cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4985198.v1
title: Barcode index number, taxonomic rank and modes of speciation: examples from fish

description: Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of <i>Co-1</i>-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (<i>R</i><sup>2</sup> ≈ 0.84–0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.
DOI: 10.6084/m9.figshare.4985177
title: A MRCC study of the isomerisation of cyclopropane

description: Mukherjee's and Brillouin-Wigner multi-reference coupled cluster methods with universal state selective (USS) corrections were used to study the isomerisation of cyclopropane to propene through a trimethylene/propylidene diradicals. Main aim was to obtain high quality ab-initio data using advanced methods that treat both static and dynamic correlation in the involved species, however, we also report implementation of the diagonal USS correction in the LPNO-MRCC code and its performance assessment. The MkCCSD(T)/cc-pV5Z lower bound of interaction energy of cyclopropane isomerisation via trimethylene is 65.6 kcal/mol (59.9 kcal/mol with ZPVE correction), in a good agreement with experimental values in the range 60–65 kcal/mol. The MkCCSD(T)/cc-pV5Z adiabatic singlet-triplet gap in trimethylene is 0.6 kcal/mol, slightly higher than previous CASPT2 result −0.7 kcal/mol by Skancke et al.
DOI: 10.6084/m9.figshare.4985180.v1
title: Quantum rotational scattering of H<sub>2</sub> and its isotopologues with He

description: Quantum close-coupling computations of the rotational quenching of H<sub>2</sub> and its isotopologues due to He impact are performed using a highly accurate potential energy surface. State-to-state cross sections are obtained in a wide range of collision energies between 10<sup>−5</sup> cm<sup>−1</sup> and 10<sup>4</sup> cm<sup>−1</sup>, and the theoretical rate coefficients are reported for temperatures ranging from 10<sup>−4</sup> K to 3000 K. Compared with previous studies, the well depth of the potential adopted in this study is larger, leading to stronger resonance effects in the cross sections of He-HD. The accurate potential was employed to investigate the isotope effects of H<sub>2</sub> in detail. The cross-section resonances shift towards lower collision energies and become stronger with increasing reduced mass. The calculated cross sections and rate coefficients of H<sub>2</sub> and its isotopic variants in collisions with He are provided to study the energy transfer in these systems.
DOI: 10.6084/m9.figshare.4985177.v1
title: A MRCC study of the isomerisation of cyclopropane

description: Mukherjee's and Brillouin-Wigner multi-reference coupled cluster methods with universal state selective (USS) corrections were used to study the isomerisation of cyclopropane to propene through a trimethylene/propylidene diradicals. Main aim was to obtain high quality ab-initio data using advanced methods that treat both static and dynamic correlation in the involved species, however, we also report implementation of the diagonal USS correction in the LPNO-MRCC code and its performance assessment. The MkCCSD(T)/cc-pV5Z lower bound of interaction energy of cyclopropane isomerisation via trimethylene is 65.6 kcal/mol (59.9 kcal/mol with ZPVE correction), in a good agreement with experimental values in the range 60–65 kcal/mol. The MkCCSD(T)/cc-pV5Z adiabatic singlet-triplet gap in trimethylene is 0.6 kcal/mol, slightly higher than previous CASPT2 result −0.7 kcal/mol by Skancke et al.
DOI: 10.6084/m9.figshare.4985165
title: Content uniformity testing for stratified samples via parametric tolerance interval testing

description: Historically in the biopharmaceutical setting, USP&lt;905&gt; has been used to establish that a batch of drug product has acceptable content uniformity. More recently, alternative approaches such as the two one-sided parametric tolerance interval test (PTI-TOST) have been proposed to establish content uniformity. Traditionally, the PTI-TOST is implemented as a sequential, two-tiered test, under the generally accepted assumption that the data are independently and identically distributed. Since the material is sequenced through the manufacturing process over a period of time, there are conceptually arguable locations within each batch, for instance: beginning, middle, and end. In such a situation, a practitioner may wish to evaluate potential effects of these batch locations, for example, during process validation. If location (stratified) differences exist within the batch and if multiple samples are taken from each location, significant within-location correlations may be induced in the data. In such a case, the traditional PTI-TOST underestimates the total variability, thereby improperly boosting the power of the test method. When there is reason to believe that location variances exist, the batch may be evaluated using stratified sampling, and the location effect may be modeled. In this paper, a two-tiered PTI-TOST that accounts for both between-location and within-location variance components is introduced. Operating characteristic curves and practical advice are given to aid the practitioner’s uptake of the proposed method.
DOI: 10.6084/m9.figshare.4985165.v1
title: Content uniformity testing for stratified samples via parametric tolerance interval testing

description: Historically in the biopharmaceutical setting, USP&lt;905&gt; has been used to establish that a batch of drug product has acceptable content uniformity. More recently, alternative approaches such as the two one-sided parametric tolerance interval test (PTI-TOST) have been proposed to establish content uniformity. Traditionally, the PTI-TOST is implemented as a sequential, two-tiered test, under the generally accepted assumption that the data are independently and identically distributed. Since the material is sequenced through the manufacturing process over a period of time, there are conceptually arguable locations within each batch, for instance: beginning, middle, and end. In such a situation, a practitioner may wish to evaluate potential effects of these batch locations, for example, during process validation. If location (stratified) differences exist within the batch and if multiple samples are taken from each location, significant within-location correlations may be induced in the data. In such a case, the traditional PTI-TOST underestimates the total variability, thereby improperly boosting the power of the test method. When there is reason to believe that location variances exist, the batch may be evaluated using stratified sampling, and the location effect may be modeled. In this paper, a two-tiered PTI-TOST that accounts for both between-location and within-location variance components is introduced. Operating characteristic curves and practical advice are given to aid the practitioner’s uptake of the proposed method.
DOI: 10.6084/m9.figshare.4985156
title: Urban Stream Vulnerability Toward PAHs and <i>n</i>-Alkanes and Their Source Identification

description: Monjolinho River is an important water body located in the central urban region of São Paulo State in southeast Brazil. The present work reports a 4-year study related to spatio-temporal distribution and source identification of polycyclic aromatic hydrocarbons (PAHs) and <i>n</i>-alkanes in surface water and sediment samples of Monjolinho River. A total of 25 sampling campaigns for water, and 10 sampling campaigns for sediment collection, were performed from 2011 to 2014. In sediment samples, total PAHs were found in the range of 2.25 µg kg<sup>−1</sup>–26,253.87 µg kg<sup>−1</sup>, while <i>n</i>-alkane concentrations ranged from 0.01 to 165.64 µg kg<sup>−1</sup>. Total PAHs' concentration in surface water was in the range of 0.17–1,348.35 ng L<sup>−1</sup>, while <i>n</i>-alkanes were detected in the range of 6.17–316.15 µg L<sup>−1</sup>. Principal component analysis was used as a statistical tool for summarizing and interpreting a huge quantity of data. It was observed that concentrations of contaminants increased along the river course in urban zone. Distribution indexes were calculated to identify possible sources of carbon pool that pointed towards petrogenic, pyrogenic, and biogenic sources. The overall concentrations of PAHs and <i>n</i>-alkanes were low compared to many previous studies done elsewhere and were mostly below the threshold effects level except in very few occasional cases, while probable effect level was violated in 1 sample during 4 years. Although adverse impacts are unexpected due to overall low contaminant concentrations, unexpected industrial, and sewage discharges make it risky for safer use as a drinking water resource, especially in dry conditions.
DOI: 10.6084/m9.figshare.4985156.v1
title: Urban Stream Vulnerability Toward PAHs and <i>n</i>-Alkanes and Their Source Identification

description: Monjolinho River is an important water body located in the central urban region of São Paulo State in southeast Brazil. The present work reports a 4-year study related to spatio-temporal distribution and source identification of polycyclic aromatic hydrocarbons (PAHs) and <i>n</i>-alkanes in surface water and sediment samples of Monjolinho River. A total of 25 sampling campaigns for water, and 10 sampling campaigns for sediment collection, were performed from 2011 to 2014. In sediment samples, total PAHs were found in the range of 2.25 µg kg<sup>−1</sup>–26,253.87 µg kg<sup>−1</sup>, while <i>n</i>-alkane concentrations ranged from 0.01 to 165.64 µg kg<sup>−1</sup>. Total PAHs' concentration in surface water was in the range of 0.17–1,348.35 ng L<sup>−1</sup>, while <i>n</i>-alkanes were detected in the range of 6.17–316.15 µg L<sup>−1</sup>. Principal component analysis was used as a statistical tool for summarizing and interpreting a huge quantity of data. It was observed that concentrations of contaminants increased along the river course in urban zone. Distribution indexes were calculated to identify possible sources of carbon pool that pointed towards petrogenic, pyrogenic, and biogenic sources. The overall concentrations of PAHs and <i>n</i>-alkanes were low compared to many previous studies done elsewhere and were mostly below the threshold effects level except in very few occasional cases, while probable effect level was violated in 1 sample during 4 years. Although adverse impacts are unexpected due to overall low contaminant concentrations, unexpected industrial, and sewage discharges make it risky for safer use as a drinking water resource, especially in dry conditions.
DOI: 10.6084/m9.figshare.4985087
title: NORDP Exercise 1 - Breakout notes- Team Gretchen

description: Pre-Conference Leadership Forum, group exercise. Making data driven decisions. Which areas should we invest in?
DOI: 10.6084/m9.figshare.4985087.v2
title: NORDP Exercise 1 - Breakout notes- Team Gretchen

description: Pre-Conference Leadership Forum, group exercise. Making data driven decisions. Which areas should we invest in?
DOI: 10.6084/m9.figshare.4985081
title: NORDP Pre-Conference breakout - Group 3 - Exercise 1

description: Pre-conference Leadership Forum. Group 3, Exercise 1. How do we identify research areas and investigators to make investments?
DOI: 10.6084/m9.figshare.4985087.v1
title: NORDP Breakout notes- GK table.docx

description: notes
DOI: 10.6084/m9.figshare.4985048
title: Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM

description: The custom-designed single nucleotide polymorphism (SNP) panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing (MPS) technology and Ion Torrent personal genome machine (PGM). SNPs were chosen from SNPforID, IISNP, HapMap, dbSNP, and related published literatures. Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls. Ten SNPs (rs4606077, rs334355, rs430046, rs2920816, rs4530059, rs1478829, rs1498553, rs7141285, rs12714757 and rs2189011) with low coverage or heterozygote imbalance should be optimized or excluded from the panel. Sequence data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS–SNP panel. A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input DNA. Mixture testing with this panel is possible through analysis of the <i>F</i><sub>MAR</sub> (frequency of major allele reads) values at most loci with enough high coverage depth and low level of sequencing noise. These results indicate the potential advantage of the custom MPS–SNP assays and Ion Torrent PGM platform for forensic study.
DOI: 10.6084/m9.figshare.4985048.v1
title: Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM

description: The custom-designed single nucleotide polymorphism (SNP) panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing (MPS) technology and Ion Torrent personal genome machine (PGM). SNPs were chosen from SNPforID, IISNP, HapMap, dbSNP, and related published literatures. Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls. Ten SNPs (rs4606077, rs334355, rs430046, rs2920816, rs4530059, rs1478829, rs1498553, rs7141285, rs12714757 and rs2189011) with low coverage or heterozygote imbalance should be optimized or excluded from the panel. Sequence data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS–SNP panel. A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input DNA. Mixture testing with this panel is possible through analysis of the <i>F</i><sub>MAR</sub> (frequency of major allele reads) values at most loci with enough high coverage depth and low level of sequencing noise. These results indicate the potential advantage of the custom MPS–SNP assays and Ion Torrent PGM platform for forensic study.
DOI: 10.6084/m9.figshare.4985081.v2
title: NORDP Pre-Conference breakout - Group 3 - Exercise 1

description: Pre-conference Leadership Forum. Group 3, Exercise 1. How do we identify research areas and investigators to make investments?
DOI: 10.6084/m9.figshare.4984217
title: Dados de Procrastinação

description: Data from 500 people from Brazil that answered to a modified version of the General Procrastination Questionnaire.
DOI: 10.6084/m9.figshare.4985081.v1
title: Tiime 1- no3- group Eck.docx

description: NORDP2017
DOI: 10.6084/m9.figshare.4984217.v1
title: Dados de Procrastinação

description: Data from 500 people from Brazil that answered to a modified version of the General Procrastination Questionnaire.
DOI: 10.6084/m9.figshare.4983392
title: Dataset for the paper High-Income Consumers May Be Less Hyperbolic When Discounting the Future

description: Dataset for the paper High-Income Consumers May Be Less Hyperbolic when Discounting the Future
DOI: 10.6084/m9.figshare.4983371
title: Genome sequencing of C. truncatum (3 kb mate-pair)

description: Long insert mate pair library of size 3kb for genome sequencing of C. truncatum.<br>
DOI: 10.6084/m9.figshare.4983368
title: Menopause Study Plos One

description: Data from a clinical trial investigating the effects of red clover isoflavone aglycones on menopausal symptoms<b></b>
DOI: 10.6084/m9.figshare.4983371.v1
title: Genome sequencing of C. truncatum (3 kb mate-pair)

description: Long insert mate pair library of size 3kb for genome sequencing of C. truncatum.<br>
DOI: 10.6084/m9.figshare.4983392.v2
title: Dataset for the paper High-Income Consumers May Be Less Hyperbolic When Discounting the Future

description: Dataset for the paper High-Income Consumers May Be Less Hyperbolic when Discounting the Future
DOI: 10.6084/m9.figshare.4983311
title: PyGBe on Localized Surface Plasmon Resonance (LSPR)

description: This file set includes three Jupyter notebooks with a summary of the preliminary results of Localized surface plasmon resonance applications obtained using PyGBe. <br><br>It also contains the figures and css style to load the notebooks properly when they are download. <br><br>The links below are:<br><br>* The github repository of the notebook's. <br>* The rendered version of the three notebooks in NBviewer<br>* The github repository of the Python library PyGBe. <br>
DOI: 10.6084/m9.figshare.4983392.v1
title: Dataset for the paper High-Income Consumers May Be Less Hyperbolic When Discounting the Future

description: Dataset for the paper High-Income Consumers May Be Less Hyperbolic when Discounting the Future
DOI: 10.6084/m9.figshare.4983257
title: Genomic DNA sequencing of C. truncatum (5kb mate-pair)

description: Long insert mate pair library of 5 kb size for genomic DNA sequencing of C. truncatum.<br>
DOI: 10.6084/m9.figshare.4983128
title: Imputed_datasets.zip

description: 10 imputed datasets of animal features: generated by mice_model_best.Rda
DOI: 10.6084/m9.figshare.4983122
title: Mos-flav data.xlsx

description: Vector status of mosquitos for several flavivirus strains
DOI: 10.6084/m9.figshare.4983257.v1
title: Genomic DNA sequencing of C. truncatum (5kb mate-pair)

description: Long insert mate pair library of 5 kb size for genomic DNA sequencing of C. truncatum.<br>
DOI: 10.6084/m9.figshare.4983128.v1
title: Imputed_datasets.zip

description: 10 imputed datasets of animal features: generated by mice_model_best.Rda
DOI: 10.6084/m9.figshare.4983122.v1
title: Mos-flav data.xlsx

description: Vector status of mosquitos for several flavivirus strains
DOI: 10.6084/m9.figshare.4983311.v1
title: PyGBe_LSPR

description: This file set includes three Jupyter notebooks with a summary of the preliminary results of Localized surface plasmon resonance applications obtained using PyGBe. <br><br>The links below are:<br><br>* The github repository of the notebook's. <br>* The rendered version of the three notebooks in NBviewer<br>* The github repository of the Python library PyGBe . <br>
DOI: 10.6084/m9.figshare.4983116
title: Flavivirus traits + key.xlsx

description: Flavivirus-related covariates and keys
DOI: 10.6084/m9.figshare.4983110
title: mice_model_best.Rda

description: R object for imputed animal features joint distribution: generates imputed datasets
DOI: 10.6084/m9.figshare.4983113
title: mosquito.csv

description: Mosquito features dataset
DOI: 10.6084/m9.figshare.4983311.v2
title: PyGBe_LSPR

description: This file set includes three Jupyter notebooks with a summary of the preliminary results of Localized surface plasmon resonance applications obtained using PyGBe. <br><br>It also contains the figures and css style to load the notebooks properly when they are download. <br><br>The links below are:<br><br>* The github repository of the notebook's. <br>* The rendered version of the three notebooks in NBviewer<br>* The github repository of the Python library PyGBe . <br>
DOI: 10.6084/m9.figshare.4983110.v1
title: mice_model_best.Rda

description: R object for imputed animal features joint distribution: generates imputed datasets
DOI: 10.6084/m9.figshare.4983104
title: flavi_small_trans.Rda

description: Animal feature dataset for primates: continuous variables transformed for closer adherence to gaussianity
DOI: 10.6084/m9.figshare.4983107
title: flavi_small.Rda

description: Animal feature dataset for primates: continuous variables untransformed
DOI: 10.6084/m9.figshare.4983107.v1
title: flavi_small.Rda

description: Animal feature dataset for primates: continuous variables untransformed
DOI: 10.6084/m9.figshare.4983098
title: flavi_prim01new.csv

description: Contains binary status of 376 primates for being reservoirs for each of the 8 flavivirus-borne diseases.
DOI: 10.6084/m9.figshare.4983104.v1
title: flavi_small_trans.Rda

description: Animal feature dataset for primates: continuous variables transformed for closer adherence to gaussianity
DOI: 10.6084/m9.figshare.4983101
title: Population Aging and Migration – History and UN Forecasts in the EU-28 and its East and South Near Neighborhood – One Century Perspective 1950 – 2050

description: Background: There is a gap in knowledge on long term pace of population aging acceleration and related net-migration rate changes in WHO European Region and its adjacent MENA countries. We decided to compare European Union (EU-28) region with the EU Near Neighborhood Policy Region East and EU Near Neighborhood Policy Region South in terms of these two essential features of third demographic transition. One century long perspective dating back to both historical data and towards reliable future forecasts was observed.Methods: United Nation’s Department of Economic and Social Affairs estimates on indicators of population aging and migration were observed. Time horizon adopted was 1950 – 2050. Targeted 44 countries belong to either one of three regions named by EU diplomacy as: European Union or EU-28, EU Near Neighborhood Policy Region East (ENP East) and EU Near Neighborhood Policy Region South (ENP South). Results: European Union region currently experiences most advanced stage of demographic aging. The latter one is the ENP East region dominated by Slavic nations whose fertility decline continues since the USSR Era back in late 1980s. ENP South region dominated by Arab League nations remains rather young compared to their northern counterparts. However as the Third Demographic Transition is inevitably coming to these societies they remain the spring of youth and positive net emigration rate. Probably the most prominent change will be the extreme fall of total fertility rate (children per woman) in ENP South countries (dominantly Arab League) from 6.72 back in 1950 to medium-scenario forecasted 2.10 in 2050. In the same time net number of migrants in the EU28 (both sexes combined) will grow from -91,000 in 1950 to +394,000 in 2050.Conclusions: Long term migration from Eastern Europe westwards and from MENA region northwards is historically present for many decades dating back deep into the Cold War Era. Contemporary large scale migrations outsourcing from Arab League nations towards rich European Protestant North is probably the peak of an iceberg in long migration routes history. However, in the decades to come acceleration of aging is likely to question sustainability of such movements of people.<br>
DOI: 10.6084/m9.figshare.4983095
title: Puma_GPS_locations

description: CSV file contains puma GPS collar locations collected at 5 minute, 15 minute, and 6 hour intervals in Southern California as part of the UC Davis Wildlife Health Center Mountain Lion Project. Fields contain unique identifiers for each individual and the X / Y location in NAD 1983 UTM Zone 11N projection.
DOI: 10.6084/m9.figshare.4983098.v1
title: flavi_prim01new.csv

description: Contains binary status of 376 primates for being reservoirs for each of the 8 flavivirus-borne diseases.