cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5624800.v1
title: Reaction paths of alane dissociation: VASP CONTCAR

description: Zipped sets of 6 intermediate images output from converged VASP climbing-image calculation, in CONTCAR format. Zip filename identifies start and end configurations which can be found in the "Alane adsorption on Si(100): VASP CONTCAR" filesets. <br>
DOI: 10.6084/m9.figshare.5624797.v1
title: MyData2

description: This is a experimental dataset.
DOI: 10.6084/m9.figshare.5624809
title: II.8" - Agrogenom clade-specific genes

description: Sets of clade-specific genes derived from the ancestral genome gene content estimations in Agrogenom database.<br>Procedure for detection of clade-specific genes from phylogenetic profiles:Clade-specific genes were defined as genes gained (or lost) by the clade ancestor and conserved (not re-gained) in all clade members since. We first identified genes marked by gain/loss events in the genome of a clade ancestor. Then, we identified clade-specific genes by searching for contrasting patterns in the phylogenetic profile of the presence or absence of each gained/lost gene. These profiles were established from the scenarios of orthologous subfamily evolution (see above and Supplementary Text, section 3, step 6). A background clade was chosen as the one corresponding to the next higher taxonomic unit (genus, species complex, etc.) in which the focal (foreground) clade was nested. Contrast was initially defined between the foreground and background clades, where foreground genomes had a consistently opposite pattern to that of genomes in the background clade. However, possible subsequent transfer or loss events in the background clade can blur the contrasting pattern in phylogenetic profiles. Clade-specific genotypes were thus identified using a relaxed definition of clade specificity, i.e. where the presence/absence contrast could be incomplete, with up to two genomes in the background clade sharing the foreground state.<br>
DOI: 10.6084/m9.figshare.5624809.v1
title: II.8" - Agrogenom clade-specific genes

description: Sets of clade-specific genes derived from the ancestral genome gene content estimations in Agrogenom database.<br>Procedure for detection of clade-specific genes from phylogenetic profiles:Clade-specific genes were defined as genes gained (or lost) by the clade ancestor and conserved (not re-gained) in all clade members since. We first identified genes marked by gain/loss events in the genome of a clade ancestor. Then, we identified clade-specific genes by searching for contrasting patterns in the phylogenetic profile of the presence or absence of each gained/lost gene. These profiles were established from the scenarios of orthologous subfamily evolution (see above and Supplementary Text, section 3, step 6). A background clade was chosen as the one corresponding to the next higher taxonomic unit (genus, species complex, etc.) in which the focal (foreground) clade was nested. Contrast was initially defined between the foreground and background clades, where foreground genomes had a consistently opposite pattern to that of genomes in the background clade. However, possible subsequent transfer or loss events in the background clade can blur the contrasting pattern in phylogenetic profiles. Clade-specific genotypes were thus identified using a relaxed definition of clade specificity, i.e. where the presence/absence contrast could be incomplete, with up to two genomes in the background clade sharing the foreground state.<br>
DOI: 10.6084/m9.figshare.5624746
title: Explaining the national differences in the level of scientific research – a review of literature

description: This paper deals with the causes of the national differences in the level of scientific research. The level of scientific research is defined as the citation-impact of publications. The paper is based on a scrutinity of the explanation models presented in the relevant literature: 1) the number of talented researchers, 2) the amount of research funding, and 3) the conditions of research environment (modes of research funding, the time available for research, the infrastructure, the economies of scale, concentration, national and international cooperation, etc.). The explanatory power of the models is critically examined based on the results of empirical studies and mutual comparison. The paper is part of a research project “Why is Finland not successful in international science comparisons?”. The empirical part of the project is carried out by comparing Finland to Switzerland, the Netherlands, Denmark, Sweden and Norway. The research includes some ideas on how to improve Finland’s position in international science comparisons. <br>
DOI: 10.6084/m9.figshare.5624746.v1
title: Explaining the national differences in the level of scientific research – a review of literature

description: This paper deals with the causes of the national differences in the level of scientific research. The level of scientific research is defined as the citation-impact of publications. The paper is based on a scrutinity of the explanation models presented in the relevant literature: 1) the number of talented researchers, 2) the amount of research funding, and 3) the conditions of research environment (modes of research funding, the time available for research, the infrastructure, the economies of scale, concentration, national and international cooperation, etc.). The explanatory power of the models is critically examined based on the results of empirical studies and mutual comparison. The paper is part of a research project “Why is Finland not successful in international science comparisons?”. The empirical part of the project is carried out by comparing Finland to Switzerland, the Netherlands, Denmark, Sweden and Norway. The research includes some ideas on how to improve Finland’s position in international science comparisons. <br>
DOI: 10.6084/m9.figshare.5624644
title: The formation of gullies on Mars today

description: Locations and brief descriptions of known active dune gullies
DOI: 10.6084/m9.figshare.5624644.v1
title: The formation of gullies on Mars today

description: Locations and brief descriptions of known active dune gullies
DOI: 10.6084/m9.figshare.5624635
title: The formation of gullies on Mars today

description: Summary of information about known gully changes on Mars.
DOI: 10.6084/m9.figshare.5624623
title: Supplementary Material

description: Supplementary Material of the Research article 'The impact of changes in day-care centres’ enrolment on<br>the dynamics of varicella transmission in France between<br>1991 and 2015'<br>
DOI: 10.6084/m9.figshare.5624635.v1
title: The formation of gullies on Mars today

description: Summary of information about known gully changes on Mars.
DOI: 10.6084/m9.figshare.5624593
title: Purification and structural analysis of volatile sesquiterpenes produced by <i>Escherichia coli</i> carrying unidentified terpene synthase genes from edible plants of the family <i>Araliaceae</i>

description: A simple method to purify volatile sesquiterpenes from recombinant <i>Escherichia coli</i> was developed using the cells that carried known sesquiterpene synthase (<i>Tps</i>) genes <i>ZzZss</i>2 (<i>ZSS</i>2) and <i>ZoTps</i>1. This method was applied for the purification and structural analyses of volatile sesquiterpenes produced by <i>E. coli</i> cells that carried unidentified <i>Tps</i> genes, which were isolated from the <i>Aralia</i>-genus edible plants belonging to the family <i>Araliaceae</i>. Recombinant cells carrying each Tps gene were cultured in the two-layer medium (<i>n</i>-octane/TB medium), and volatile sesquiterpenes trapped in <i>n</i>-octane were purified through two-phase partition, silica gel column chromatography, and reversed-phase preparative high-performance liquid chromatography, if necessary. Further, their structures were confirmed by nuclear magnetic resonance, [α]<sub>D</sub>, and gas chromatography–mass spectrometry analyses. Herein, the products of <i>E. coli</i> cells that carried two <i>Tps</i> gene (named <i>AcTps</i>1 and <i>AcTps</i>2) in <i>Araria cordata</i> “Udo” and a <i>Tps</i> gene (named <i>AeTps</i>1) in <i>Aralia elata</i> “Taranoki” were studied resulting in identifying functionalities of these cryptic <i>Tps</i> genes. Purification and structural analysis of volatile sesquiterpenes produced by <i>Escherichia coli</i> carrying unidentified terpene synthase genes from edible plants of the family <i>Araliaceae</i>.
DOI: 10.6084/m9.figshare.5624602
title: Whole-transcriptome analysis of oxidative stress response genes in carotenoid-producing <i>Enterococcus gilvus</i>

description: Whole-transcriptome analysis of aerobic stress response gene in <i>Enterococcus gilvus</i> was performed using RNA-sequencing to identify carotenoid-based stress response genes in lactic acid bacteria. The expression of gene responsible for pyruvate dehydrogenase complex synthesis was highly upregulated after aerobic treatment. In addition, the expression of transcriptional regulator <i>spx</i> and genes encoding UvrABC system protein was also upregulated.
DOI: 10.6084/m9.figshare.5624593.v1
title: Purification and structural analysis of volatile sesquiterpenes produced by <i>Escherichia coli</i> carrying unidentified terpene synthase genes from edible plants of the family <i>Araliaceae</i>

description: A simple method to purify volatile sesquiterpenes from recombinant <i>Escherichia coli</i> was developed using the cells that carried known sesquiterpene synthase (<i>Tps</i>) genes <i>ZzZss</i>2 (<i>ZSS</i>2) and <i>ZoTps</i>1. This method was applied for the purification and structural analyses of volatile sesquiterpenes produced by <i>E. coli</i> cells that carried unidentified <i>Tps</i> genes, which were isolated from the <i>Aralia</i>-genus edible plants belonging to the family <i>Araliaceae</i>. Recombinant cells carrying each Tps gene were cultured in the two-layer medium (<i>n</i>-octane/TB medium), and volatile sesquiterpenes trapped in <i>n</i>-octane were purified through two-phase partition, silica gel column chromatography, and reversed-phase preparative high-performance liquid chromatography, if necessary. Further, their structures were confirmed by nuclear magnetic resonance, [α]<sub>D</sub>, and gas chromatography–mass spectrometry analyses. Herein, the products of <i>E. coli</i> cells that carried two <i>Tps</i> gene (named <i>AcTps</i>1 and <i>AcTps</i>2) in <i>Araria cordata</i> “Udo” and a <i>Tps</i> gene (named <i>AeTps</i>1) in <i>Aralia elata</i> “Taranoki” were studied resulting in identifying functionalities of these cryptic <i>Tps</i> genes. Purification and structural analysis of volatile sesquiterpenes produced by <i>Escherichia coli</i> carrying unidentified terpene synthase genes from edible plants of the family <i>Araliaceae</i>.
DOI: 10.6084/m9.figshare.5624602.v1
title: Whole-transcriptome analysis of oxidative stress response genes in carotenoid-producing <i>Enterococcus gilvus</i>

description: Whole-transcriptome analysis of aerobic stress response gene in <i>Enterococcus gilvus</i> was performed using RNA-sequencing to identify carotenoid-based stress response genes in lactic acid bacteria. The expression of gene responsible for pyruvate dehydrogenase complex synthesis was highly upregulated after aerobic treatment. In addition, the expression of transcriptional regulator <i>spx</i> and genes encoding UvrABC system protein was also upregulated.
DOI: 10.6084/m9.figshare.5624536
title: An open-treatment six-week study of the clinical effectiveness of Paliperidone Palmitate in schizophrenia: data from acute units in Spain (SHADOW study)

description: <b>Objectives:</b> To evaluate clinical evolution of patients with schizophrenia admitted in acute units because of a relapse and treated with once-monthly Paliperidone Palmitate (PP1M). <b>Methods:</b> This multicentre, open-label, prospective observational study followed patients with schizophrenia treated with PP1M in acute psychiatric units for up to 6 weeks. <b>Results:</b> Out of the 280 enrolled patients, 61 received PP1M as antipsychotic monotherapy, and 219 in combination with other antipsychotics. The average Clinical Global Impression–Schizophrenia (CGI-SCH) score decreased from 4.7 at baseline to 3.3 at final visit (<i>p</i> p <b>Conclusions:</b> PP1M was effective and well tolerated in treatment of acute episodes of schizophrenia both in monotherapy and in combination with other antipsychotics in clinical setting. Early start of PP1M therapy in acute schizophrenia episodes might help to shorten hospital stay.
DOI: 10.6084/m9.figshare.5624530
title: A good practice guide for translating and adapting hearing-related questionnaires for different languages and cultures

description: <i>Objectives</i>: To raise awareness and propose a good practice guide for translating and adapting any hearing-related questionnaire to be used for comparisons across populations divided by language or culture, and to encourage investigators to publish detailed steps. <i>Design</i>: From a synthesis of existing guidelines, we propose important considerations for getting started, followed by six early steps: (1) Preparation, (2, 3) Translation steps, (4) Committee Review, (5) Field testing and (6) Reviewing and finalising the translation. <i>Study sample</i>: Not applicable. <i>Results</i>: Across these six steps, 22 different items are specified for creating a questionnaire that promotes equivalence to the original by accounting for any cultural differences. Published examples illustrate how these steps have been implemented and reported, with shared experiences from the authors, members of the International Collegium of Rehabilitative Audiology and TINnitus research NETwork. <i>Conclusions</i>: A checklist of the preferred reporting items is included to help researchers and clinicians make informed choices about conducting or omitting any items. We also recommend using the checklist to document these decisions in any resulting report or publication. Following this step-by-step guide would promote quality assurance in multinational trials and outcome evaluations but, to confirm functional equivalence, large-scale evaluation of psychometric properties should follow.
DOI: 10.6084/m9.figshare.5624536.v1
title: An open-treatment six-week study of the clinical effectiveness of Paliperidone Palmitate in schizophrenia: data from acute units in Spain (SHADOW study)

description: <b>Objectives:</b> To evaluate clinical evolution of patients with schizophrenia admitted in acute units because of a relapse and treated with once-monthly Paliperidone Palmitate (PP1M). <b>Methods:</b> This multicentre, open-label, prospective observational study followed patients with schizophrenia treated with PP1M in acute psychiatric units for up to 6 weeks. <b>Results:</b> Out of the 280 enrolled patients, 61 received PP1M as antipsychotic monotherapy, and 219 in combination with other antipsychotics. The average Clinical Global Impression–Schizophrenia (CGI-SCH) score decreased from 4.7 at baseline to 3.3 at final visit (<i>p</i> p <b>Conclusions:</b> PP1M was effective and well tolerated in treatment of acute episodes of schizophrenia both in monotherapy and in combination with other antipsychotics in clinical setting. Early start of PP1M therapy in acute schizophrenia episodes might help to shorten hospital stay.
DOI: 10.6084/m9.figshare.5623669
title: Multi-clonal evolution of MDR/XDR M. tuberculosis in a high prevalence setting of Papua New Guinea for over three decades

description: Beauti raw file anlyzed using BEAST 1.8<br>
DOI: 10.6084/m9.figshare.5623705
title: R code and raw data for Clark et al Parasites & Vectors

description: These files provide sample R scripts and raw data necessary to calculate flea functional-phylogenetic host specificity and analyse flea infestation probability in wild mammals using phylogenetic glmms. The pdf files contain the code necessary for completing analyses.
DOI: 10.6084/m9.figshare.5623669.v1
title: Multi-clonal evolution of MDR/XDR M. tuberculosis in a high prevalence setting of Papua New Guinea for over three decades

description: Beauti raw file anlyzed using BEAST 1.8<br>
DOI: 10.4225/03/5a14df30afcab
title: Textual apparatus for "The Fortunes of Richard Mahony"

description: The Textual Apparatus (TA) is a public record of how the editors established their new text of Richardson's three novels, at the level of individual words and punctuation. It displays to the reader the choices that confronted the editors, and shows the materials on which they based their decisions: it also records Richardson's own first, second, third, and sometimes subsequent thoughts over various states of the typed and printed text, from the earliest surviving typescript (TS), its revision (TSR), to the first London edition (E1) and first American edition (A1).
DOI: 10.6084/m9.figshare.5623705.v1
title: R code and raw data for Clark et al Parasites & Vectors

description: These files provide sample R scripts and raw data necessary to calculate flea functional-phylogenetic host specificity and analyse flea infestation probability in wild mammals using phylogenetic glmms. The pdf files contain the code necessary for completing analyses.
DOI: 10.6084/m9.figshare.5623513
title: #ItsNotInYourHead Campaign Materials - Provoked Vestibulodynia

description: #ItsNotInYourHead is the hashtag associated with a campaign for a condition called Provoked Vestibulodynia (PVD), initiated by Dr. Lori Brotto and the Women's Health Research Institute in Vancouver, British Columbia. PVD is characterized by provoking pain with touch to the vulvar area, and affects up to 10% of women. The campaign aims to raise awareness about this condition and share evidenced-based research of psychological treatments that can help manage female genital pain.<br>These materials are meant to help promote the #ItsNotInYourHead campaign. They can be downloaded from this site - please be sure to use the hashtag and/or tag @NotInYourHead17 in all of your tweets!<br>
DOI: 10.6084/m9.figshare.5623531
title: Multiple Local Solutions and Geomin Rotation

description: In exploratory factor analysis, factor rotation is conducted to improve model interpretability. A promising and increasingly popular factor rotation method is geomin rotation. Geomin rotation, however, frequently encounters multiple local solutions. We report a simulation study that explores the frequency of local solutions in geomin rotation and the implications of such phenomena. The findings include: (1) multiple local solutions exist for geomin rotation in a variety of situations; (2) ϵ = .01 provides satisfactory rotated factor loadings in most situations; (3) 100 random starts appear sufficient to examine the multiple solution phenomenon; and (4) a population global solution may correspond to a sample local solution rather than the sample global solution.
DOI: 10.6084/m9.figshare.5623531.v1
title: Multiple Local Solutions and Geomin Rotation

description: In exploratory factor analysis, factor rotation is conducted to improve model interpretability. A promising and increasingly popular factor rotation method is geomin rotation. Geomin rotation, however, frequently encounters multiple local solutions. We report a simulation study that explores the frequency of local solutions in geomin rotation and the implications of such phenomena. The findings include: (1) multiple local solutions exist for geomin rotation in a variety of situations; (2) ϵ = .01 provides satisfactory rotated factor loadings in most situations; (3) 100 random starts appear sufficient to examine the multiple solution phenomenon; and (4) a population global solution may correspond to a sample local solution rather than the sample global solution.
DOI: 10.6084/m9.figshare.5621494
title: How does technology pathway choice influence economic viability and environmental impacts of lignocellulosic biorefineries?

description: Background: The need for liquid fuels in the transportation sector is increasing, and it is essential to develop industriallysustainable processes that simultaneously address the tri-fold sustainability metrics of technological feasibility, economic viability, and environmental impacts. Biorefineries based on lignocellulosic feedstocks could yield high value products such as ethyl acetate, dodecane, ethylene, and hexane. This work focuses on assessing biochemicaland biomass to electricity platforms for conversion of Banagrass and Energycane into valuable fuels and chemicals using the tri-fold sustainability metrics.<br>Results: The production cost of various products produced from Banagrass was $1.19/kg ethanol, $1.00/kg ethylacetate, $3.01/kg dodecane (jet fuel equivalent), $2.34/kg ethylene and $0.32/kW-h electricity. The production cost ofdifferent products using Energycane as a feedstock was $1.31/kg ethanol, $1.11/kg ethyl acetate, $3.35/kg dodecane, and $2.62/kg ethylene. The sensitivity analysis revealed that the price of the main product, feedstock cost and cost of ethanol affected the profitability the overall process. Banagrass yielded 11% higher ethanol compared to Energycane, which could be attributed to the differences in the composition of these lignocellulosic biomass sources. Acidification potential was highest when ethylene was produced at the rate of 2.56 × 10−2 and 1.71 × 10−2 kg SO2 eq. for Banagrass and Energycane, respectively. Ethanol production from Banagrass and Energycane resulted in a global warming potential of − 12.3 and − 40.0 g CO2 eq./kg ethanol.<br>Conclusions: Utilizing hexoses and pentoses from Banagrass to produce ethyl acetate was the most economical scenario with a payback period of 11.2 years and an ROI of 8.93%, respectively. Electricity production was the most unprofitable scenario with an ROI of − 29.6% using Banagrass/Energycane as a feedstock that could be attributed to high feedstock moisture content. Producing ethylene or dodecane from either of the feedstocks was not economical. The moisture content and composition of biomasses affected overall economics of the various pathways studied. Producing ethanol and ethyl acetate from Energycane had a global warming potential of − 3.01 kg CO2 eq./kg ethyl acetate.
DOI: 10.6084/m9.figshare.5621455
title: Alignments

description: A zip file containing all gene alignments used in MK-style analyses. Each species (e.g. Palmeretal2017Alignments/insects/Apis) has two subdirectories: polymorphism and divergence. Polymorphism includes alignments of ingroup genes and were used to calculate within-species polymorphism, while divergence are alignments between the ingroup consensus sequence and the outgroup outlined in Palmer et al, 2017.<br>
DOI: 10.6084/m9.figshare.5621368
title: data.zip

description: Coding files of virtual experiments, data generated from virtual experiments and analysis files<br>
DOI: 10.6084/m9.figshare.5621455.v1
title: Alignments

description: A zip file containing all gene alignments used in MK-style analyses. Each species (e.g. Palmeretal2017Alignments/insects/Apis) has two subdirectories: polymorphism and divergence. Polymorphism includes alignments of ingroup genes and were used to calculate within-species polymorphism, while divergence are alignments between the ingroup consensus sequence and the outgroup outlined in Palmer et al, 2017.<br>
DOI: 10.6084/m9.figshare.5621371
title: all.data.final.csv

description: pre.cjk { font-family: "Courier New", monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } <pre>Data for paper "Rural Protein Insufficiency <br>in a Wildlife-Depleted West African <br>Farm-Forest Landscape"</pre>
DOI: 10.6084/m9.figshare.5621368.v1
title: data.zip

description: Coding files of virtual experiments, data generated from virtual experiments and analysis files<br>
DOI: 10.6084/m9.figshare.5621371.v1
title: all.data.final.csv

description: pre.cjk { font-family: "Courier New", monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } <pre>Data for paper "Rural Protein Insufficiency <br>in a Wildlife-Depleted West African <br>Farm-Forest Landscape"</pre>