the way for advancements in preventative and interventional strategies to enhance the quality of life for preterm infants.
DOI: 10.17632/v566mwcn6f.1
title: Raw data on Teachers' competencies to design and implement online courses

description: This raw data was obtained on teachers competencies to design and implement online courses
DOI: 10.17632/7z4s4srxry.1
title: Comentario al libro "Universidad, sentido y crítica"

description: CRÍTICA AL LIBRO "UNIVERSIDAD SENTIDO Y CRITICA"
DOI: 10.17632/t7r9zncvxm.1
title: FINANCIAL BEHAVIOURAL INTENTIONS

description: FINANCIAL BEHAVIOURAL INTENTIONS IN CORRELATION WITH CONTEXTUAL CUES AND FINANCIAL LITERACY – A HUNGARIAN EMPIRICAL STUDY
DOI: 10.17632/vv5fcxk5rn.1
title: Representative Sets of Singular Non-Hemolytic and Non-Toxic AMPs from Cephalopods' Posterior Salivary Glands Extracted via Network Centralities.

description: These datasets comprise the most representative peptides extracted from a singular set of non-hemolytic and non-toxic antimicrobial peptides (AMPs) sourced from Cephalopods (doi: 10.17632/8mttp4pvmc.1). The selection process involved employing network centrality measures, specifically harmonic and hub-bridge centralities, calculated on the Half-Space Proximal Network used for projecting 5,466 singular AMPs. The smaller dataset (808 peptides) was generated from the peptides identified by both centrality measures, whereas the extended set (2,114 peptides) includes peptides extracted by either centrality measure.
DOI: 10.5281/zenodo.8420587
title: iGEM Leiden 2023 - Fluorescence microscopy pictures for PHA visualization

description: Raw data files of fluorescence microscopy of <em>Methylobacterium extorquens</em> AM1 stained with Nile Red to visualize PHA granules.
DOI: 10.5281/zenodo.8420586
title: iGEM Leiden 2023 - Fluorescence microscopy pictures for PHA visualization

description: Raw data files of fluorescence microscopy of <em>Methylobacterium extorquens</em> AM1 stained with Nile Red to visualize PHA granules.
DOI: 10.5281/zenodo.8417573
title: Raw Data from Puerto Madryn Patagonia Argentina

description: The file is composed by temperature maximum, minimum and mean value, pressure and relative humidity for the period 1902-1915
DOI: 10.5281/zenodo.8417572
title: Raw Data from Puerto Madryn Patagonia Argentina

description: The file is composed by temperature maximum, minimum and mean value, pressure and relative humidity for the period 1902-1915
DOI: 10.5281/zenodo.8423134
title: iGEM Leiden 2023 - Methylobacterium extorquens cultivation

description: Raw data of effect of culture conditions for <em>Methylobacterium extorquens</em> on PHA production.
DOI: 10.5281/zenodo.8423133
title: iGEM Leiden 2023 - Methylobacterium extorquens cultivation

description: Raw data of effect of culture conditions for <em>Methylobacterium extorquens</em> on PHA production.
DOI: 10.5281/zenodo.8400422
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB]

description: Submitted and raw files of the interlab study (all experiments)
DOI: 10.5281/zenodo.8400423
title: iGEM-Leiden-2023-Supplementary Experiments [INTERLAB] Calibration Experiment Submitted Data

description: <strong>Submitted and Raw files of the interlab studies </strong>
DOI: 10.5281/zenodo.8400468
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB]

description: Submitted and raw files of the interlab study (all experiments)
DOI: 10.5281/zenodo.8422731
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Experiment 3

description: Experiment 3 of Interlab study
DOI: 10.5281/zenodo.8422730
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Experiment 3

description: Experiment 3 of Interlab study
DOI: 10.5281/zenodo.8422723
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Experiment 2

description: Experiment 2 of Interlab study
DOI: 10.5281/zenodo.8422722
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Experiment 2

description: Experiment 2 of Interlab study
DOI: 10.5281/zenodo.8422719
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Experiment 1

description: Experiment 1 of Interlab study
DOI: 10.5281/zenodo.8422718
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Experiment 1

description: Experiment 1 of Interlab study
DOI: 10.5281/zenodo.8422709
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Calibration

description: Calibration of interlab study
DOI: 10.5281/zenodo.8422708
title: iGEM Leiden 2023 - Supplementary experiments [INTERLAB] - Calibration

description: Calibration of interlab study
DOI: 10.5281/zenodo.8422542
title: iGEM Leiden 2023 - phaC, groEL and groES overexpression PHA quantification

description: Raw data of the PHA quantification of the phaC, groEL, groES overexpression strains of Methylobacterium extorquens using Nile Red staining. Data includes OD, biomass and fluorescence intensity data per experiment.
DOI: 10.5281/zenodo.8422541
title: iGEM Leiden 2023 - phaC, groEL and groES overexpression PHA quantification

description: Raw data of the PHA quantification of the phaC, groEL, groES overexpression strains of Methylobacterium extorquens using Nile Red staining. Data includes OD, biomass and fluorescence intensity data per experiment.
DOI: 10.25345/c56h4d16c
title: MassIVE MSV000093071 - RIME Analysis of HNF4A binding partners in the intestinal epithelium
title: The mechanisms driving gene expression changes during intestinal differentiation are unclear. Our studies have shown differential recruitment and occupancy of Pol II to be a major driver of these gene expression changes. Additionally, we have identified the transcription factor HNF4 as a key player in shaping this phenomenon. To gain insights into the protein-based mechanisms underlying HNF4-mediated Pol II recruitment, we performed RIME (Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins) using anti-HNF4A antibodies in primary mouse epithelium.
DOI: 10.22003/xfel.eu-data-004462-00
title: Single particle imaging of laser-aligned (bio-) nanoparticles
DOI: 10.5281/zenodo.8420881
title: iGEM Leiden 2023 - Inducible autolysis system experiment 1

description: Raw data of colony counting of uninduced and induced autolysis systems in <em>Methylobacterium extorquens </em>AM1.
DOI: 10.5281/zenodo.8420880
title: iGEM Leiden 2023 - Inducible autolysis system experiment 1

description: Raw data of colony counting of uninduced and induced autolysis systems in <em>Methylobacterium extorquens </em>AM1.
DOI: 10.5281/zenodo.8420816
title: iGEM Leiden 2023 - Inducible autolysis system experiment 2

description: Raw data of spot growth test of <em>Methylobacterium extorquens</em> AM1 with an inducible autolysis system. The effect of the inducible autolysis system on solvent resistance of <em>M. extorquens</em> was determined.
DOI: 10.5281/zenodo.8420815
title: iGEM Leiden 2023 - Inducible autolysis system experiment 2

description: Raw data of spot growth test of <em>Methylobacterium extorquens</em> AM1 with an inducible autolysis system. The effect of the inducible autolysis system on solvent resistance of <em>M. extorquens</em> was determined.
DOI: 10.5281/zenodo.8420742
title: iGEM Leiden 2023 - Promoter characterization

description: Promoter characterization data in <em>Methylobacterium extorquens</em> AM1 of three growth assay experiments (fluorescence and OD measured over time).
DOI: 10.5281/zenodo.8420741
title: iGEM Leiden 2023 - Promoter characterization

description: Promoter characterization data in <em>Methylobacterium extorquens</em> AM1 of three growth assay experiments (fluorescence and OD measured over time).
DOI: 10.34740/kaggle/dsv/6650382
title: mendical insurance and malpratice
DOI: 10.5281/zenodo.8420645
title: iGEM Leiden 2023 - MALDI-TOF data for PHA identification

description: Raw data of MALDI-TOF experiment aimed at identifying PHA in <em>Methylobacterium extorquens</em> AM1.
DOI: 10.5281/zenodo.8420644
title: iGEM Leiden 2023 - MALDI-TOF data for PHA identification

description: Raw data of MALDI-TOF experiment aimed at identifying PHA in <em>Methylobacterium extorquens</em> AM1.
DOI: 10.5281/zenodo.8408573
title: DockGame: Cooperative Games for Multimeric Rigid Protein Docking

description: Raw datasets used for DB5.5 dataset and DIPS dataset used in DockGame, with associated code at https://github.com/vsomnath/dockgame These datasets can also be downloaded from https://zlab.umassmed.edu/benchmark (DB5.5) and https://www.dropbox.com/s/sqknqofy58nlosh/DIPS.zip?dl=0 (DIPS). Note that our organization would be slightly different from these downloaded versions. We follow EquiDock (https://github.com/octavian-ganea/equidock_public) for the DB5 dataset splits. <strong>Paper Abstract</strong> Protein interactions and assembly formation are fundamental to most biological processes. Predicting the assembly structure from constituent proteins -- referred to as the protein docking task -- is thus a crucial step in protein design applications. Most traditional and deep learning methods for docking have focused mainly on binary docking, following either a search-based, regression-based, or generative modeling paradigm. In this paper, we focus on the less-studied multimeric (i.e., two or more proteins) docking problem. We introduce DockGame, a novel game-theoretic framework for docking -- we view protein docking as a cooperative game between proteins, where the final assembly structure(s) constitute stable equilibria w.r.t. the underlying game potential. Since we do not have access to the true potential, we consider two approaches - i) learning a surrogate game potential guided by physics-based energy functions and computing equilibria by simultaneous gradient updates, and ii) sampling from the Gibbs distribution of the true potential by learning a diffusion generative model over the action spaces (rotations and translations) of all proteins. Empirically, on the Docking Benchmark 5.5 (DB5.5) dataset, DockGame has much faster runtimes than traditional docking methods, can generate multiple plausible assembly structures, and achieves comparable performance to existing binary docking baselines, despite solving the harder task of coordinating multiple protein chains.