cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3153505
title: Bronchodilator responsiveness in wheezy infants predicts continued early childhood respiratory morbidity

description: <i>Objective</i>: Spirometry including bronchodilator responsiveness is considered routine in the workup of asthma in older children. However, in wheezy infants the existence of bronchodilator responsiveness and its prognostic significance remain unclear. <i>Methods</i>: Infants (&lt; 2 years) with chronic or recurrent wheezing or coughing were evaluated by infant pulmonary function testing (PFT). Maximal expiratory flow at the point of functional residual capacity (V̇<sub>max</sub>FRC) was measured before and 20 minutes after salbutamol administration. Only infants with an obstructive profile (V̇<sub>max</sub>FRC &lt; 80% predicted) were included. The infants were divided into two groups with regard to whether or not a response to salbutamol was observed on PFT. A response was defined as a mean V̇maxFRC after salbutamol administration exceeding the upper confidence interval limit of individual pre-bronchodilator V̇<sub>max</sub>FRC measurements. Follow-up data was gathered after a mean of 2 years. <i>Measurements and Main Results</i>: Sixty infants were included in the study of which 32 (53%) demonstrated responsiveness to bronchodilators. The infants in the responsive group had a significantly higher frequency of physician visits for wheezing than the non-responders (3.0 mean visits/yr vs. 1.5 respectively, <i>P</i> = 0.03), and had a higher likelihood of having received asthma medication in the last year of the follow-up period (84% vs. 50% respectively, RR: 1.68[1.10–2.56]). At the end of the follow-up period, more parents in the responsive group reported continued respiratory disease (71% vs. 22%, RR:3.21[1.30–7.95]). <i>Conclusions</i>: Bronchodilator responsiveness can be demonstrated by infant PFT in infants with recurrent wheezing and can predict increased respiratory morbidity until 3 years of age.
DOI: 10.6084/m9.figshare.3153493
title: Functional Alterations in Order Short-Term Memory Networks in Adults With Dyslexia

description: Dyslexia is characterized not only by reading impairment but also by short-term memory (STM) deficits, and this particularly for the retention of serial order information. Here, we explored the functional neural correlates associated with serial order STM performance of adults with dyslexia for verbal and visual STM tasks. Relative to a group of age-matched controls, the dyslexic group showed abnormal activation in a network associated with order STM encompassing the right intraparietal and superior frontal sulcus, and this for both verbal and visual order STM conditions. This study highlights long-lasting alterations in non-language neural substrates and processes in dyslexia.
DOI: 10.6084/m9.figshare.3153505.v1
title: Bronchodilator responsiveness in wheezy infants predicts continued early childhood respiratory morbidity

description: <i>Objective</i>: Spirometry including bronchodilator responsiveness is considered routine in the workup of asthma in older children. However, in wheezy infants the existence of bronchodilator responsiveness and its prognostic significance remain unclear. <i>Methods</i>: Infants (&lt; 2 years) with chronic or recurrent wheezing or coughing were evaluated by infant pulmonary function testing (PFT). Maximal expiratory flow at the point of functional residual capacity (V̇<sub>max</sub>FRC) was measured before and 20 minutes after salbutamol administration. Only infants with an obstructive profile (V̇<sub>max</sub>FRC &lt; 80% predicted) were included. The infants were divided into two groups with regard to whether or not a response to salbutamol was observed on PFT. A response was defined as a mean V̇maxFRC after salbutamol administration exceeding the upper confidence interval limit of individual pre-bronchodilator V̇<sub>max</sub>FRC measurements. Follow-up data was gathered after a mean of 2 years. <i>Measurements and Main Results</i>: Sixty infants were included in the study of which 32 (53%) demonstrated responsiveness to bronchodilators. The infants in the responsive group had a significantly higher frequency of physician visits for wheezing than the non-responders (3.0 mean visits/yr vs. 1.5 respectively, <i>P</i> = 0.03), and had a higher likelihood of having received asthma medication in the last year of the follow-up period (84% vs. 50% respectively, RR: 1.68[1.10–2.56]). At the end of the follow-up period, more parents in the responsive group reported continued respiratory disease (71% vs. 22%, RR:3.21[1.30–7.95]). <i>Conclusions</i>: Bronchodilator responsiveness can be demonstrated by infant PFT in infants with recurrent wheezing and can predict increased respiratory morbidity until 3 years of age.
DOI: 10.6084/m9.figshare.3153619.v1
title: Statistical Analysis of Bodytmronic measurements

description: Data set used for statistical analysis of reliability of bodytronic measurement for circumference and volume of the lower extremity.
DOI: 10.6084/m9.figshare.3153619.v3
title: Statistical analysis of bodytronic measurements of circumference and volume of the lower extremity

description: Data set used for statistical analysis of reliability of Bodytronic measurement for circumference and volume of the lower extremity.
DOI: 10.6084/m9.figshare.3153493.v1
title: Functional Alterations in Order Short-Term Memory Networks in Adults With Dyslexia

description: Dyslexia is characterized not only by reading impairment but also by short-term memory (STM) deficits, and this particularly for the retention of serial order information. Here, we explored the functional neural correlates associated with serial order STM performance of adults with dyslexia for verbal and visual STM tasks. Relative to a group of age-matched controls, the dyslexic group showed abnormal activation in a network associated with order STM encompassing the right intraparietal and superior frontal sulcus, and this for both verbal and visual order STM conditions. This study highlights long-lasting alterations in non-language neural substrates and processes in dyslexia.
DOI: 10.6084/m9.figshare.3153619.v2
title: Statistical analysis of bodytronic measurements of circumference and Volume of the lower extremity

description: Data set used for statistical analysis of reliability of Bodytronic measurement for circumference and volume of the lower extremity.
DOI: 10.6084/m9.figshare.3153454
title: Integrative taxonomy of <i>Peniculus</i>, <i>Metapeniculus</i>, and <i>Trifur</i> (Siphonostomatoida: Pennellidae), copepod parasites of marine fishes from Chile: species delimitation analyses using DNA barcoding and morphological evidence

description: Pennellidae is a family of copepod parasites of widely distributed marine fishes. The pennellid species are usually morphologically differentiated by cephalothorax, neck, trunk, and abdomen shape. These characters, however, show high polymorphism and therefore using only this type of data, delimitation at species level of this genus is difficult. In this study, we explored the genetic distances calculated from sequences of a DNA barcoding marker (COI mt) (678 base pairs). We also explored the genetic distances of 25 <i>Peniculus</i> specimens associated within nine marine fish species, four <i>Metapeniculus</i> specimens associated within one marine fish species, and four <i>Trifur</i> specimens associated within one marine fish species. All specimens were collected in Antofagasta Bay, Chile and were calculated from sequences of a DNA barcoding marker (COI mt) (678 base pairs). The genetic distance among the <i>Peniculus</i> specimens was 0.95% from the different host species, the <i>Metapeniculus</i> specimens distance was 0.44% and the <i>Trifur</i> specimens was 2.25%. Genetic difference between <i>Peniculus</i> and <i>Metapeniculus</i> was 17.86% and <i>Peniculus</i> differ from <i>T</i>. <i>tortuosus</i> by 18.16%. We analysed the barcoding gene fragment using Bayesian Inference (BI) for phylogenetic reconstruction using three outgroups. Based on the phylogenetic analysis an ultrametric tree was built and a general mixed Yule-coalescent (bGMYC) model was conducted for species delimitation. Morphometrics analyses were made with Bayesian statistics. Mean and credibility limit (95%) for each parameter was calculated. Results show that based on morphology the individuals collected can be assigned to <i>P.</i> cf. <i>fistula</i> von Nordmann, 1832, <i>Metapeniculus antofagastensis</i> Castro-Romero & Baeza-Kuroki, 1985, and <i>Trifur</i> cf. <i>tortuosus</i> Wilson, 1917. High morphological polymorphism was observed for the lineage of <i>Peniculus</i> associated to several host species of marine fishes. Similar results were obtained for <i>Trifur</i> cf. <i>tortuosus</i> parasites on Chilean marine fishes.
DOI: 10.15131/shef.data.3153442
title: ICASSP 2016 - Experiment results for the paper "Groupwise learning for ASR k-best list reranking in spoken language translation"

description: The compressed folder contains the experiment output described in Table 1 and Table 2 in the paper "Groupwise learning for ASR k-best list reranking in spoken language translation" DOI: 10.1109/ICASSP.2016.7472853.<br><br>In the top level there are two files,<br>"E12.filelist" contains the 1124 segments used in the experiments. Each segment is named after the convention (TALK)_(SPEAKER)_(STARTTIME in 10ms)_(ENDTIME in 10ms). The segments are identical to those from the IWSLT 2012 evaluation (http://hltshare.fbk.eu/IWSLT2012/IWSLT12.TED.SLT.testsets.tgz) <br>"E12.tc.fr.reference" contains the reference French translation of these 1124 sentences.<br><br>Experiments results were organised into subfolders. <br>Results from which TABLE 1 was generated could be found in the folder TABLE_1/Setting_[A or B or C] accordingly. For each Setting, 8 regression experiments (predicsvcpermute*) and 14 classification experiments (predicsvrpermute*) were conducted. The translation outputs are recorded in the files prefixed "rerank.merged.*" and the translation scores are recorded in the files prefixed "best-results.fullset.*"<br><br>The folders TABLE_2/Groupwise+LDA/Setting_[A or B or C] contain the translation outputs "rerank.merged.*" and translation scores "best-results.fullset.*" for the Groupwise+LDA results described in Table 2 in the paper. For Setting A, B and C, the corresponding optimal LDA dimensions are 3, 5 and 4 respectively. These are also reflected in the filename in the uploaded data. <br><br><br><br><br>
DOI: 10.15131/shef.data.3153442.v1
title: ICASSP 2016 - Experiment results for the paper "Groupwise learning for ASR k-best list reranking in spoken language translation"

description: The compressed folder contains the experiment output described in Table 1 and Table 2 in the paper "Groupwise learning for ASR k-best list reranking in spoken language translation" DOI: 10.1109/ICASSP.2016.7472853.<br><br>In the top level there are two files,<br>"E12.filelist" contains the 1124 segments used in the experiments. Each segment is named after the convention (TALK)_(SPEAKER)_(STARTTIME in 10ms)_(ENDTIME in 10ms). The segments are identical to those from the IWSLT 2012 evaluation (http://hltshare.fbk.eu/IWSLT2012/IWSLT12.TED.SLT.testsets.tgz) <br>"E12.tc.fr.reference" contains the reference French translation of these 1124 sentences.<br><br>Experiments results were organised into subfolders. <br>Results from which TABLE 1 was generated could be found in the folder TABLE_1/Setting_[A or B or C] accordingly. For each Setting, 8 regression experiments (predicsvcpermute*) and 14 classification experiments (predicsvrpermute*) were conducted. The translation outputs are recorded in the files prefixed "rerank.merged.*" and the translation scores are recorded in the files prefixed "best-results.fullset.*"<br><br>The folders TABLE_2/Groupwise+LDA/Setting_[A or B or C] contain the translation outputs "rerank.merged.*" and translation scores "best-results.fullset.*" for the Groupwise+LDA results described in Table 2 in the paper. For Setting A, B and C, the corresponding optimal LDA dimensions are 3, 5 and 4 respectively. These are also reflected in the filename in the uploaded data. <br><br><br><br><br>
DOI: 10.6084/m9.figshare.3153406
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: CRMs]

description: This repository contains the positive and negative training sets generated from the ChIP-seq transcription factor and histone post-translational modification data. Such sets of data were run as input to the RFECS software. RFECS is a tailor-made random forest model for making cis-regulatory module (CRM) predictions. The random forest model used for making the predictions is also available in this repository as a binary MATLAB file.<br>The references below explain specifically how to (1) access a MATLAB file and (2), how to use the current model file to predict the CRMs. For more details about the RFECS algorithm itself, take a look at reference (3).<br>
DOI: 10.6084/m9.figshare.3153427
title: Molecular and Structural Considerations of TF-DNA Binding for the Generation of Biologically Meaningful and Accurate Phylogenetic Footprinting Analysis: the LysR-Type Transcriptional Regulator Family as a Study Model

description: 5' upstream region of orthologous genes from the LysR-type transcription factor family.<br>
DOI: 10.6084/m9.figshare.3153454.v1
title: Integrative taxonomy of <i>Peniculus</i>, <i>Metapeniculus</i>, and <i>Trifur</i> (Siphonostomatoida: Pennellidae), copepod parasites of marine fishes from Chile: species delimitation analyses using DNA barcoding and morphological evidence

description: Pennellidae is a family of copepod parasites of widely distributed marine fishes. The pennellid species are usually morphologically differentiated by cephalothorax, neck, trunk, and abdomen shape. These characters, however, show high polymorphism and therefore using only this type of data, delimitation at species level of this genus is difficult. In this study, we explored the genetic distances calculated from sequences of a DNA barcoding marker (COI mt) (678 base pairs). We also explored the genetic distances of 25 <i>Peniculus</i> specimens associated within nine marine fish species, four <i>Metapeniculus</i> specimens associated within one marine fish species, and four <i>Trifur</i> specimens associated within one marine fish species. All specimens were collected in Antofagasta Bay, Chile and were calculated from sequences of a DNA barcoding marker (COI mt) (678 base pairs). The genetic distance among the <i>Peniculus</i> specimens was 0.95% from the different host species, the <i>Metapeniculus</i> specimens distance was 0.44% and the <i>Trifur</i> specimens was 2.25%. Genetic difference between <i>Peniculus</i> and <i>Metapeniculus</i> was 17.86% and <i>Peniculus</i> differ from <i>T</i>. <i>tortuosus</i> by 18.16%. We analysed the barcoding gene fragment using Bayesian Inference (BI) for phylogenetic reconstruction using three outgroups. Based on the phylogenetic analysis an ultrametric tree was built and a general mixed Yule-coalescent (bGMYC) model was conducted for species delimitation. Morphometrics analyses were made with Bayesian statistics. Mean and credibility limit (95%) for each parameter was calculated. Results show that based on morphology the individuals collected can be assigned to <i>P.</i> cf. <i>fistula</i> von Nordmann, 1832, <i>Metapeniculus antofagastensis</i> Castro-Romero & Baeza-Kuroki, 1985, and <i>Trifur</i> cf. <i>tortuosus</i> Wilson, 1917. High morphological polymorphism was observed for the lineage of <i>Peniculus</i> associated to several host species of marine fishes. Similar results were obtained for <i>Trifur</i> cf. <i>tortuosus</i> parasites on Chilean marine fishes.
DOI: 10.6084/m9.figshare.3153427.v1
title: Molecular and Structural Considerations of TF-DNA Binding for the Generation of Biologically Meaningful and Accurate Phylogenetic Footprinting Analysis: the LysR-Type Transcriptional Regulator Family as a Study Model

description: 5' upstream region of orthologous genes from the LysR-type transcription factor family.<br>
DOI: 10.6084/m9.figshare.3153400
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: DHPTMs]

description: This repository contains the various scripts and files used to identify differential histone post-translational modifications (DHPTMs).<br>The complete details about the various scripts and files in this repository, as well as the set of commands used to run the analysis, are included in the file README.txt<br>
DOI: 10.6084/m9.figshare.3153364
title: A higher aspect ratio enhanced bioaccumulation and altered immune responses due to intravenously-injected aluminum oxide nanoparticles

description: Aluminum oxide nanoparticles (AlO NP) have been widely utilized in a variety of areas, including in the optical, biomedical and electronic fields and in the overall development of nanotechnologies. However, their toxicological profiles are still not fully developed. This study compared the distribution and immunotoxicity of two rod-types of AlO NP. As reported previously, the two types of AlO NP had different aspect ratios (long-type: 6.2 ± 0.6, short-type: 2.1 ± 0.4), but the size and surface charge were very similar. On Day 14 after a single intravenous (IV) injection (1.25 or 5 mg/kg), both AlO NP accumulated primarily in the liver and spleen and altered the levels of redox response-related elements. The accumulated level was higher in mice exposed to the long-type AlO NP compared to the short-type. Additionally, it was noted that the levels of IL-1<i>β</i>, IL-8 and MCP-1 were enhanced in the blood of mice exposed to both types of AlO NP and the percentages of neutrophils and monocytes among all white blood cells were increased only in mice injected with the long-type AlO NP (5 mg/kg). In addition, as compared to the control, co-expression of CD80 and CD86 (necessary for antigen presentation) on splenocytes together with a decreased expression of chemotaxis-related marker (CD195) was attenuated by exposure to the AlO NP, especially the long-type. Taken together, the data suggest that accumulation following a single IV injection with rod-types of AlO NP is strengthened by a high aspect ratio and, subsequently, this accumulation has the potential to influence immune functions in an exposed host.
DOI: 10.6084/m9.figshare.3153364.v1
title: A higher aspect ratio enhanced bioaccumulation and altered immune responses due to intravenously-injected aluminum oxide nanoparticles

description: Aluminum oxide nanoparticles (AlO NP) have been widely utilized in a variety of areas, including in the optical, biomedical and electronic fields and in the overall development of nanotechnologies. However, their toxicological profiles are still not fully developed. This study compared the distribution and immunotoxicity of two rod-types of AlO NP. As reported previously, the two types of AlO NP had different aspect ratios (long-type: 6.2 ± 0.6, short-type: 2.1 ± 0.4), but the size and surface charge were very similar. On Day 14 after a single intravenous (IV) injection (1.25 or 5 mg/kg), both AlO NP accumulated primarily in the liver and spleen and altered the levels of redox response-related elements. The accumulated level was higher in mice exposed to the long-type AlO NP compared to the short-type. Additionally, it was noted that the levels of IL-1<i>β</i>, IL-8 and MCP-1 were enhanced in the blood of mice exposed to both types of AlO NP and the percentages of neutrophils and monocytes among all white blood cells were increased only in mice injected with the long-type AlO NP (5 mg/kg). In addition, as compared to the control, co-expression of CD80 and CD86 (necessary for antigen presentation) on splenocytes together with a decreased expression of chemotaxis-related marker (CD195) was attenuated by exposure to the AlO NP, especially the long-type. Taken together, the data suggest that accumulation following a single IV injection with rod-types of AlO NP is strengthened by a high aspect ratio and, subsequently, this accumulation has the potential to influence immune functions in an exposed host.
DOI: 10.6084/m9.figshare.3153280
title: Declaring a tuberculosis outbreak over with genomic epidemiology

description: Text file commands used in reference alignment and variant calling and fasta file of the final dataset of variants as published in<i> Microbial Genomics </i>in the following article: 'Declaring a tuberculosis outbreak over with genomic epidemiology'
DOI: 10.6084/m9.figshare.3153217
title: Need for Speed RSOS

description: Steering bias of human travelling down a virtual road with biased optic flow. Optic flow speed was altered, as was optic flow asymmetry.<br>Results and analysis published in:Kountouriotis, Mole, Merat & Wilkie (2016) The need for speed: global optic flow speed influences steering. Royal Society Open Science
DOI: 10.6084/m9.figshare.3153181
title: Using Google Earth to improve management of threatened limestone karst ecosystems in Peninsular Malaysia

description: Biodiversity conservation is now about prioritisation, especially in a world with limited resources and so many habitats and species in need of protection. However, we cannot prioritise effectively if historical and current information on a particular habitat or species remains scattered. Several good platforms have been created to help users to find, use and create biodiversity information. However, good platforms for sharing habitat information for threatened ecosystems are still lacking. Limestone hills are an example of threatened ecosystems that harbour unique biodiversity, but are facing intensifying anthropogenic disturbances. As limestone is a vital resource for the construction industry, it is not possible to completely halt forest degradation and quarrying in developing countries such as Malaysia, where 445 limestone hills have been recorded in the peninsula to date. As such, there is an urgent need to identify which hills must be prioritised for conservation. To make decisions based on sound science, collating spatial and biological information on limestone hills into a publicly accessible database is critical. Here, we compile Malaysia’s first limestone hill GIS map for 445 limestone hills in the peninsula based on information from geological reports and scientific literature. To assist in conservation prioritisation efforts, we quantify characteristics of limestone hills in terms of size, degree of isolation, and spatial distribution patterns and also assessed the degree of habitat disturbance of each limestone hill in terms of buffer area forest degradation and quarrying activity. All this information is stored in a KMZ file and can be accessed through the Google Earth interface. This product should not be viewed as a final output containing basic limestone hill information. Rather, this database is a foundational platform for users to collect, store, update and manipulate spatial and biological data from limestone hills to better inform decisions regarding their management.
DOI: 10.6084/m9.figshare.3153406.v2
title: CODE: CRMs

description: This repository contains binary *mat file that contains the trained RFECS forest used to make CRM predictions.<br>Please consult the README.txt file for instructions on how to use this file.
DOI: 10.6084/m9.figshare.3153193
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: Pre-processing]

description: This repository contains the scripts and files used to generate the alignment files used for downstream analyses, the bigWig files used to visualise the data and various Quality Control (QC) results used to address the quality of the various samples.<br><br>The complete details about the various scripts and files in this repository, as well as the set of commands used to run the analysis, are included in the file README.txt