cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3188497.v1
title: Variations in HDL-carried miR-223 and miR-135a concentrations after consumption of dietary trans fat are associated with changes in blood lipid and inflammatory markers in healthy men - an exploratory study

description: A high consumption of trans fatty acids (TFAs) is associated with an increased risk of cardiovascular diseases (CVDs). High-density lipoproteins (HDLs) have many cardioprotective properties and transport functional microRNAs (miRNAs) to recipient cells. We hypothesized that dietary TFAs modify the HDL-carried miRNA profile, therefore modulating its cardioprotective properties. We assessed whether consumption of dietary TFAs modifies HDL-carried miR-223-3p and miR-135a-3p concentration and the inter-relationship between diet-induced changes in HDL-carried miRNA concentration and CVD risk markers. In a double blind, randomized, crossover, controlled study, 9 men were fed each of 3 experimental isoenergetic diets: 1) High in industrial TFA (iTFA; 3.7% energy); 2) High in TFA from ruminants (rTFA; 3.7% energy); 3) Low in TFA (control; 0.8% energy) for 4 weeks each. HDLs were isolated by ultracentrifugation and miRNAs were quantified by RT-qPCR. Variations in HDL-miR-223-3p concentration were negatively correlated with variations in HDL-cholesterol after the iTFA diet (r<sub>s</sub>=0.82; <i>P=</i>0.007), and positively correlated with variations in Creactive protein concentration after the rTFA diet (r<sub>s</sub>=0.75; <i>P</i>=0.020). Variations in HDL-miR-135a-3p concentration were positively correlated with variations in total triglyceride (TG) concentration following the iTFA diet (r<sub>s</sub>=0.82; <i>P</i>=0.007), and with variations in low-density lipoprotein (LDL)-TG concentration following the rTFA diet (r<sub>s</sub>=0.83; <i>P</i>=0.005), compared to the control diet. However, the consumption of dietary TFAs has no significant unidirectional impact on HDL-carried miR-223-3p and miR-135a-3p concentrations. Our results suggest that the variability in the HDL-carried miRNAs response to TFA intake, by being associated with variations in CVD risk factors, might reflect physiological changes in HDL functions.
DOI: 10.6084/m9.figshare.3188497.v3
title: Variations in HDL-carried miR-223 and miR-135a concentrations after consumption of dietary trans fat are associated with changes in blood lipid and inflammatory markers in healthy men - an exploratory study

description: A high consumption of trans fatty acids (TFAs) is associated with an increased risk of cardiovascular diseases (CVDs). High-density lipoproteins (HDLs) have many cardioprotective properties and transport functional microRNAs (miRNAs) to recipient cells. We hypothesized that dietary TFAs modify the HDL-carried miRNA profile, therefore modulating its cardioprotective properties. We assessed whether consumption of dietary TFAs modifies HDL-carried miR-223-3p and miR-135a-3p concentration and the inter-relationship between diet-induced changes in HDL-carried miRNA concentration and CVD risk markers. In a double blind, randomized, crossover, controlled study, 9 men were fed each of 3 experimental isoenergetic diets: 1) High in industrial TFA (iTFA; 3.7% energy); 2) High in TFA from ruminants (rTFA; 3.7% energy); 3) Low in TFA (control; 0.8% energy) for 4 weeks each. HDLs were isolated by ultracentrifugation and miRNAs were quantified by RT-qPCR. Variations in HDL-miR-223-3p concentration were negatively correlated with variations in HDL-cholesterol after the iTFA diet (r<sub>s </sub>= 0.82; <i>P = </i>0.007), and positively correlated with variations in C-reactive protein concentration after the rTFA diet (r<sub>s</sub> = 0.75; <i>P</i> = 0.020). Variations in HDL-miR-135a-3p concentration were positively correlated with variations in total triglyceride (TG) concentration following the iTFA diet (r<sub>s</sub> = −0.82; <i>P</i> = 0.007), and with variations in low-density lipoprotein (LDL)-TG concentration following the rTFA diet (r<sub>s</sub> = 0.83; <i>P</i> = 0.005), compared to the control diet. However, the consumption of dietary TFAs has no significant unidirectional impact on HDL-carried miR-223-3p and miR-135a-3p concentrations. Our results suggest that the variability in the HDL-carried miRNAs response to TFA intake, by being associated with variations in CVD risk factors, might reflect physiological changes in HDL functions.
DOI: 10.6084/m9.figshare.3188326.v1
title: 2015 Organic Letters SI.pdf

description: Microwave synthesis of NIR squaraine photosensitizers<br>
DOI: 10.6084/m9.figshare.3188497.v2
title: Variations in HDL-carried miR-223 and miR-135a concentrations after consumption of dietary trans fat are associated with changes in blood lipid and inflammatory markers in healthy men - an exploratory study

description: A high consumption of trans fatty acids (TFAs) is associated with an increased risk of cardiovascular diseases (CVDs). High-density lipoproteins (HDLs) have many cardioprotective properties and transport functional microRNAs (miRNAs) to recipient cells. We hypothesized that dietary TFAs modify the HDL-carried miRNA profile, therefore modulating its cardioprotective properties. We assessed whether consumption of dietary TFAs modifies HDL-carried miR-223-3p and miR-135a-3p concentration and the inter-relationship between diet-induced changes in HDL-carried miRNA concentration and CVD risk markers. In a double blind, randomized, crossover, controlled study, 9 men were fed each of 3 experimental isoenergetic diets: 1) High in industrial TFA (iTFA; 3.7% energy); 2) High in TFA from ruminants (rTFA; 3.7% energy); 3) Low in TFA (control; 0.8% energy) for 4 weeks each. HDLs were isolated by ultracentrifugation and miRNAs were quantified by RT-qPCR. Variations in HDL-miR-223-3p concentration were negatively correlated with variations in HDL-cholesterol after the iTFA diet (r<sub>s </sub>= 0.82; <i>P = </i>0.007), and positively correlated with variations in C-reactive protein concentration after the rTFA diet (r<sub>s</sub> = 0.75; <i>P</i> = 0.020). Variations in HDL-miR-135a-3p concentration were positively correlated with variations in total triglyceride (TG) concentration following the iTFA diet (r<sub>s</sub> = −0.82; <i>P</i> = 0.007), and with variations in low-density lipoprotein (LDL)-TG concentration following the rTFA diet (r<sub>s</sub> = 0.83; <i>P</i> = 0.005), compared to the control diet. However, the consumption of dietary TFAs has no significant unidirectional impact on HDL-carried miR-223-3p and miR-135a-3p concentrations. Our results suggest that the variability in the HDL-carried miRNAs response to TFA intake, by being associated with variations in CVD risk factors, might reflect physiological changes in HDL functions.
DOI: 10.6084/m9.figshare.3188242
title: [OLD] Psychosocial predictors of painful HIV-associated sensory neuropathy and quality of life

description: This repository has been superceded by: http://dx.doi.org/10.6084/m9.figshare.4555474. The new repository is linked directly to the originating GitHub repo for the data.
DOI: 10.6084/m9.figshare.3188107
title: Intranasal dexmedetomidine as a sedative premedication for patients undergoing suspension laryngoscopy: A randomized double-blind study

description: <b>The date includes many items. </b> <b>Including:</b> 1、Baseline Characteristic Data(Age Weight Height Sex ASA status ) 2、Duration time Duration from intranasal drug administration to arrival at operating room Duration from intranasal drug administration to anesthesia intubation Duration of anesthesia Duration of surgery 3、Modified OAA S scores（Before intranasal drugs At Pre-induction After extubation） Anxiety scores (Before intranasal drugs At Pre-induction) Satisfaction scores 4、Bradycardiac episode Tachycardiac episode Hypotensive episode Hypertensive episode 5、Predicted Effect-site Concentrations of Propofol Predicted Effect-site Concentrations of Remifentanil 6、Anesthesia recovery time 7、HR （Before Intranasal Drugs At Pre-induction） 8、Number of Participants With Anxiety Score &gt;2 Number of participants with VAS &gt;50 Number of participants with postoperative nausea Number of participants with Postoperative Vomiting Number of participants with Postoperative Shivering Number of participants with Intra-operative Awareness 9、 Visual Analogue Scale (VAS)
DOI: 10.6084/m9.figshare.3188155
title: Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing

description: Excavation of resistance genes is one of the most effective and environment-friendly measures to control the devastating rice disease caused by <i>Magnaporthe oryzae</i>. Many resistance genes have been mapped and characterized in the last century. Nevertheless, only a few of the total resistance genes could be really applied in the rice breeding program. Huazhan (HZ) is a new native rice restorer line developed in China and widely used in hybrid rice in recent years. HZ and its crossed combinations usually show a broad spectrum of resistance against rice blast in different rice ecosystems in China. Dissection of the genetic background of HZ is very useful for its further application. In this study, a combined method based on bulked segregation analysis (BSA) and specific length amplified fragment sequencing (SLAF-seq) was used to identify blast resistance gene(s) in HZ. A total of 56,187 SLAFs labels were captured and 9051 polymorphic SLAFs markers were analysed and procured in this study. One trait associated with candidate resistance genes region on chromosome 12 overlapping 10.2–17.6 Mb has been identified, in which 10 NBS-LRR (nucleotide-binding site-leucine-rich repeat) coding genes were used as resistance gene candidates. Our result indicated that SLAF-seq with BSA is a rapid and effective method for initial identification of blast resistance genes. The identification of resistance gene in HZ will improve its molecular breeding and resistance variety application.
DOI: 10.6084/m9.figshare.3188155.v1
title: Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing

description: Excavation of resistance genes is one of the most effective and environment-friendly measures to control the devastating rice disease caused by <i>Magnaporthe oryzae</i>. Many resistance genes have been mapped and characterized in the last century. Nevertheless, only a few of the total resistance genes could be really applied in the rice breeding program. Huazhan (HZ) is a new native rice restorer line developed in China and widely used in hybrid rice in recent years. HZ and its crossed combinations usually show a broad spectrum of resistance against rice blast in different rice ecosystems in China. Dissection of the genetic background of HZ is very useful for its further application. In this study, a combined method based on bulked segregation analysis (BSA) and specific length amplified fragment sequencing (SLAF-seq) was used to identify blast resistance gene(s) in HZ. A total of 56,187 SLAFs labels were captured and 9051 polymorphic SLAFs markers were analysed and procured in this study. One trait associated with candidate resistance genes region on chromosome 12 overlapping 10.2–17.6 Mb has been identified, in which 10 NBS-LRR (nucleotide-binding site-leucine-rich repeat) coding genes were used as resistance gene candidates. Our result indicated that SLAF-seq with BSA is a rapid and effective method for initial identification of blast resistance genes. The identification of resistance gene in HZ will improve its molecular breeding and resistance variety application.
DOI: 10.6084/m9.figshare.3188389.v2
title: Material complementario a la comunicación "Escala y modelización: ¿Cuál es la relación entre la escala de la cartografía LULC empleada y la extensión del área modelada?

description: Se incluyen diferentes tablas que amplían los resultados mostrados en la comunicación (área total y número de polígonos de cambios a nivel de región para las cuatro simulaciones efectuadas) así como la leyenda jerárquica creada para vincular las dos cartografías (CORINE y SIOSE) y las transiciones consideradas en el modelo, con sus correspondientes tasas de cambio.Se incluyen finalmente los cuatro mapas LULC (<i>Land Use Land Cover</i>, Usos y Coberturas del Suelo) utilizados (dos para cada cartografía) así como los mapas de cambios resultado de las modelizaciones efectuadas.
DOI: 10.6084/m9.figshare.3188242.v2
title: [OLD] Psychosocial predictors of painful HIV-associated sensory neuropathy and quality of life

description: This repository has been superceded by: http://dx.doi.org/10.6084/m9.figshare.4555474. The new repository is linked directly to the originating GitHub repo for the data.
DOI: 10.6084/m9.figshare.3188389.v1
title: Material complementario a la comunicación "Escala y modelización: ¿Cuál es la relación entre la escala de la cartografía LULC empleada y la extensión del área modelada?

description: La influencia de la escala en el análisis y representación de los datos espaciales, a pesar de su importancia y de ser señalada como una línea de investigación prioritaria, permanece aún sin una adecuada comprensión. Son numerosos los conceptos a los que podemos hacer referencia cuando hablamos de escala. En la presente comunicación nos centramos en dos de ellos (escala cartográfica y su asociada unidad mínima cartografiable, así como la extensión del área de estudio), analizando la relación entre ambos y la modelización LULC (<i>Land Use Land Cover</i>, Usos y Coberturas del Suelo). A través del empleo de las métricas de la ecología del paisaje, la herramienta VALIDATE del software IDRISI, así como la matriz propuesta por Pontius y Millones, se ha analizado la influencia de los dos citados conceptos de escala en los escenarios creados a través del modelo Dinamica EGO. Se han efectuado cuatro simulaciones: dos para cada base de datos utilizada (SIOSE 1.25.0000 y CORINE 1.100.000), realizando para cada una de ellas una simulación para el conjunto del área de estudio y otra creando un submodelo para cada municipio dentro del área modelada. Los resultados pretender ayudar a aquellos investigadores en el ámbito de la modelización LULC en la parametrización inicial de sus modelos. Del mismo modo, se busca alcanzar una mejor comprensión de la relación que existe entre los distintos conceptos de escala.
DOI: 10.6084/m9.figshare.3188242.v1
title: Psychosocial predictors of painful HIV-associated sensory neuropathy and quality of life

description: Data, analysis scripts and script outputs for a study investigating predictors of painful versus non-painful HIV-associated sensory neuropathy, and predictors of quality of life in these patients.
DOI: 10.6084/m9.figshare.3187909
title: SMILE Twitter Emotion dataset

description: This dataset is collected and annotated for the SMILE project http://www.culturesmile.org. This collection of tweets mentioning 13 Twitter handles associated with British museums was gathered between May 2013 and June 2015. It was created for the purpose of classifying emotions, expressed on Twitter towards arts and cultural experiences in museums. <br>It contains 3,085 tweets, with 5 emotions namely anger, disgust, happiness, surprise and sadness. Please see our paper "SMILE: Twitter Emotion Classification using Domain Adaptation" for more details of the dataset.<br>License: The annotations are provided under a CC-BY license, while Twitter retains the ownership and rights of the content of the tweets.<br>
DOI: 10.6084/m9.figshare.3187903
title: FOOD resources: ontologies and data

description: This dataset is the outcome of an e-government project named FOOD, FOod in Open Data, which was carried out in the context of a collaboration between the Institute of Cognitive Sciences and Technologies of the Italian National Research Council, the Italian Ministry of Agriculture (MIPAAF) and the Italian Digital Agency (AgID). In particular, we implemented several ontologies for describing protected names of products (wine, pasta, fish, oil, etc.). In addition, we present the process carried out for producing and publishing a LOD dataset containing data extracted from existing Italian policy documents on such products and compliant with the aforementioned ontologies.<br><br>This dataset contains all the excel files, the ontologies, accompanied by their HTML documentation (in English and Italian) and diagrams, and data developed in the context of the Italian project "FOOD: Food in Open Data".<br>
DOI: 10.6084/m9.figshare.3187897
title: Molecular dynamics study of the membrane interaction of a membranotropic dengue virus C protein-derived peptide

description: Dengue virus C protein, essential in the dengue virus life cycle, possesses a segment, peptide PepC, known to bind membranes composed of negatively charged phospholipids. To characterize its interaction with the membrane, we have used the molecular dynamics HMMM membrane model system. This approach is capable of achieving a stable system and sampling the peptide/lipid interactions which determine the orientation and insertion of the peptide upon membrane binding. We have been able to demonstrate spontaneous binding of PepC to the 1,2-divaleryl-sn-glycero-3-phosphate/1,2-divaleryl-sn-glycero-3-phosphocholine membrane model system, whereas no binding was observed at all for the 1,2-divaleryl-sn-glycero-3-phosphocholine one. PepC, adopting an α-helix profile, did not insert into the membrane but did bind to its surface through a charge anchor formed by its three positively charged residues. PepC, maintaining its three-dimensional structure along the whole simulation, presented a nearly parallel orientation with respect to the membrane when bound to it. The positively charged amino acid residues Arg-2, Lys-6, and Arg-16 are mainly responsible for the peptide binding to the membrane stabilizing the structure of the bound peptide. The segment of dengue virus C protein where PepC resides is a fundamental protein–membrane interface which might control protein/membrane interaction, and its positive amino acids are responsible for membrane binding defining its specific location in the bound state. These data should help in our understanding of the molecular mechanism of DENV life cycle as well as making possible the future development of potent inhibitor molecules, which target dengue virus C protein structures involved in membrane binding.
DOI: 10.6084/m9.figshare.3187894
title: DGE tool TPR/FPR performance with 2 replicates

description: This figure is an expansion on Figure 2 from our paper in RNA "How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?". The figure shows the comparison of the true positive rate (TPR) and false positive rate (FPR) performance for each of the DGE tools for extremely low-replication (n_r=2) RNA-seq data. As for Figure 2 in the paper, the TPRs & FPRs for each tool are calculated by comparing the mean number of true and false positive (TPs and FPs) calculated over 100 bootstrap iterations to the number of TPs and FPs calculated from the same tool using the full clean dataset (error-bars are 1 standard deviation). Although the TPRs and FPRs from each tool are calculated by comparing each tool against itself rather than a tool-independent ‘gold standard’ (albeit with the full clean dataset) the results are comparable across tools (see the paper for more details).
DOI: 10.6084/m9.figshare.3187903.v1
title: New draft item

description: This dataset contains all the ontologies and data developed in the context of the Italian project "FOOD: Food in Open Data".<br>
DOI: 10.6084/m9.figshare.3187894.v2
title: DGE tool TPR/FPR performance with 2 replicates

description: This figure is an expansion on Figure 2 from our paper in RNA "How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?". The figure shows the comparison of the true positive rate (TPR) and false positive rate (FPR) performance for each of the DGE tools for extremely low-replication (n_r=2) RNA-seq data. As for Figure 2 in the paper, the TPRs & FPRs for each tool are calculated by comparing the mean number of true and false positive (TPs and FPs) calculated over 100 bootstrap iterations to the number of TPs and FPs calculated from the same tool using the full clean dataset (error-bars are 1 standard deviation). Although the TPRs and FPRs from each tool are calculated by comparing each tool against itself rather than a tool-independent ‘gold standard’ (albeit with the full clean dataset) the results are comparable across tools (see the paper for more details).
DOI: 10.6084/m9.figshare.3187897.v2
title: Molecular dynamics study of the membrane interaction of a membranotropic dengue virus C protein-derived peptide

description: Dengue virus C protein, essential in the dengue virus life cycle, possesses a segment, peptide PepC, known to bind membranes composed of negatively charged phospholipids. To characterize its interaction with the membrane, we have used the molecular dynamics HMMM membrane model system. This approach is capable of achieving a stable system and sampling the peptide/lipid interactions which determine the orientation and insertion of the peptide upon membrane binding. We have been able to demonstrate spontaneous binding of PepC to the 1,2-divaleryl-sn-glycero-3-phosphate/1,2-divaleryl-sn-glycero-3-phosphocholine membrane model system, whereas no binding was observed at all for the 1,2-divaleryl-sn-glycero-3-phosphocholine one. PepC, adopting an α-helix profile, did not insert into the membrane but did bind to its surface through a charge anchor formed by its three positively charged residues. PepC, maintaining its three-dimensional structure along the whole simulation, presented a nearly parallel orientation with respect to the membrane when bound to it. The positively charged amino acid residues Arg-2, Lys-6, and Arg-16 are mainly responsible for the peptide binding to the membrane stabilizing the structure of the bound peptide. The segment of dengue virus C protein where PepC resides is a fundamental protein–membrane interface which might control protein/membrane interaction, and its positive amino acids are responsible for membrane binding defining its specific location in the bound state. These data should help in our understanding of the molecular mechanism of DENV life cycle as well as making possible the future development of potent inhibitor molecules, which target dengue virus C protein structures involved in membrane binding.
DOI: 10.6084/m9.figshare.3187903.v2
title: FOOD resources: ontologies and data

description: This dataset contains all the ontologies and data developed in the context of the Italian project "FOOD: Food in Open Data".<br>