cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19125863
title: Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

description: <strong>These are the supplementary files and scripts used in the the manuscript "Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants"</strong> <br> <strong>Abstract </strong> During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyze more than 1,600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.
DOI: 10.6084/m9.figshare.19125863.v1
title: Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

description: <strong>These are the supplementary files and scripts used in the the manuscript "Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants"</strong> <br> <strong>Abstract </strong> During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyze more than 1,600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.
DOI: 10.5281/zenodo.3834602
title: Perfiles de investigación y su implantación en la Universidad Pública de Navarra en 2018

description: Control de la presencia del personal investigador de la UPNA en las principales plataformas de perfiles de investigación, no solo en las más evidentes como Google Scholar Citation, Researcher ID, Scopus ID y ORCID, y también en otros servicios que, en la práctica, funcionan como perfiles de investigación, como Mendeley, Linkedin, ResearchGate, Academia.edu y Academica-e. Usando como base el censo de personal investigador de la universidad suministrado por el Vicerrectorado de Investigación, se ha comprobado, para cada autor o autora, la existencia o no de un perfil en los diferentes servicios estudiados. Los resultados se han ido tabulando en un fichero Excel para poder analizarlos posteriormente. Los datos han sido tomados en marzo de 2018 para Orcid, ResearcherID, ScopusID, Google Scholar Citations y Mendeley. En Noviembre de 2018 se tomaron los datos de Academica-e, Academia.edu, ResearchGate y Linkedin. Para cada uno de los perfiles, se ha utilizado, cuando era posible, una búsqueda por la adscripción institucional, para disponer de un primer listado de personal investigador de la UPNA con ese perfil. Posteriormente, se realizaba una búsqueda, persona por persona, del resto del personal investigador que no aparecía en ese primer listado. Los datos marcan la existencia o no de un perfil en los diferentes servicos, marcado con un "1" en caso afirmativo, o un "0" en caso negativo.
DOI: 10.5281/zenodo.3834601
title: Perfiles de investigación y su implantación en la Universidad Pública de Navarra en 2018

description: Control de la presencia del personal investigador de la UPNA en las principales plataformas de perfiles de investigación, no solo en las más evidentes como Google Scholar Citation, Researcher ID, Scopus ID y ORCID, y también en otros servicios que, en la práctica, funcionan como perfiles de investigación, como Mendeley, Linkedin, ResearchGate, Academia.edu y Academica-e. Usando como base el censo de personal investigador de la universidad suministrado por el Vicerrectorado de Investigación, se ha comprobado, para cada autor o autora, la existencia o no de un perfil en los diferentes servicios estudiados. Los resultados se han ido tabulando en un fichero Excel para poder analizarlos posteriormente. Los datos han sido tomados en marzo de 2018 para Orcid, ResearcherID, ScopusID, Google Scholar Citations y Mendeley. En Noviembre de 2018 se tomaron los datos de Academica-e, Academia.edu, ResearchGate y Linkedin. Para cada uno de los perfiles, se ha utilizado, cuando era posible, una búsqueda por la adscripción institucional, para disponer de un primer listado de personal investigador de la UPNA con ese perfil. Posteriormente, se realizaba una búsqueda, persona por persona, del resto del personal investigador que no aparecía en ese primer listado. Los datos marcan la existencia o no de un perfil en los diferentes servicos, marcado con un "1" en caso afirmativo, o un "0" en caso negativo.
DOI: 10.6084/m9.figshare.21085150.v2
title: Data from: Nutrient enrichment promotes invasion success of alien plants via increased growth and suppression of chemical defence

description: Data from: Nutrient enrichment promotes invasion success of alien plants via increased growth and suppression of chemical defence
DOI: 10.5281/zenodo.6502723
title: Optimizing parametric factors in CIELAB and CIEDE2000 color-difference formulas for 3D printed spherical objects

description: Forty-five spherical samples were printed using a Stratasys J750 3D color printer, and 82 pairs of 3D samples were produced to investigate the human color perception of the lightness, chroma and hue differences of 3D spherical objects, and to optimize the current CIELAB and CIEDE2000 color-difference formulas. This file contains the CIELAB values of the 45 spherical samples and the calculated colour differences as well as visual colour-difference data of 82 pairs of 3D samples. Optimizations of parametric factors in CIELAB and CIEDE2000 colour-difference formulas were performed based on the colour-difference data provided.
DOI: 10.5281/zenodo.6502724
title: Optimizing parametric factors in CIELAB and CIEDE2000 color-difference formulas for 3D printed spherical objects

description: Forty-five spherical samples were printed using a Stratasys J750 3D color printer, and 82 pairs of 3D samples were produced to investigate the human color perception of the lightness, chroma and hue differences of 3D spherical objects, and to optimize the current CIELAB and CIEDE2000 color-difference formulas. This file contains the CIELAB values of the 45 spherical samples and the calculated colour differences as well as visual colour-difference data of 82 pairs of 3D samples. Optimizations of parametric factors in CIELAB and CIEDE2000 colour-difference formulas were performed based on the colour-difference data provided.
DOI: 10.6084/m9.figshare.20751642
title: A Polish five-year-old with protracted phonological development

description: This case study examines the phonology of a five-year-old Polish-speaking boy with protracted phonological development. A multi-tier analysis of his phonology revealed that word length, stress patterns, vowels and most consonants were largely compatible with the adult target while coronal consonants requiring fine control of tongue shape (fricatives, affricates, liquids) and most consonant clusters posed difficulty for the child in all word positions. Labial and dorsal features were well-established; in fact, [Labial] outcompeted other places of articulation in problematic sequences of both singletons and clusters. The case profile demonstrates asynchronous development of individual phonological elements and tiers. A proposed treatment plan exploits the child’s strengths to address his needs and minimise the discrepancy between the tiers.
DOI: 10.6084/m9.figshare.20751642.v1
title: A Polish five-year-old with protracted phonological development

description: This case study examines the phonology of a five-year-old Polish-speaking boy with protracted phonological development. A multi-tier analysis of his phonology revealed that word length, stress patterns, vowels and most consonants were largely compatible with the adult target while coronal consonants requiring fine control of tongue shape (fricatives, affricates, liquids) and most consonant clusters posed difficulty for the child in all word positions. Labial and dorsal features were well-established; in fact, [Labial] outcompeted other places of articulation in problematic sequences of both singletons and clusters. The case profile demonstrates asynchronous development of individual phonological elements and tiers. A proposed treatment plan exploits the child’s strengths to address his needs and minimise the discrepancy between the tiers.
DOI: 10.6084/m9.figshare.21089568.v1
title: Interdentals to the rescue: a German four-year-old with protracted phonological development

description: This paper examines the phonology of a German four-year-old with asynchronous phonological development: age-level word structure and vowels, but a restricted consonantal inventory. Both expected and unexpected developmental patterns were evident. While the absence of dorsal non-continuants and most coronal and labiodental fricatives and affricates is not unexpected in four-year-olds with PPD, less expected was his mastery of more marked /l/ and /ʁ/ and the pervasive use of ungrooved interdental fricatives (or affricates) as substitutions. Ungrooved interdentals often replace grooved fricatives and affricates, but in his system, they also replaced stops in more marked prosodic positions (unstressed initial syllables and clusters) and labiodental /f/. His case profile demonstrates the autonomy of phonological tiers (levels) but also the restrictive interactions that occur when one tier dominates, in his case, word structure. A proposed treatment plan targets new feature combinations and consonant sequences in order to address the asynchrony.
DOI: 10.6084/m9.figshare.21089568
title: Interdentals to the rescue: a German four-year-old with protracted phonological development

description: This paper examines the phonology of a German four-year-old with asynchronous phonological development: age-level word structure and vowels, but a restricted consonantal inventory. Both expected and unexpected developmental patterns were evident. While the absence of dorsal non-continuants and most coronal and labiodental fricatives and affricates is not unexpected in four-year-olds with PPD, less expected was his mastery of more marked /l/ and /ʁ/ and the pervasive use of ungrooved interdental fricatives (or affricates) as substitutions. Ungrooved interdentals often replace grooved fricatives and affricates, but in his system, they also replaced stops in more marked prosodic positions (unstressed initial syllables and clusters) and labiodental /f/. His case profile demonstrates the autonomy of phonological tiers (levels) but also the restrictive interactions that occur when one tier dominates, in his case, word structure. A proposed treatment plan targets new feature combinations and consonant sequences in order to address the asynchrony.
DOI: 10.6084/m9.figshare.20751645
title: Uncommon timing variation in the speech of an Icelandic-speaking child with protracted phonological development

description: The following paper presents an Icelandic-speaking child with protracted phonological development (PPD) over an intervention period (age 4;10 to 5;3) as a contribution to a special crosslinguistic issue describing individual profiles in PPD. Along with typical mismatch (“error”) patterns, the child showed one pervasive and rare mismatch for Icelandic: compensatory lengthening of vowels when postvocalic consonant sequences reduced. Segment length is phonemic in Icelandic; thus, this pattern decreased her intelligibility considerably. A constraints-based nonlinear phonological framework served as a basis for analysis and intervention planning. Need addressed across the phonological hierarchy were: (1) accurate mapping between the timing tier (word structure level) and consonant and vowel tiers, through a focus on word-medial (WM) pre-aspirated stops; (2) onset complexity (word-initial (WI) /s/-clusters); and (3) a positional target, WI /f/. During intervention (17 sessions), she successfully produced training words for all targets. Monthly probes and a post-test at 5;3 revealed generalization to untrained words for pre-aspirated stops and labiodentals but not for /s/-clusters. Overall, compensatory vowel lengthening reduced substantially. The nonlinear analysis pointed specifically to the nature of the timing mismatches, supporting system-wide change.
DOI: 10.6084/m9.figshare.16832795
title: Consonants lost: a Swedish girl with protracted phonological development

description: This paper addresses the phonology of a Swedish girl, aged 3 years 10 months, with extensive phonological difficulties that include an unusual phonological pattern. She had relatively well-developed phonological building blocks in terms of features, stress pattern and word length (number of syllables), but had extensive difficulties regarding syllable and word shapes, with frequent deletions of both segments and whole syllables. Word-initial position was dominated by non-continuant consonants, both voiced and voiceless, with extensive deletion. Word-medial position was dominated by voiceless obstruents, with extensive use of [j] in place of voiced consonants. Word-final position was similar to word-medial, but with more deletion than [j]. Non-initial stressed syllables resemble word-initial syllables. Consonant clusters mirrored singletons, i.e. with similar substitution patterns or deletions. We present a non-linear analysis of her speech production, and a plan for intervention targeting her special difficulties.
DOI: 10.6084/m9.figshare.20751651.v1
title: When codas trump onsets: an English-speaking child with atypical phonological development before and after intervention

description: This case study presents an English-speaking preschooler with severely protracted phonological development (PPD) before and after two six-week blocks of intervention (36 sessions). Pre-treatment (3;8), he showed very low whole word, singleton consonant, vowel, and word shape matches. He had two major uncommon patterns: (1) higher accuracy for word-final consonants compared with word-initial (WI) and word-medial (WM); and (2) frequent substitution of onset consonants with glottals [h] or [ʔ]. Goals and treatment strategies were selected using a nonlinear phonological approach. Post-treatment, there was a notable decrease in frequency of glottal substitutions and concomitant increase in word shape, consonant, and vowel match. Pre- and post-treatment data are presented and discussed in terms of theoretical and clinical implications.
DOI: 10.6084/m9.figshare.20751651
title: When codas trump onsets: an English-speaking child with atypical phonological development before and after intervention

description: This case study presents an English-speaking preschooler with severely protracted phonological development (PPD) before and after two six-week blocks of intervention (36 sessions). Pre-treatment (3;8), he showed very low whole word, singleton consonant, vowel, and word shape matches. He had two major uncommon patterns: (1) higher accuracy for word-final consonants compared with word-initial (WI) and word-medial (WM); and (2) frequent substitution of onset consonants with glottals [h] or [ʔ]. Goals and treatment strategies were selected using a nonlinear phonological approach. Post-treatment, there was a notable decrease in frequency of glottal substitutions and concomitant increase in word shape, consonant, and vowel match. Pre- and post-treatment data are presented and discussed in terms of theoretical and clinical implications.
DOI: 10.6084/m9.figshare.20751654
title: Complexity resolved: profile of a Slovenian child with protracted phonological development over an intervention period

description: This paper describes the complex phonological patterns of one Slovenian-speaking girl with protracted phonological development who received phonological intervention. At 4;6, the child’s word length, stress and vowels were age-level, but she showed reduced match levels (accuracy) for syllable structure and consonants. Unusual constraints on word position and sequences, particularly concerning fricatives and stops, resulted in many assimilations, reduplications and metatheses. Addressing these constraints in the first intervention period (to 4;9) led to higher overall accuracy and a transition from less typical to more typical mismatches (“errors”), e.g., sibilant grooving (stridency) and rhotic production as singletons and in clusters. The profile focuses on that initial pre- and post-treatment period, giving a brief overview of the follow-up intervention and outcomes and reflecting on implications for future research and clinical practice.<sup>1</sup><sup>1</sup>The abstract is available in Slovenian language (see Supplementary material). The abstract is available in Slovenian language (see Supplementary material).
DOI: 10.6084/m9.figshare.20751654.v1
title: Complexity resolved: profile of a Slovenian child with protracted phonological development over an intervention period

description: This paper describes the complex phonological patterns of one Slovenian-speaking girl with protracted phonological development who received phonological intervention. At 4;6, the child’s word length, stress and vowels were age-level, but she showed reduced match levels (accuracy) for syllable structure and consonants. Unusual constraints on word position and sequences, particularly concerning fricatives and stops, resulted in many assimilations, reduplications and metatheses. Addressing these constraints in the first intervention period (to 4;9) led to higher overall accuracy and a transition from less typical to more typical mismatches (“errors”), e.g., sibilant grooving (stridency) and rhotic production as singletons and in clusters. The profile focuses on that initial pre- and post-treatment period, giving a brief overview of the follow-up intervention and outcomes and reflecting on implications for future research and clinical practice.<sup>1</sup><sup>1</sup>The abstract is available in Slovenian language (see Supplementary material). The abstract is available in Slovenian language (see Supplementary material).
DOI: 10.6084/m9.figshare.16832795.v2
title: Consonants lost: a Swedish girl with protracted phonological development

description: This paper addresses the phonology of a Swedish girl, aged 3 years 10 months, with extensive phonological difficulties that include an unusual phonological pattern. She had relatively well-developed phonological building blocks in terms of features, stress pattern and word length (number of syllables), but had extensive difficulties regarding syllable and word shapes, with frequent deletions of both segments and whole syllables. Word-initial position was dominated by non-continuant consonants, both voiced and voiceless, with extensive deletion. Word-medial position was dominated by voiceless obstruents, with extensive use of [j] in place of voiced consonants. Word-final position was similar to word-medial, but with more deletion than [j]. Non-initial stressed syllables resemble word-initial syllables. Consonant clusters mirrored singletons, i.e. with similar substitution patterns or deletions. We present a non-linear analysis of her speech production, and a plan for intervention targeting her special difficulties.
DOI: 10.6084/m9.figshare.20751645.v2
title: Uncommon timing variation in the speech of an Icelandic-speaking child with protracted phonological development

description: The following paper presents an Icelandic-speaking child with protracted phonological development (PPD) over an intervention period (age 4;10 to 5;3) as a contribution to a special crosslinguistic issue describing individual profiles in PPD. Along with typical mismatch (“error”) patterns, the child showed one pervasive and rare mismatch for Icelandic: compensatory lengthening of vowels when postvocalic consonant sequences reduced. Segment length is phonemic in Icelandic; thus, this pattern decreased her intelligibility considerably. A constraints-based nonlinear phonological framework served as a basis for analysis and intervention planning. Need addressed across the phonological hierarchy were: (1) accurate mapping between the timing tier (word structure level) and consonant and vowel tiers, through a focus on word-medial (WM) pre-aspirated stops; (2) onset complexity (word-initial (WI) /s/-clusters); and (3) a positional target, WI /f/. During intervention (17 sessions), she successfully produced training words for all targets. Monthly probes and a post-test at 5;3 revealed generalization to untrained words for pre-aspirated stops and labiodentals but not for /s/-clusters. Overall, compensatory vowel lengthening reduced substantially. The nonlinear analysis pointed specifically to the nature of the timing mismatches, supporting system-wide change.
DOI: 10.6084/m9.figshare.20751645.v1
title: Uncommon timing variation in the speech of an Icelandic-speaking child with protracted phonological development

description: The following paper presents an Icelandic-speaking child with protracted phonological development (PPD) over an intervention period (age 4;10 to 5;3) as a contribution to a special crosslinguistic issue describing individual profiles in PPD. Along with typical mismatch (“error”) patterns, the child showed one pervasive and rare mismatch for Icelandic: compensatory lengthening of vowels when postvocalic consonant sequences reduced. Segment length is phonemic in Icelandic; thus, this pattern decreased her intelligibility considerably. A constraints-based nonlinear phonological framework served as a basis for analysis and intervention planning. Need addressed across the phonological hierarchy were: (1) accurate mapping between the timing tier (word structure level) and consonant and vowel tiers, through a focus on word-medial (WM) pre-aspirated stops; (2) onset complexity (word-initial (WI) /s/-clusters); and (3) a positional target, WI /f/. During intervention (17 sessions), she successfully produced training words for all targets. Monthly probes and a post-test at 5;3 revealed generalization to untrained words for pre-aspirated stops and labiodentals but not for /s/-clusters. Overall, compensatory vowel lengthening reduced substantially. The nonlinear analysis pointed specifically to the nature of the timing mismatches, supporting system-wide change.