cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/7d2fb4m7gn.1
title: BindDB: Pseudogenes Case Study

description: As a negative control for BindDB, we uploaded a list of 76 pseudogene names, identified by the 'ps' extension to the gene symbols in the Refseq annotation, to the multi-gene query form of BindDB and selected to query their proximal promoter regions. Overall, the epigenetic profile of these pseudogenes was that of inactive chromatin. Sorting by the "Enrichment" column of the positive results table shows depletion of epigenetic marks that are associated with active transcription such as H3K4me1, H3K36me3, H3K27ac and H3K79me2 (Figure S2A). In agreement, the heatmap shows very little evidence of factor binding to most of the pseudogenes and the prominent yellow color of the sidebar indicates that there is no evidence of RNA expression coming from these regions either(Figure S2B). Yet, a handful of pseudogenes, including Rpl34-ps and Pisd-ps1/2,display evidence of H3K4me3 and RNAP II bindingas well as RNA expression (Figure S2B, top cluster).These pseudogenes are also bound by many transcription factors, including those from the pluripotent network, such as OCT4, indicating that this small group of genes are likely expressed in ESCs and may be inaccurately annotated as "pseudogenes". In the case of Rpl34-ps, its annotation completely overlaps the non-pseudo gene version of the same gene, such that it shares its epigenetics with Rpl34 itself, a key ribosomal protein that is expressed in ESCs. For Pisd-ps1/2, the Refseq and Ensembl annotations have categorized it as a non-coding transcript, hence misleadingly termed a pseudogene. By clicking the gene name, Pisd-ps1, on the BindDB results page, the UCSC genome browser(Kent et al., 2002)opens up at the gene's genomic location along with the ENCODE/LICR Histone Mods(ENCODE, 2012) and RNA-seq tracks for E14 ESCs(Mortazavi et al., 2008) providing a more focused view on this gene (Figure S2C). Its active epigenetic profile, including OCT4 binding, makes it an interesting candidate for the study of ncRNA in ESCs. Running the same analysis on a larger cohort of ~5500 non-overlapping pseudogenes in the Ensembl annotation, reassuringly replicated the same general lack of factor binding and histone gene modifications at their promoters (data not shown).
DOI: 10.17632/j6z69cyyyy.1
title: BindDB: LincRNAs Case Study

description: Epigenetic Classification of Novel Genes Provides Insights into Functional Subgroups The introduction of NGS platforms has greatly facilitated the discovery of novel genes, especially non-coding genes, which were under the radar of the previous methodologies. By combining epigenetic analysis to the regions of novel transcription, 1000s of novel long intervening non-coding RNAs, or lincRNAs, residing in intergenic regions were discovered (Guttman et al., 2009; Khalil et al., 2009). The understanding that histone marks can point to areas of active and functional transcription enabled the use of a minimal epigenetic profile ("K4-K36"), to locate regions with H3K4me3 marking a promoter region, followed by H3K36me3 within the potential coding region. But, epigenetic regulation of active genes could be far more complex. We applied the BindDB analysis capabilities to this novel group of genes in order to ask whether their promoters are regulated similarly to protein-coding genes and test if we could expand it beyond the basic "K4-K36" profile. We uploaded a list of 2074 genomic regions (in BED format since many are not annotated with gene symbols) classified as lincRNAs in the Ensembl annotation (Hubbard et al., 2002) according to the algorithms in Guttman et al. (Guttman et al., 2009), yet also include strand information from which promoter regions can be deduced. These regions were merged by BindDB into 1729 non-overlapping proximal promoter regions. It is striking to see a noticeable enrichment for almost all factors beyond H3K4me3 (1.55-2.65-fold, log2 scale, see Supplemental Experimental Procedures) and H3K36me3 (0.04-1.25-fold) (FigureS3). The low enrichment of H3K36me3 persisted when we examined only lincRNA bodies compared to all gene bodies in a separate analysis (0.54-1.92), indicating that lincRNAs have similar levels of H3K36me3 as in protein-coding genes. The clustered heatmap view of all factors and histone modification along all lincRNA promoters (Figure1B) gives us two important insights into this large group. First, there is quite an extensive epigenetic profile for many of them involving active histone modification and transcription factors. Second, there are as much as 20% of lincRNA annotations that do not display such a profile (Figure1B, orange star). This group also exhibits none to low levels of RNA expression and may include lincRNAs specific to non-ESC types or false-positives resulting from the extensive statistical methods applied in search of the "K4-K36" profile along with some regions that have only the minimal "K4-K36" profile. We can speculate that this minimal profile may not be enough to support bona-fide regulated transcription, at least not in ESCs, but the deposit of histone modifications may be a byproduct of another process.
DOI: 10.17632/xz6gv65m6d.2
title: Reproducible experiments on dynamic resource allocation in cloud data centers

description: In Wolke et al. we compare the efficiency of different resource allocation strategies experimentally. We focused on dynamic environments where virtual machines need to be allocated and deallocated to servers over time. In this companion paper, we describe the simulation framework and how to run simulations to replicate experiments or run new experiments within the framework.
DOI: 10.17632/z9vv7tvpfp.1
title: BindDB: Oct4 Case Study

description: Epigenomic Profiling of Oct4 Promoter Due to the flexibility of the BindDB platform, more general questions related to epigenetic regulation in the ESC context can be asked. For example, how are the alternative promoters of the stem cell specific transcription factor OCT4 regulated? In both mESCs and hESCs, two main isoforms of Oct4 exist (Oct4A, Oct4B), which differ by approximately 3kb in their 5' regions and have the potential to be regulated by two distinct promoter regions (Wang and Dai, 2010). Interestingly, Oct4A and Oct4B display different temporal and spatial expression patterns (Cauffman et al., 2006). It has been hypothesized that the Oct4A is the pluripotent promoter, whereas, Oct4B is related to stress responses (Wang et al., 2009). To study these promoters in greater depth, we queried ‘Pou5f1’ in BindDB (Figure 2A). The tool automatically discerns the presence of two alternative promoters while searching for the gene's genomic location and directs the user to a heatmap of per-promoter results. From the heatmap, it is apparent that both promoters share some of their epigenetic signature including H3K4me3, H3K27ac and H3K9ac active chromatin marks (Figure 2B). Also, the OCT4 protein itself binds both of its promoters, along with other pluripotent factors such as UTX and KLF4. Beyond this common epigenetic core, the two promoters differ widely: The Oct4A promoter of the longer isoform displays binding for a plethora of factors and evidence of RNAPII suggests that Oct4 is actively transcribed in ESCs. In general, this type of large-scale epigenetic profile is characteristic of active gene regulation and goes far beyond the simple histone modification code. On the other hand, the Oct4B promoter exhibits binding for an entirely different set of factors including SMC1, SMC3, SA1, SA2, RAD21, and CTCF, the main components of the structural Cohesin complex. It is also bound by ZC3H11A, which we found to cluster globally with the Cohesin complex (data not shown). Cohesin binding to the Oct4B promoter suggests that a specific enhancer may be driving the expression of this second isoform in ESCs. On the other hand, the mediator proteins MED1 and MED12 bind the first promoter and do not cluster with the Cohesin complex as they are proposed to do. These findings may be particularly insightful into discovering the molecular mechanisms governing alternative promoter regulation of Oct4 and genes in general.
DOI: 10.17632/xz6gv65m6d.3
title: Reproducible experiments on dynamic resource allocation in cloud data centers

description: In Wolke et al. we compare the efficiency of different resource allocation strategies experimentally. We focused on dynamic environments where virtual machines need to be allocated and deallocated to servers over time. In this companion paper, we describe the simulation framework and how to run simulations to replicate experiments or run new experiments within the framework.
DOI: 10.17632/khtbbvg6xx.1
title: The Act of Teaching Writing - A literary review on this skill

description: Communication is a process that requires constant practice. Without the communication of ideas, the world would be in chaos. Scholars of all over the world had discovered this, and they have exploited some characteristics of this. But, the problem starts when people wants to communicate ideas to others in another language. Nowadays, with the plenty access of data online, is not a mind breaker to discover that most of the articles people fnd at the Internet were writen by language technicians who are not native speakers. Here is when the process of teaching the beter way to teach how to write in English takes a part of the game. Moreover, teaching skills, like writing requires some schemes that need to be followed. And also it is necessary to teach them to the frst critical population: the student corpus. Simple basic stuf such as grammar, spelling and word choice becomes an important part of the curriculum for this topic. Nonetheless many teachers tend to confuse some exercises with other which does not have part in this skill. Te critical task for teachers is to recognize efectively which exercises are compatible for enhancing writen performance. Finally, at the end is all about communication. Old conventions for writing tend to be deprecated when we think that most of the technology today has come for only one purpose, to make things easy. We should teach rapid and efective ways of writing clearly and fuently. Although, in some part of our lives we need to appeal to our wisdom in order to do an academically research, it is something we do not deal every single day. Te thing is to create a balance between the strict ways of teaching how to write, aside the new conventions for writing, which have modifed the language during the present times.
DOI: 10.14469/hpc/174
title: Molecule1

description: Anhydride
DOI: 10.14469/hpc/175
title: ttest

description: test
DOI: 10.15468/ci43bl
title: Colección Teriológica y Ornitológica  de la Universidad Tecnológica del Chocó

description: Actualmente la Colección reúne cerca de 2670 especímenes (Mamiferos y Aves), los cuales cuentan con un nivel de identificación hasta especie en un 98% aproximadamente. Los especímenes de esta colección son irremplazables, por lo que se emplean técnicas adecuadas de inclusión, organización, sistematización y preservación, que aseguren la conservación a largo plazo de los especímenes depositados en ella, ya que esto dependerá, en buena parte, la investigación taxonómica del futuro. La información de cada ejemplar es almacenada en una base de datos basada en el software Specify, en la cual se incluyen datos de taxonomía, captura, morfometría e imágenes, ademas estos ejemplares fueron georreferenciados y publicados a través del portal del SiB Colombia.
DOI: 10.5525/gla.researchdata.229
title: Photon-sparse microscopy: Visible light imaging using infrared illumination
DOI: 10.5281/zenodo.33776
title: Mappingzeroinflateddata: First Release

description: Code and data associated with Lyashevska, Brus, and van der Meer Ecology and Evolution paper: Mapping species abundance by a spatial zero-inflated Poisson 2 model. A case study in the Wadden Sea, Netherlands
DOI: 10.5281/zenodo.27871
title: Allergic Non-Asthmatic Adults Have Regional Pulmonary Responses To Segmental Allergen Challenge

description: Data reported in the manuscript, 'Allergic Non-Asthmatic Adults have Regional Pulmonary Responses to Segmental Allergen Challenge' published in PLOS One. November 2015
DOI: 10.5880/tr32db.16
title: Raster-based Crop Rotation Map of the Rur catchment (2008-2012)

description: This data set contains a raster-based Crop Rotation Map
      (2008-2012) for the study area of the CRC/Transregio 32: "Patterns in
      Soil-Vegetation-Atmosphere Systems: monitoring, modelling and data assimilation", which
      corresponds to the catchment of the river Rur. The study area is mainly situated in the
      western part of North Rhine-Westphalia (Germany) and parts of the Netherlands and Belgium,
      covering an area of approximately 2365 square kilometers. The crop rotation map provides the
      succession of the major agricultural crops (winter wheat, winter barley, winter rapeseed,
      sugar beet, maize, Potato, Spring Barley) on a year to year basis for every raster cell. The
      crop rotation map is provided in GeoTIFF format. Spatial resolution: 15 m; Projection: WGS84,
      UTM Zone 32N.
DOI: 10.17632/xz6gv65m6d.4
title: Reproducible experiments on dynamic resource allocation in cloud data centers

description: In Wolke et al. we compare the efficiency of different resource allocation strategies experimentally. We focused on dynamic environments where virtual machines need to be allocated and deallocated to servers over time. In this companion paper, we describe the simulation framework and how to run simulations to replicate experiments or run new experiments within the framework.
DOI: 10.5065/d62j68z6
title: Ethane measurements in air extracted from Greenland and Antarctic ice cores, Version 1.0

description: This dataset contains the results of ethane (C2H6) analysis in air extracted from 27 ice core samples from Summit, Greenland (GISP2B ice core) and 33 samples from West Antarctic Ice Sheet Divide, Antarctica (WDC-05A ice core). The data is in Excel (.xlsx) format with data from the two sites provided in separate worksheets named after the ice cores. In addition to ethane, dichlorodifluoromethane (CFC-12) measurements are also reported for all samples. The presence of CFC-12 can indicate presence of modern air in an ice core sample.
DOI: 10.5287/bodleian:st74cq573
title: Nature-themed Apps, 2013
DOI: 10.5281/zenodo.33862
title: Image Dataset

description: Dataset de prueba para imágenes
DOI: 10.5281/zenodo.33864
title: Text Dataset

description: Dataset de prueba para texto
DOI: 10.15129/5dddf224-deaa-4b4b-aeb2-ef60c0d910c9
title: VCS-data

description: VCS-data: Vehicle Crew Scheduling Data

This set contains 240 test instances we generated using all different combinations of important problem parameters for a crew scheduling problem apparent for off-shore supply vessels (OSVs).

The documentation file provides thorough detail regarding problem parameters and different values used for each of these, and it also presents an MIP formulation of the problem to clarify the use of the data in a problem setting.  Each data instance has a text file with defined parameters, please see the .zip file that contains all instances.

The data is in a format that allows parameters to be readable for optimization software FICO XPress-MP.  The same software was used to generate the individual data instances based on the detailed description available in the documentation file.
DOI: 10.15468/mtqcuq
title: NEOTROPICMYXO. A database of Myxomycetes from the Neotropics

description: This is a database of the Myxomycetes recorded from the Neotropical region. This large biogeographical region includes the continent of America, from Mexico to Tierra del Fuego (Argentina and Chile). The region has the greatest biodiversity in the World and includes several biodiversity hotspots. The database NEOTROPICMYXO was developed in 2015 and includes all the species of Myxomycete (Amoebozoa) recorded in the literature as well as the data from herbaria and other recognised collections. The information included, apart from the species name, is the up-to-date nomenclatural status, bibliographic and geographic information, and also substrate data and where the material is located. The database is currently a reference for the MYXOTROPIC Project.
DOI: 10.17632/6n2tfgxcgb.1
title: Yugoslav Stats

description: This dataset contains statistics from Yugoslavia between 1943 and 1989. Data was extracted manually from three main sources and, in some cases, series are not complete. Some columns are manual calculations to analyse the variation of specific indicators). The main objective of this research was to understand how data could relate political changes taking place in the country. The study focused on three critical junctures: 1948, 1968 and 1974. The sources are "Statistical Book of Yugoslavia" Editions of 1988 and 1991 Lenard Cohen, 1983 I hope the dataset is useful and that can be completed in the future. There is a promising visualization if you compare unemployment and affiliation to the Communist Party!
DOI: 10.5281/zenodo.33973
title: Location Choice With Longitudinal Wifi Data: Research Data

description: This document describes the softwares, data, models and raw results associated to


Danalet, A., Tinguely, L., de Lapparent, M., & Bierlaire, M. (2015). <em>Location choice with longitudinal WiFi data</em>. Technical report TRANSP-OR 131002. Transport and Mobility Laboratory, ENAC, EPFL. Lausanne, Switzerland.
description: {"references": ["Bierlaire, M. (2003). BIOGEME: a free package for the estimation of discrete choice models, Proceedings of the 3rd Swiss Transportation Research Conference, Monte Verita\u0300, Ascona, Switzerland.", "Bierlaire, M. and Fetiarison, M. (2009). Estimation of discrete choice models: extend- ing BIOGEME., Swiss Transport Research Conference (STRC), Monte Verita\u0300, Ascona, Switzerland.", "Danalet, A. (2015). A Bayesian Approach to Detect Pedestrian Destination-Sequences from WiFi Signatures: Data (Transp. Res. Part C, 2014).", "Danalet, A., Farooq, B. and Bierlaire, M. (2014). A Bayesian approach to detect pedestrian destination-sequences from WiFi signatures, Transportation Research Part C 44: 146\u2013 170.", "Danalet, A., Tinguely, L., de Lapparent, M. and Bierlaire, M. (2015). Location choice with longitudinal WiFi data, Technical report TRANSP-OR 151110, Submitted for pub- lication in the Journal of Choice Modeling, Transport and Mobility Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fe\u0301dr\u0301ale de Lausanne, Lausanne, Switzerland.", "Wooldridge, J. M. (2005). Simple solutions to the initial conditions problem in dynamic, nonlinear panel data models with unobserved heterogeneity, Journal of Applied Econo- metrics 20(1): 39\u201354."]}
DOI: 10.15468/u552fh
title: Marie-Victorin Herbarium (MT) - Bryophytes

description: The Marie-Victorin Herbarium (MT) is the second largest university herbarium in Quebec and ranks fourth among all Canadian herbaria. It includes about 50,000+ bryophytes. About half of the material is Canadian, but representation is global. The current dataset includes the ca. 26,000 digitized specimens from the collection.
DOI: 10.5281/zenodo.31516
title: Dataset From Annual Acoustic Presence Of Fin Whale (Balaenoptera Physalus) Offshore Eastern Sicily, Central Mediterranean Sea

description: This dataset is form the study: 

Sciacca V., Caruso F.,Beranzoli L., Chierici F., De Domenico E., Embriaco D., Favali P., Giovanetti G., Larosa G., Marinaro G., Papale E., Pavan G., Pellegrino C., Pulvirenti S., Simeone F., Viola S., and G. Riccobene. "Annual Acoustic Presence of Fin Whale (<em>Balaenoptera physalus</em>) Offshore Eastern Sicily, Central Mediterranean Sea." PLoS ONE 10(11): e0141838. doi:10.1371/journal.pone.0141838

The archives labeled YYYYMM_Spectrograms.zip contain the data from each  month of passive acoustic recording -MM- of the years -YYYY- 2012 and 2013. Data consist of the spectrograms (1-50 Hz) of 10-min audio recordings, in PNG format files. These data were used in the cited study to verify the presence of fin whale calls.

The archive labeled "NoiseData.zip" consists of two matrix (ASCII format) containing the recorded values of acoustic noise within the fin whale call frequency band.
DOI: 10.5281/zenodo.34020
title: Interaction Between Unidirectional Quantized Vortex Rings

description: All data included in a paper on "Interactions between unidirectional quantized vortex rings". This paper is currently being prepared for submission.
DOI: 10.5281/zenodo.34062
title: Pathway Dataset

description: Depth maps from kinect streams
DOI: 10.17632/xz6gv65m6d.5
title: Reproducible experiments on dynamic resource allocation in cloud data centers

description: In Wolke et al. we compare the efficiency of different resource allocation strategies experimentally. We focused on dynamic environments where virtual machines need to be allocated and deallocated to servers over time. In this companion paper, we describe the simulation framework and how to run simulations to replicate experiments or run new experiments within the framework.
DOI: 10.15468/demitt
title: A phylogenetic classification of jumping spiders (Araneae: Salticidae)

description: A phylogenetic classification of jumping spiders (Araneae: Salticidae)
DOI: 10.5281/zenodo.34086
title: Middlesex Convicts Delivered For Transportation 1785-92

description: Between July 1789 and October 1792 the keeper of Newgate gaol, Richard Akerman, submitted to the Justices of the Peace at the Middlesex Sessions of the Peace a series of lists of convicts sentenced to transportation whom he had conveyed from Newgate to various vessels along the Thames or south coast ports, along with his detailed accounts of the substantial expenses incurred in the process. Akerman's lists named a total of 1515 offenders convicted at the Old Bailey and Middlesex Sessions whom he conveyed from Newgate and delivered to a number of destinations between January 1785 and July 1792.
description: The dataset has been created using the transcriptions of the Order Books published at London Lives http://www.londonlives.org. I am grateful to Tim Hitchcock and Bob Shoemaker, the London Lives project directors, for agreeing to share this data.
DOI: 10.15128/fq977t77k
title: Geo-healthcare access database

description: Data sources

Pharmacy data obtained from General Pharmaceutical Council. http://www.pharmacyregulation.org/ 

GP practice data obtained from http://data.gov.uk/dataset/england-nhs-connecting-for-health-organisation-data-service-data-files-of-general-medical-practices

IMD and Urban Rural classification from ONS

Postcode data aggregated to LSOA from ONS Postcode Directory Office of National Statistics. 
https://geoportal.statistics.gov.uk/geoportal/catalog/main/home.page;jsessionid=DA42EA7C669D7CC91FBA9C13AD511DFB
DOI: 10.5281/zenodo.34122
title: Secuencia Fotos

description: Secuencia de imaxes tomadas fora da nave 4 feita coas cámaras Xenics, Flir e Photonfocus o venres 20 de Novembro.
DOI: 10.5287/bodleian:3f462612m
title: Ultrahigh and persistent optical depths of cesium in Kagomé-type hollow-core photonic crystal fibres