cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15971353
title: simulated_msa v1.0: simulated multiple sequence alignments with known phylogenies for benchmarking MSA tools

description: This dataset contains 1,860 simulated multiple sequence alignments (MSAs) with known phylogenies. The alignments were generated using the AliSim tool from IQ-TREE v2.4.0.

The simulation parameters span a broad range of conditions:



Number of sequences: 1,000–100,000

Substitution models: LG, JTT, and WAG

Sequence lengths: 400–2,000 residues

Sequence identities: 8%–75%

Gap fractions: 0%–99%


Directory structure

The dataset contains three main directories:



fasta/ – unaligned protein sequences [FASTA format]

msa/ – aligned protein sequences (reference MSAs) [FASTA format]

tree/ – phylogenetic trees corresponding to each simulated MSA (reference trees) [Newick format]


A metadata file (metadata.tsv) is also included, providing detailed information for each simulated MSA

Metadata

A metadata file (metadata.tsv) is included, containing detailed information for each simulated MSA. It provides:



id – unique MSA identifier

seqs_count – number of sequences in the MSA

alisim_length – seed sequence length

alisim_rlen_min / mean / max – relative branch length parameters

alisim_ins / alisim_del – insertion and deletion rates

alisim_model – substitution model (LG, JTT, WAG)

alisim_model_type – model configuration used by AliSim

mean_identity_percent – average sequence identity [%]

mean_gaps_percent – average fraction of gaps [%]

min_seq_length / mean_seq_length / max_seq_length – sequence length statistics
DOI: 10.5281/zenodo.17543275
title: Trajectories of reef coral morphological traits during the early Paleogene hothouse reveal the predictive limits of fossil analogues in a rapidly changing climate - PECT Dataset

description: PalEoCoralTraits (PECT) dataset with all raw data from the paper: 

Bosellini, F. R., Mariani, L. and Benedetti, A., 2026. Trajectories of reef coral morphological traits during the early Paleogene hothouse reveal the predictive limits of fossil analogues in a rapidly changing climate, Palaeogeography, Palaeoclimatology, Palaeoecology, v. 683, 113472. https://doi.org/10.1016/j.palaeo.2025.113472
DOI: 10.5281/zenodo.17543276
title: Trajectories of reef coral morphological traits during the early Paleogene hothouse reveal the predictive limits of fossil analogues in a rapidly changing climate - PECT Dataset

description: PalEoCoralTraits (PECT) dataset with all raw data from the paper: 

Bosellini, F. R., Mariani, L. and Benedetti, A., 2026. Trajectories of reef coral morphological traits during the early Paleogene hothouse reveal the predictive limits of fossil analogues in a rapidly changing climate, Palaeogeography, Palaeoclimatology, Palaeoecology, v. 683, 113472. https://doi.org/10.1016/j.palaeo.2025.113472
DOI: 10.11587/ovn6wr
title: Schulpartnerschaft: Jugendstudie 1997 (1997-04-16 - 1997-06-09)
title: Schulpartnerschaft

description: Mehrere Bände: Thema: Schulpartnerschaft Jugendstudie
description: Schulpartnerschaft
DOI: 10.15468/dl.zkbfs9
title: Occurrence Download

description: A dataset containing 94450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Nezara viridula"
 ]
}

 The dataset includes 94450 records from 530 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005457-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17697904
title: Required datasets for The Relative Productivity Index V2

description: Data resources to run R code for the analysis in Lomax, Guy A., Thomas W.R. Powell, Timothy M. Lenton, and Andrew M. Cunliffe, (under review) ‘The relative productivity index for assessing local impacts on rangeland condition: refinement and evaluation’.

Instructions



Clone the repository from GitHub

Set up project environment using renv.

Unzip data.zip to the main project directory.

Run analysis scripts in numerical order.
DOI: 10.5281/zenodo.17697905
title: Required datasets for The Relative Productivity Index V2

description: Data resources to run R code for the analysis in Lomax, Guy A., Thomas W.R. Powell, Timothy M. Lenton, and Andrew M. Cunliffe, (under review) ‘The relative productivity index for assessing local impacts on rangeland condition: refinement and evaluation’.

Instructions



Clone the repository from GitHub

Set up project environment using renv.

Unzip data.zip to the main project directory.

Run analysis scripts in numerical order.
DOI: 10.15468/dl.xpaqfu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Heterosentis zdzitowieckii",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005581-260126135527185/datasets/export for details.
DOI: 10.34780/ofknfr29
title: Supplementary Material: Charred Plant Remains from Jawa

description: The table gives the results of identifications obtained from the charred remains from the 1970 season at Jawa. The 14C samples were selected from them. Only dry sieving (as opposed to flotation) was possible due to lack of water during the excavation. Charred remains were hand-picked from the sieved material which inevitably resulted in a limited data set. Despite this, the results demonstrate that a typical assemblage of cultivated cereals and pulses were in use at Jawa during the Early Bronze Age. Fuel was obtained from forest species which today grow on the western slopes of the Jebel Druze between 1100 and 1500 m a.s.l. situated between 40 and 50 km northwest of Jawa. During the Early Bronze Age these trees may have been growing further east and would have been nearer the site.
DOI: 10.15468/dl.uce3qt
title: Occurrence Download

description: A dataset containing 4511 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rosa montana"
 ]
}

 The dataset includes 4511 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005582-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/awma1g
title: Household costs of hospitalized dengue illness in semi-rural Thailand

description: Household costs of hospitalized dengue illness in semi-rural Thailand
DOI: 10.7910/dvn/egri79
title: House Unpassed Legislation 1891, committee on rules - leave to withdraw, SC1/series 230, Petition of T.W. Curtis

description: &lt;p&gt;Petition subject: School discrimination &lt;/p&gt; &lt;p&gt;Original: &lt;a href="http://nrs.harvard.edu/urn-3:FHCL:25763590"&gt;http://nrs.harvard.edu/urn-3:FHCL:25763590&lt;/a&gt; &lt;/p&gt; &lt;p&gt;Date of creation: (unknown) &lt;/p&gt; &lt;p&gt;Petition location: Massachusetts &lt;/p&gt; &lt;p&gt;Legislator, committee, or address that the petition was sent to: Josiah Quincy, Quincy &lt;/p&gt; &lt;p&gt;Selected signatures:&lt;ol&gt;&lt;li&gt;T.W. Curtis&lt;/li&gt;&lt;/ol&gt; &lt;/p&gt; &lt;p&gt;Total signatures: 1 &lt;/p&gt; &lt;p&gt;Legal voter signatures (males not identified as non-legal): 1 &lt;/p&gt; &lt;p&gt;Female only signatures: No &lt;/p&gt; &lt;p&gt;Identifications of signatories: The Nationalist League of Massachusetts, secretary, Nationalist League of Mass, citizens &lt;/p&gt; &lt;p&gt;Prayer format was &lt;a href="http://en.wikipedia.org/wiki/Printing"&gt;printed&lt;/a&gt; vs. &lt;a href="http://en.wikipedia.org/wiki/Manuscript"&gt;manuscript&lt;/a&gt;: Printed &lt;/p&gt; &lt;p&gt;Additional non-petition or unrelated documents available at archive: additional documents available &lt;/p&gt; &lt;p&gt;Additional archivist notes: compulsory school age, attendance, training, labor, education, plants, manufacture of gas and electricity, lands, habitation, dwellings, rental, industries, unemployment, Republic of Switzerland, referendum, popular initiative, imperative mandate, equitable method of minority representation for all public elections, more representative and democratic form of government, convenience, welfare, original intent of equality for all citizens, equality of opportunity, distinctions based upon class, race, social conditions, public school system, England, Springfield, Swiss principles, direct participation &lt;/p&gt; &lt;p&gt;Location of the petition at the Massachusetts Archives of the Commonwealth: House Unpassed 1891, committee on rules - leave to withdraw &lt;/p&gt; &lt;p&gt;Acknowledgements: Supported by the National Endowment for the Humanities (PW-5105612), Massachusetts Archives of the Commonwealth, Radcliffe Institute for Advanced Study at Harvard University, Center for American Political Studies at Harvard University, Institutional Development Initiative at Harvard University, and Harvard University Library.&lt;/p&gt;
DOI: 10.7910/dvn/ehqzx1
title: Artificial Intelligence Based Machine Learning Models Predict Sperm parameter Upgrading after Varicocele Repair: A Multi-Institutional Analysis

description: Purpose: Varicocele repair is recommended in the presence of a clinical varicocele together with at least one abnormal semen parameter, and male infertility. Unfortunately, up to 50% of men who meet criteria for repair will not see meaningful
benefit in outcomes despite successful treatment. We developed an artificial intelligence (AI) model to predict which men with varicocele will benefit from treatment.
Materials and Methods: We identified men with infertility, clinical varicocele, and at least one abnormal semen parameter from two large urology centers in North America (Miami and Toronto) between 2006 and 2020. We collected pre and postoperative clinical and hormonal data following treatment. Clinical upgrading was defined as an increase in sperm concentration that would allow a couple to access previously unavailable reproductive options. The tiers used for upgrading were: 1–5 million/mL (ICSI/IVF), 5–15 million/mL (IUI) and &gt;15 million/mL (natural conception). Thus moving from ICSI/IVF to IUI, or from IUI to natural conception, would be considered an upgrade. AI models were trained and tested using R to predict which patients were likely to upgrade after surgery. The model sorted men into categories that defined how likely they were to upgrade after surgery (likely, equivocal, and unlikely).
Results: Data from 240 men were included from both centers. A total of 45.6% of men experienced an upgrade in sperm concentration following surgery, 48.1% did not change, and 6.3% downgraded. The data from Miami were used to create a random
forest model for predicting upgrade in sperm concentration. On external validation using Toronto data, the model accurately predicted upgrade in 87% of men deemed likely to improve, and in 49% and 36% of men who were equivocal and unlikely to
improve, respectively. Overall, the personalized prediction for patients in the validation cohort was accurate (AUC 0.72).
Conclusions: A machine learning model performed well in predicting clinically meaningful post-varicocelectomy sperm parameters using pre-operative hormonal, clinical, and semen analysis data. To our knowledge, this is the first prediction
model to show the utility of hormonal data, as well as the first to use machine learning models to predict clinically meaningful upgrading. This model will be published online as a clinical calculator that can be used in the preoperative counseling of patients.
DOI: 10.7910/dvn/fhmutt
title: Unified Astronomy Thesaurus

description: The Unified Astronomy Thesaurus (UAT) is an open, interoperable and community-supported thesaurus that unifies the existing Astronomy
&amp; Astrophysics thesauri into a single, freely-available open thesaurus for astronomical objects and concepts. &lt;br /&gt;&lt;br /&gt; These files introduce the UAT and describe the unique combination of conditions that lead to its development, as well as the people, organizations and tools involved in its construction. Because astronomy and astrophysics are fast-moving fields (terms such as 'exoplanets' and 'dark energy' were relatively unknown 10 years ago), the poster will also describe the ways tha
t the UAT will leverage expertise from astronomers, physicists and librarians to keep the thesaurus both current and accurate.
&lt;br /&gt;&lt;br /&gt; One of the primary drivers behind the creation of the UAT is the wish to support semantic enrichment of astronomy literature and databases. We anticipate it will be used as a common language across publishers and platforms, to connect articles and data sets. We also hope this unified vocabulary will inspire a new range of cross-silo data sharing. &lt;br /&gt;&lt;br /&gt; The UAT began as a collaboration between the American Institute of Physics (AIP) and Institute of Physics (IOP), which dona
ted their collection astronomy of terms to the AAS. SPIE has also donated their astronomy terms towards the effort. Our plans include providing a community-supported mechanism for reviewing, discussing, and evaluating the continuous evolution of terminology in astronomy and astrophysics.
&lt;br /&gt;&lt;br /&gt; See &lt;a href="http://astrothesaurus.org/"&gt;http://astrothesaurus.org/&lt;/a&gt; for more information.
DOI: 10.7910/dvn/jow4f1
title: Replication Data for: The ecology of immigrant naturalisation: a life course approach in the context of institutional conditions.

description: Traditionally, immigrants’ propensity to naturalize is attributed to individual characteristics and the origin country. Recently scholars increasingly recognise that naturalisation decisions do not take place in a vacuum: they are conditioned both by the individual life course of immigrants, such as the age at migration and family situation, as well as the opportunity structure set by citizenship policies of the destination country. Yet it is less clear what impact specific policy changes have, and to whom these changes matter most. In this paper we address these questions by analysing citizenship acquisition among first generation immigrants in the Netherlands in light of a restriction in citizenship policy in 2003. We employ unique micro-level longitudinal data from Dutch municipal population registers between 1995 until 2012, which allow us to track naturalisation among different immigration cohorts. We find evidence that indeed naturalisation is part of a larger life course trajectory: immigrants who arrive at a younger age in the Netherlands naturalise more often and so do immigrants with a native partner, or a foreign-born partner who also naturalises. Policy also matters: migrants naturalise later and less often under more restrictive institutional conditions, especially migrants from less developed and politically unstable countries of origin.
description: Peters, F., Vink, M., & Schmeets, H. (2016). The Ecology of Immigrant Naturalisation: A Life Course Approach in the Context of Institutional Conditions. Journal of Ethnic and Migration Studies, 42(3), 359-381. DOI: https://doi.org/10.1080/1369183X.2015.1103173.

In this version, files have been systematized to facilitate replication transparency.
DOI: 10.7910/dvn/m4eyfo
title: Replication Data for: It’s a matter of timing. How the timing of politicians’ information subsidies affects what becomes news

description: The file contains all material (STATA data + do-file) to replicate the results reported in the paper.
DOI: 10.7910/dvn/now6sg
title: How Annals of Dermatology Has Improved the Scientific Quality and Ethical Standards of its Articles in the Two-Year Period since October 2018

description: Annals of Dermatology has not been deposited in PubMed Central (PMC) since October 2018 due to inadequate scientific quality, including the absence of informed consent in three case reports with patients’ photos. This study examined the readiness of Annals of Dermatology to be deposited in PMC again by analyzing the 13 issues published from October 2018 to August 2020. The journal’s scientific quality and ethical standards were assessed, and adherence to these standards was documented. In total, 259 articles were analyzed for ethical standards, including institutional review board (IRB) approval, an informed consent statement, and disclosure of conflicts of interest. Scientific quality was also checked for each article. Of the 129 original articles or brief reports presenting research on human subjects or human-derived materials, 111 studies received IRB approval and/or obtained informed consent. The other seven studies were data analyses or studies of purchased cultured cells. One study that used a post-circumcision foreskin sample contained no statement describing permission from the patient’s family, but the researchers were found to have obtained informed consent. In all 152 case presentations, the authors obtained informed consent. All seven animal experiments received Institutional Animal Care and Use Committee approval. One review article did not disclose conflicts of interest, but this was an editorial error. Two systematic reviews adopted the PRISMA guidelines. In conclusion, the present publication policies, scientific quality, and ethical standards of the journal are top-tier internationally. Annals of Dermatology may be ready to apply to PMC again.
DOI: 10.7910/dvn/oqnzye
title: Replication Data for: 'The Slope of the Phillips Curve: Evidence from U.S. States'

description: The programs replicate tables and figures from "The Slope of the Phillips Curve: Evidence from U.S. States", by Hazell, Herreno, Nakamura, and Steinsson. Please see the read_me_codes_to_share file for additional details.
DOI: 10.7910/dvn/oyzjc4
title: When unionisation is profitable for firms in network industries

description: In an industry characterised by the presence of network effects, this paper investigates a duopolistic game in which firms may choose whether to bargain over wages and employment with unions or to face a competitive labour market (i.e. without unions). If unions are sufficiently risk-averse, it is shown that the presence of strong network effects makes unionisation the Pareto-efficient sub-game perfect Nash equilibrium outcome for firms. The issue of entry is also investigated.
DOI: 10.7910/dvn/surrjq
title: Replication Data for: High-throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays

description: This dataset contains raw data micrographs and videographs and code for the scientific article "High-throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays".

See the file 'data_file_list.xlsx' for a list of all files, which article figure each file corresponds to and the experimental metadata for each file.

This dataset has been made according to the FAIR principles (https://www.go-fair.org/fair-principles/) and TOP guidelines (https://www.cos.io/initiatives/top-guidelines)
DOI: 10.7910/dvn/zdeoz5
title: Risk factors for major external structural birth defects among children in Kiambu County, Kenya: a case-control study

description: 2_mesbds_kmbu_ke_questionnaire.pdf
2_mesbds_kmbu_ke.do
DOI: 10.7910/dvn/awihsr
title: Replication Data for: Compulsory Voting and Dissatisfaction with Democracy

description: This code replicates the models in the paper "Compulsory Voting and Dissatisfaction with Democracy", by Shane Singh, which appears in the British Journal of Political Science. All models estimated in Stata 13.
DOI: 10.7910/dvn/iwrkdk
title: Bootstrap current and parallel ion velocity in imperfectly optimized stellarators

description: A novel derivation of the parallel ion velocity, and the bootstrap and Pfirsch-Schlüter currents in an imperfectly optimized (that is, almost omnigenous) stellarator magnetic field, \vec B, is presented. It is shown that, when the conventional radially local form of the drift kinetic equation is employed, the flow velocity and the bootstrap current acquire a spurious contribution proportional to ω /ν , where ω denotes the \vec E × \vec B rotation frequency (due to the radial electric field E ) and ν the collision frequency. This contribution is particularly large in the squareroot ν regime and at smaller collisionalities, where ω /ν &gt; 1 , and is presumably present in most numerical calculations, but it disappears if a more accurate drift kinetic equation is used.
description: PSFC REPORT PSFC/JA-19-23<br><br>This work is supported by the US Department of Energy, Grant No. DE-FG02-91ER54109
DOI: 10.7910/dvn/jqjxqw
title: Replication data for: Presidents and the Politics of Agency Design: Administrative Agency Insulation Data Set, 2003

description: This is a data set of United States government administrative agencies created between 1946 and 1997. The data were used for all quantitative analysis in the book. Each agency created during this period is 1 observation. The data set excludes advisory, quasi-official, multi-lateral, educational and research agencies, and support offices common to all cabinet departments. An explanation of the data set, how the data was collected, and a description of the variables is included in the codebook below. Stata batch files for the models estimated in chapters 2, 5 are also included below. All users are advised to look at the data update before using the data for new projects. Please report any problems or questions to me.
DOI: 10.7910/dvn/sbqlva
title: Replication Data and Code for: Sensor Selection and State Estimation of Continuous mAb Production Processes

description: Replication Data and Code for: Sensor Selection and State Estimation of Continuous mAb Production Processes
DOI: 10.7910/dvn/zdrmxk
title: PPR Obesity DASS data Malaysia

description: A retrospective cohort study among B40 community in Kuala Lumpur, Malaysia to explore the impact of prolonged COVID-19 lockdown on obesity and mental health.
DOI: 10.7910/dvn/5sfs4h
title: hou02665c00818

description: Baptism documents, Julián de Zulueta of the Junta de Gobierno de la Casa de Beneficencia y Maternidad de la Habana, Havana
description: URN-3:FHCL.HOUGH:100958271
DOI: 10.7910/dvn/awwbc8
title: M-M Sexual Offending in Western Australia 1829-1914

description: Dataset of male on male sexual offending in Western Australia 1829-1914
description: Draft article submitted to Journal of Legal History 28 January 2021
DOI: 10.7910/dvn/axgdjo
title: Replication Data for: Financial stability in response to climate change in a northern temperate economy - Climate Projections

description: The monthly and provincial climate projections from the MARS model. Data projections are also divided into climate normals. Data is provided in trade and combined GDP values.