cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2538021
title: Patients data for meta-analysis of genotype-phenotype associations in Bardet-Biedl Syndrome

description: Data used for metaanalysis of the genotype-phenotype relationship in Bardet Biedl Syndrome.

File "EV table 1 literature.xlsx" describes studies that were included in the metaanalysis. File "EV table 2 dataset.xlsx" contains individual patient data. Each row corresponds to a patient. If the same patient was reported in more than 1 study, their data were merged into one row. The columns are as follows:

* source - a citation to the study the patient originated in

* FamilyID - randomly generated ID of a family (unique over the dataset), two persons with the same FamilyID are related.

* source case n. - A unique identifier of the patient within the study

* gene - A gene carrying the principal BBSome related mutation

* nucleotide change (allele 1,2)  - description of the mutations in DNA individual alleles of the gene, in HGVS nomenclature

* protein change (allele 1,2)  - description of how the mutations in DNA change the resulting protein, in HGVS nomenclature

* type of mut allele 1,2 - whether the given mutation  is considered missense (MS) or large truncation (trunc)

* mut/mut - combination of mutations for both alleles

* additional mutations - mutations in other BBSome-related genes. Format is "gene: DNA mutation, protein mutation"

* sex - "F" or "M"  (where reported)

* age group - age group (where reported)

* age - age in years. Contains fractions, decimal values and "5 month"

* RD, OBE, PD, CI, REP, REN, HEART, LIV, DD - presense or absence of phenotypes, if reported. RD – retinal dystrophy, OBE – obesity, PD – polydactyly, CI – cognitive impairment , REP – reproductive system anomalies, REN – renal anomalies, HRT – heart disease, LIV – liver anomalies, DD - Developmental delay. Values are "" (not reported), "0" (no phenotype), "1" (phenotype present), "1!" conflicting reports of phenotype in multiple studies (some patients were involved in multiple studies)

* ethnicity - ethnicity of the patient, if reported

* ethinc group - grouping of the ethnicities into 8 larger groups (see paper for details)

* note - miscellanous text, in particular contains notes on patients merged from multiple studies

====

The protocol for this meta-analysis was pre-registered with PROSPERO (CRD42018096099).

PubMed and Google Scholar databases were searched in May 2018 for the following keywords: [bardet-biedl syndrome AND (genotype phenotype OR cohort)]. Other suitable records were identified by snowball searching, in particular, by retrieving relevant articles from the references of the studied full-texts. In addition, all the references included in the publicly available Euro-Wabb database (https://lovd.euro-wabb.org/home.php) were covered. Our search was limited to the literature published in English language and covered the period from the inception of each database to the 21st of May 2018.
DOI: 10.5281/zenodo.2538154
title: Single Nucleotide Polymorphisms (SNPs) identified from the whole genome sequences of hilsa shad (Tenualosa ilisha) of the Bay of Bengal

description: The data file contains 792,939 isolated SNPs identified by discoSnp++ v2.3.x (Uricaru et al., 2015) from the whole genome sequence of T. ilisha of the Bay of Bengal. The central sequence of length 2k-1 is seen in upper case, while the flanking sequences are seen in lower case. SNP_higher/lower: one of the two alleles. id: id of the SNP (each SNP has a unique id).

FOR SNPs:

P_i:pos_Alt1/Alt2: Information about a ith SNP (If more than a unique SNP is found, the following format is used: P_1:pos_Alt1/Alt2,P_2:pos_Alt1/Alt2,...

pos: position of the SNP with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.

Alt1: One of the two alleles

Alt2: the other

FOR INDELs:

P_1:pos_size_repeatSize

pos: predicted position of the indel with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.

size: predicted size of the indel

repeatSize: Size of the longest sequence both prefix of the indel and prefix of the sequence located just after the insertion.

high/low: sequence complexity. If the sequence if of low complexity (e.g. ATATATATATATATAT) this variable would be low

nb_pol: number of polymorphism.

left_unitig_length: size of the full left extension.

right_unitig_length: size of the right extension.

left_contig_length: size of the full left extension.

right_contig_length: size of the right extension.

C1: number of reads mapping the central upper case sequence from the first read set.

C2: number of reads mapping the central upper case sequence from the second read set.

Q1 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the first read set.

Q2 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the second read set.

G1: Genotype of the variant in the first read set.

G2: Genotype of the variant in the second read set.

rank: ranks the predictions according to their read coverage in each condition favoring SNPs that are discriminant between conditions.
DOI: 10.5281/zenodo.2538155
title: Single Nucleotide Polymorphisms (SNPs) identified from the whole genome sequences of hilsa shad (Tenualosa ilisha) of the Bay of Bengal

description: The data file contains 792,939 isolated SNPs identified by discoSnp++ v2.3.x (Uricaru et al., 2015) from the whole genome sequence of T. ilisha of the Bay of Bengal. The central sequence of length 2k-1 is seen in upper case, while the flanking sequences are seen in lower case. SNP_higher/lower: one of the two alleles. id: id of the SNP (each SNP has a unique id).

FOR SNPs:

P_i:pos_Alt1/Alt2: Information about a ith SNP (If more than a unique SNP is found, the following format is used: P_1:pos_Alt1/Alt2,P_2:pos_Alt1/Alt2,...

pos: position of the SNP with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.

Alt1: One of the two alleles

Alt2: the other

FOR INDELs:

P_1:pos_size_repeatSize

pos: predicted position of the indel with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.

size: predicted size of the indel

repeatSize: Size of the longest sequence both prefix of the indel and prefix of the sequence located just after the insertion.

high/low: sequence complexity. If the sequence if of low complexity (e.g. ATATATATATATATAT) this variable would be low

nb_pol: number of polymorphism.

left_unitig_length: size of the full left extension.

right_unitig_length: size of the right extension.

left_contig_length: size of the full left extension.

right_contig_length: size of the right extension.

C1: number of reads mapping the central upper case sequence from the first read set.

C2: number of reads mapping the central upper case sequence from the second read set.

Q1 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the first read set.

Q2 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the second read set.

G1: Genotype of the variant in the first read set.

G2: Genotype of the variant in the second read set.

rank: ranks the predictions according to their read coverage in each condition favoring SNPs that are discriminant between conditions.
DOI: 10.5281/zenodo.2539375
title: The influence of lattice termination on the edge states of the quantum spin Hall insulator monolayer 1T'-WTe_2

description: We study the influence of sample termination on the electronic properties of the novel quantum spin Hall insulator monolayer 1T'-WTe<sub>2</sub>. For this purpose, we construct an accurate, minimal 4-orbital tight-binding model with spin-orbit coupling by employing a combination of density-functional theory calculations, symmetry considerations, and fitting to experimental data. Based on this model, we compute energy bands and 2-terminal conductance spectra for various ribbon geometries with different terminations, with and without magnetic field.

The provided repository contains all code and data to reproduce the results of this study.
DOI: 10.17029/36c868da-c107-4929-85d1-817402ccb541
title: Dataset for 'Passive elastic contribution of hip extensors to joint moments during walking in people with low back pain'.

description: The files provide data :
passive flexion moment and power of the hips - Flexion_Moments_100.xlsx, Flexion_Power_100.xlsx
the hip and knee angles - Hip_Angle_100.xlsx, Knee_Angle_100.xlsx
and total moment and power of the hip Ð Moments_100.xlsx, Power_100.xlsx
of all subjects (listed in columns) from 0-100% of the gait cycle (listed in row), together with the mean, SD and confidence interval.

(Publication post-print embargoed until 14/10/19.)
DOI: 10.5281/zenodo.2539398
title: VERTEX 2.0 Rat Neocortex Simulation Results

description: The results of simulations of electric field stimulation in rat neocortex.

Three stimulation paradigms have been used, a single pulse, a paired pulse, and theta burst stimulation.

The VERTEX simulator code that generated these results is available at https://github.com/haeste/Vertex_2.
DOI: 10.17632/4cc4p693cd.1
title: Scholarly Communication Tools Data Note

description: Responses obtained from the faculty through survey questionnaire. This is the raw data of the study. We have removed the names of the teaching faculty in line with Mendeley's conditions for confidentiality.
DOI: 10.17632/mr6byfs3jf.1
title: Dataset and code of AnyLogic model for ecological modelling of air pollutants dynamics interacting with greenery in the city of Yerevan, Armenia

description: Content Dataset on Yerevan (XLS): 1. List of activities of enerprises of Yerevan, Aremenia 2. List of main enterprises of Yerevan, Armenia 3. List of main kindergartens of Yerevan, Armenia 4. List of node coordinates of main roads of Yerevan, Armenia 5. Data on initial radiuses of object-emissions 6. Data on harmful emissions produced by enterprises of Yerevan, Armenia 7. Data on absoprion characteristics of trees planted in Yerevan, Armenia Content AnyLogic model (ZIP): 1) Yerevan_kindergartents.alp - the main file of the simulation that can be opened in AnyLogic tool Content EcModel2 (ZIP): 1) EcModel2.bak - the database file in the MS SQL Server format that should be installed before running AnyLogic model.
DOI: 10.17632/rh7kc84htz.1
title: Android Permissions and malware applications

description: This data set contain unique Android applications and their extracted permissions
DOI: 10.17632/ts398wdyys.1
title: Data for: HYDROGEN ISOTOPE INVESTIGATION OF AMPHIBOLE AND BIOTITE PHENOCRYSTS IN SILICIC MAGMAS ERUPTED AT LASSEN VOLCANIC CENTER, CALIFORNIA

description: This raw data includes the electron microprobe analyses, and other chemical and hydrogen isotopic content for phenocrysts for the samples used in this paper. In the hydrogen isotope file, the raw data for a similar study of amphiboles in Mount Saint Helens (Washington State, USA) are also included because the isotopic standards are included in those runs.
DOI: 10.17632/9kjx9d7ycm.2
title: Hydrological Reanalysis Across the 20th Century: A Case Study of the Amazon Basin

description: We make available the daily discharge dataset of the Hydrological Reanalysis across the 20th Century for the Amazon Basin in its v1.0 version, which correspond to the HRXX_Amz.nc file. The matrix of daily discharge contains 36890 columns (one per day, starting at 01Jan/1910) and 12466 rows (one per catchment). Authors: Sly Wongchuig Correa Rodrigo Cauduro Dias de Paiva Vinícius Siqueira Walter Collischonn Institute of Hydraulic Research - (IPH/UFRGS) Brazil - November 2018 Citation: When using these data, please refer to the following paper: Wongchuig, C.S.; Paiva, R.C.D.; Siqueira, V.; Collischonn, W. 2018. Hydrological Reanalysis Across the 20th Century: A Case Study of the Amazon Basin. Journal of Hydrology.
DOI: 10.17632/cy9r9b2ffv.1
title: Energy saving and users satisfaction for a new advanced public lighting system

description: These data are referred to the work based on the analysis of energy saving and users satisfaction for a new advanced public lighting system in the Campus of the University of Palermo
DOI: 10.17632/gsmh4pmr24.1
title: Grouthtruth Images for testing character segmentation algorithms from palm leaf images

description: This dataset consists of manually segmented grantha characters from palmleaflets.Grantha characters was the script used in southern India to write sanskrit language.This dataset will serve as ground truth for testing segmentation algorithms for extraction of characters from palm leaf images.The palm leaflets are taken from the manuscript "Isadi Upanishad" obtained from Oriental Research Institute under University of Kerala,India.It consists of two input palm leaflets and the corresponding cropped characters of each line arranged in different folders.
DOI: 10.17632/gsmh4pmr24.2
title: Groudtruth Images for testing character segmentation algorithms from palm leaf images

description: This dataset consists of manually segmented grantha characters from palmleaflets.Grantha characters was the script used in southern India to write sanskrit language.This dataset will serve as ground truth for testing segmentation algorithms for extraction of characters from palm leaf images.The palm leaflets are taken from the manuscript "Isadi Upanishad" obtained from Oriental Research Institute under University of Kerala,India.It consists of two input palm leaflets and the corresponding cropped characters of each line arranged in different folders.
DOI: 10.17632/m4p8c9pxbb.1
title: Lisa Test Collection

description: There are 6004 documents and 35 queries with relevance judgements. Data provided by Dr. Peter Willett of Sheffield University on 28 June 1988.
DOI: 10.17632/htrm97jts4.1
title: Placial analysis of events: a case study on criminological places

description: The data folder includes crime reports in Dallas from 1 June 2014 to 31 May 2018. With corrected geographic coordinates for each incidence. The result folder includes all rose graphs and maps created from placial analysis in the study. The script folder includes all R codes we developed and used in the study.
DOI: 10.17632/vmpb2t8h4c.1
title: Value Co-creation Behaviour Instrument dataset

description: The data in this study aims to explore a new dimensional abstraction of value co-creation behavior for the service institutions especially in the context of higher education institutions. The items used for data collection reflect the students' value co-creation behavior as a whole rather than specific dimensions mentioned by Yi and Gong (2013) such as participate behavior and citizenship behavior. Factor analysis was done with 16 items in participation behavior and 13 items of citizenship behavior developed by Yi & Gong(2013) together and check the response among the international students in the private and public higher education institutions in Malaysia. As Malaysia is considered one of the emerging HUB in Asia it would be possible to encounter students from different countries and cultures to experiment their psychology towards the value co creation behavior items in their respective university context. The aim is to experiment whether the items fall under the similar dimensions separately for the participation and citizenship behaviors or there is any integration between the items. Besides that, the study wants to explore the number of extracted factors especially for the higher educational perspectives how the items differ from the original measurement scale developed by Yi & Gong(2013). The data was gathered personally by the researcher with the help of student representative council members in the respective universities. Both postgraduate and undergraduate students participated in the survey. They have shared their value co-creation experience with their respective universities. The findings of the study have interesting insights. The items of citizenship behaviour fall with the items of participation behaviour. This reflects that students' participation behavior and citizenship behavior cannot be seen as individual entities. They rather have to be taken as an integrated phenomenon for successful value co creation behaviour. The exploratory factor analysis also reveals that the number of factors extracted for the value co-creation behaviour in higher education context is also different from the original dimensions of Yi & Gong(2013).
DOI: 10.17632/w89ntfnwtz.1
title: Impact of salpingectomy for ectopic pregnancy on the ovarian response during IVF

description: Impact of salpingectomy for ectopic pregnancy on the ovarian response during IVF
DOI: 10.17632/7g9p7ryvh8.3
title: Data for Manuscript"Nonlinear vibration of imperfect functionally graded sandwich nanobeams based on nonlocal strain gradient theory"

description: Data for Manuscript--Nonlinear free vibration of geometrically imperfect functionally graded sandwich nanobeams based on nonlocal strain gradient theory
DOI: 10.17632/b3sph5cbh7.1
title: The Geology and Mineral Resources of Northern Haïti.

description: The geology of Northern Haïti corresponds to a volcanic arc of Meso-Cenozoic Age that can be traced from Central Cuba, through the Dominican Republic and forms part of the mountains of the Massif du Nord Group in Haïti oriented NW-SE. This group is composed of volcanic tuffs and lavas from the volcanic belt, ranging in composition from felsic, through intermediate, to mafic and ultramafic rocks. The belt is composed of numerous lenticular bodies of lavas and pyroclastic material of felsic composition, varying from dacite to rhyolite, embedded in a thick series of andesites with lesser amounts of basalts and with numerous intercalations of radiolarians cherts, carbonate rocks, and tuffs. Copper and gold are the two main ore types in the area. Copper is usually found associated with the porphyritic facies, the apophyses microtonalitics, and the silicified zones, filling fissures and fractures, as well as disseminated. Within the quartz vein systems, the copper is contained in the chalcopyrite, while the gold appears both as native gold and as a very fine disseminated gold in the sulphide zone. It can also form spectacular concentrations on the oxidised cap. Gold is usually found associated with the chlorite, as well as in grains of pyrite and chalcopyrite. A second generation of gold is found associated to the quartz and the chlorite. The gold content is extremely variable, with some samples reaching up to 226 g/t on surface. As a rule of thumb, the more chalcopyrite, the greater the gold content. However, the reverse is not always true, since there is also gold associated to quartz and chlorite. Gold rich quartz veins are usually enriched in Cu, Pb, Zn, Ba, Mn, Mo, Cr, and Ti, and depleted of Ag, Hg, As, Bi, Th, U, Sr, Rb, Ir, Se, and F. The Author conducted a thorough exploration program while he was working for St. Genéviève Resources Ltd. (SGV). The program included geological mapping, geophysical and geochemical surveys, trenching and diamond drilling, as well as metallurgical studies. The program stopped when the political situation in Haïti deteriorated to a point when SGV was forced to leave the country. We systematically drilled the known targets and discovered several new mineralized points elsewhere within the limits of the studied area. Also, the Author completed a compilation of all the data from the UN and the BRG exploration programs in the region. The ore potential of Northern Haïti remains important and with a more stable political situation and with the latest advances in the hydrometallurgical process to produce both copper and gold presented by Inotel Inc., I believe that the work should be completed.
DOI: 10.17632/hjtps2gfmn.1
title: Nutrient resorption from leaves of wetland plants in a constructed wetland depends on green leaf nutrient content and life form
DOI: 10.17632/jmfmdf2jv3.1
title: Stereotactic system for accurately targeting deep brain structures in awake head-fixed mice

description: Contain intracellular, juxtacellular recorded data and also CAD files of the system.
DOI: 10.17632/k4h8h86gwt.1
title: Data for : Metabolomics dataset of Underutilized Indonesian Fruits; Rambai (Baccaurea motleyana), Nangkadak (Artocarpus nangkadak), Rambutan (Nephelium lappaceum) and Sidempuan Salak (Salacca sumatrana) using GCMS and LCMS
DOI: 10.17632/4djmkmy69c.1
title: reSolve — A transverse momentum resummation tool

description: In this note, we introduce the new tool reSolve, a Monte Carlo differential cross-section and parton-level event generator whose main purpose is to add transverse momentum resummation to a general class of inclusive processes at hadron colliders, namely all those which do not involve hadrons or jets in the measured final state. This documentation refers to the first main version release, which will form the basis for continued developments, consequently it only implements the key features of those we plan to ultimately include. This article acts as a manual for the program; describing in detail its use, structure, validation and results; whilst also highlighting key aspects of the resummation formalism applied. It details the two classes of processes so far included; these are diphoton production and Drell–Yan production. A main concept behind the development of the tool is that it is a hands-on white box for the user: significant effort has been made to give the program a modular structure, making the various parts which comprise it independent of each other as much as possible and ensuring they are transparently documented, customisable and, in principle, replaceable with something that may better serve the user’s needs. reSolve is a new C++ program, based on an evolution of the private Fortran code 2gres, it is also influenced by the DYRes Fortran code. This initial version calculates the low transverse momentum contribution to the fully differential cross-section for two main categories of processes; the inclusive production of two photons, and inclusive Drell–Yan production. In all cases resummation up to Next-to-Next-to-Leading Logarithm (NNLL) is included. We aim to extend the program to several more processes in the near future. The program is publicly available on Github.
DOI: 10.17632/7xfxhr9mg6.1
title: AMBiT: A programme for high-precision relativistic atomic structure calculations

description: We present the AMBiT software package for general atomic structure calculations. This software implements particle–hole configuration interaction with many-body perturbation theory (CI+MBPT) for fully relativistic calculations of atomic energy levels, electric- and magnetic-multipole transition matrix elements, g-factors and isotope shifts. New numerical methods and modern high-performance computing techniques employed by this software allow for the calculation of open-shell systems with many valence-electrons (N greater than or equal to 5) to a high degree of accuracy and in a highly computationally efficient manner.