cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1590988
title: Human Impact on Plant Abundance

description: This data was collected in the course of two days. The first was Monday October 19th, from 2:30-4:30, and the second day was Monday October 26th within the same time frame. Both days were chilly, around 15 degrees Celcius, and cloudy with some sun. The wind on both days was quite fast, around 5-6 on the Beaufort Wind Scale. The data was collected around Danby woods at York University. Specifically, it was completed in the grassland, just South of the woods and West of Keele street. The area that was encompassed was up to 200 feet West of Keele street and around 150 feet South of Danby woods. The plant species that was chosen was <em>T officinale</em>, more commonly known as dandelions. This species was chosen due to its hardiness and ability to survive in difficult conditions. If there was a change in abundance, it would be because of extreme conditions such as air pollution or soil damage. Quadrats were used for the random sampling technique. This was done to simplify what pieces of garbage were counted. Only those inside the placed quadrat were considered to have an effect on plant abundance. The area was divided into three categories of differing distances: 0-60 feet, 60-110 feet, and 110-200 feet. This was done to see if proximity to gasoline and air pollution had any harmful effects on plant abundance. 50 quadrats were placed in each section of distances, and plants were counted inside the quadrat. If any pieces of garbage were present, they were also counted. This lab goes further to help develop and complete a self-designed experiment, using random sampling techniques. Lab partners were Abera, Sufyan, Alex, and Frankie.
DOI: 10.6084/m9.figshare.1590977
title: Abdominal muscle activity during mechanically ventilation increases lung injury in severe acute respiratory distress syndrome

description: This is the supplements of《Abdominal muscle activity during mechanically ventilation increases lung injury in severe acute respiratory distress syndrome》
DOI: 10.6084/m9.figshare.1590988.v1
title: Human Impact on Plant Abundance

description: This data was collected in the course of two days. The first was Monday October 19th, from 2:30-4:30, and the second day was Monday October 26th within the same time frame. Both days were chilly, around 15 degrees Celcius, and cloudy with some sun. The wind on both days was quite fast, around 5-6 on the Beaufort Wind Scale. The data was collected around Danby woods at York University. Specifically, it was completed in the grassland, just South of the woods and West of Keele street. The area that was encompassed was up to 200 feet West of Keele street and around 150 feet South of Danby woods. The plant species that was chosen was <em>T officinale</em>, more commonly known as dandelions. This species was chosen due to its hardiness and ability to survive in difficult conditions. If there was a change in abundance, it would be because of extreme conditions such as air pollution or soil damage. Quadrats were used for the random sampling technique. This was done to simplify what pieces of garbage were counted. Only those inside the placed quadrat were considered to have an effect on plant abundance. The area was divided into three categories of differing distances: 0-60 feet, 60-110 feet, and 110-200 feet. This was done to see if proximity to gasoline and air pollution had any harmful effects on plant abundance. 50 quadrats were placed in each section of distances, and plants were counted inside the quadrat. If any pieces of garbage were present, they were also counted. This lab goes further to help develop and complete a self-designed experiment, using random sampling techniques. Lab partners were Abera, Sufyan, Alex, and Frankie.
DOI: 10.6084/m9.figshare.1590977.v1
title: Abdominal muscle activity during mechanically ventilation increases lung injury in severe acute respiratory distress syndrome

description: This is the supplements of《Abdominal muscle activity during mechanically ventilation increases lung injury in severe acute respiratory distress syndrome》
DOI: 10.6084/m9.figshare.1590982
title: Making Plots and Diagrams for Presentations, Papers, and Theses

description: Presentation on making plots and diagrams for presentations, papers, and theses. The primary audience, at the present time, is undergraduate and graduate students in STEM fields. The source for the presentation, its diagrams, and the Jupyter/IPython notebook to make the plots are at the provided GitHub link and are licensed CC BY 4.0. The current version of the presentation is named current.pdf. The other versions are stored by as version_X.pdf where X is the version. Note that this figshare replaces http://dx.doi.org/10.6084/m9.figshare.1590009 which had file naming issues. The abstract is below Plots and diagrams are a common visual means of conveying information in scientific talks, papers, and theses. A good plot or diagram conveys the desired information clearly and in a way that gives understanding that would be lacking in a table or description giving the same information by itself. In addition, the plot or diagram should be understandable to people with various types of colorblindness and when printed on a printer (color or greyscale) or shown on a projector. A bad plot or diagram can serve as a distraction and cause confusion, or be otherwise difficult to read. This presentation will show how to make plots and diagrams more clear and readable. In addition, computer and printing considerations will be discussed. These include screens and projectors, printers, fonts, etc.<br>
DOI: 10.6084/m9.figshare.1590966
title: Spatial walking bouts and walkability

description: This is the dataset for Peer J submission. R script used in analysis: glmmadmb(formula = Bout ~ WS + Sex + Age + BMI + Income, data = Data,<br>family = "nbinom", random = ~1 | Famid, zeroInflation = TRUE)
DOI: 10.6084/m9.figshare.1590966.v1
title: Spatial walking bouts and walkability

description: This is the dataset for Peer J submission. R script used in analysis: glmmadmb(formula = Bout ~ WS + Sex + Age + BMI + Income, data = Data,<br>family = "nbinom", random = ~1 | Famid, zeroInflation = TRUE)
DOI: 10.6084/m9.figshare.1590962
title: A Textual-based Technique for Smell Detection

description: In this paper, we present TACO (Textual Analysis for Code Smell Detection), a technique that exploits textual analysis to detect a family of smells of different nature and different levels of granularity. We run TACO on 10 open source projects, comparing its performance with existing smell detectors purely based on structural information extracted from code components. The analysis of the results indicate that TACO’s precision ranges between 67% and 77%, while its recall ranges between 72% and 84%. Also, TACO often outperforms alternative structural approaches confirming, once again, the usefulness of information that can be derived from the textual part of code components.
DOI: 10.6084/m9.figshare.1590045
title: Influence of treatment of vulvovaginal atrophy with intravaginal prasterone on the male partner

description: ABSTRACT<i>Objective</i> The aim was to analyze the opinion of the male partner of women treated for vulvovaginal atrophy (VVA) with intravaginal 0.50% DHEA (prasterone), thus providing information on both members of the couple.<i>Methods</i> On a voluntary basis, in a prospective, randomized, double-blind and placebo-controlled phase-III clinical trial, the male partner filled a questionnaire at baseline and at 12 weeks stating his observations related to his penis and intercourse before and after VVA treatment.<i>Results</i> Sixty-six men having a partner treated with intravaginal DHEA and 34 others having a partner treated with placebo answered the questionnaires. Concerning the feeling of vaginal dryness of their female partner, the severity score following DHEA treatment improved by 81% (0.76 units) over placebo (<i>p</i> = 0.0347). Thirty-six percent of men having a partner treated with DHEA did not feel the vaginal dryness of the partner at the end of treatment compared to 7.8% in the placebo group. When analyzing the situation at 12 weeks compared to baseline, an improved score of 1.09 units was the difference found for the DHEA group compared to 0.76 for the placebo group (<i>p</i> = 0.05 vs. placebo). In the DHEA group, 38% of men scored very improved compared to 18% in the placebo group. No adverse event has been reported.<i>Conclusion</i> The male partner had a very positive evaluation of the treatment received by his female partner.
DOI: 10.6084/m9.figshare.1590048
title: Distribution and Abundance of Birds on York University

description: Data for this experiment was collected over two days, one week apart, between 2:45 pm and 4:45 pm. This was done to account for factors that could not be controlled (such as weather) which may have affected the abundance and distribution of birds on a particular day. Day 1, on Tuesday October 13th, 2015, was cloudy and moderately windy with a temperature of 15°C. Day 2, on Tuesday October 20th, 2015, was cloudy with light rain and low wind with a temperature of 16 °C. All data was gathered from grasslands, woodlots, and urbanized parts of York University's Keele Campus. On Day 1, a total of 16 transects 120 m long were randomly placed along Keele Campus. Eight were placed in urban areas where at least 75% of the area being surveyed was pavement and/or buildings, and eight were placed in natural areas where at least 75% of the area being surveyed was vegetation. On Day 2, a total of 20 transects also 120 m long were randomly placed along Keele Campus. Ten in urban areas and ten in natural areas which matched the same criteria as those in day 1. Each 120 m long transect was measured out using a transect measuring tape and was walked along. Birds that were visually approximated to be within 25 m of either side of the transect and within 15 m of the ground were considered to be using the area and were counted. This entire area (25 m on either side of, and 15 m above the entire 125 m long transect) is considered the area being surveyed upon which the urban and natural areas were defined. Every bird seen was visually categorized into species with reference to a bird identification guide. The number of each species were counted and recorded as each transect was walked along. At the end of each transect, the total number of different species and total number of birds were also counted and recorded. This process was performed for every transect.
DOI: 10.6084/m9.figshare.1590962.v1
title: One Technique to Smell Them All: A Textual-based Technique for Code and Test Smell Detection

description: Bad smells are symptoms of poor design or implementation choises that may affect both production and test code. Several previous studies demonstrated the huge impact of these smells on change- and fault-proneness, comprehensibility and, more in general, on maintainability. These are the reasons why researchers spent a lot of effort on the definition of metrics-based techniques able to detect them by exploiting structural properties of the source code. However, code and test smell detection have always been treated as separate problems, since for detecting different smells, different tools relying on a different ah-hoc set of metrics are required. To overcome such limitations, we propose a textual-based smell detector able to detect both code and test smells through IR methods measuring the probability that a code component is affected by a given smell. We run the proposed approach, named TACO (Textual Analysis for Code Smell Detection), on 20 open source projects, comparing its performances with existing state-of-the-art smell detectors purely based on structural analysis. Our findings indicate that TACO’s precision ranges between 57% and 75%, while its recall ranges between 68% and 85%. Moreover, we observed that the proposed detector often outperforms competitive structural approaches, being able to identify smell instances that can not be detected by solely using structural analysis.
DOI: 10.6084/m9.figshare.1590047
title: Sunlight exposure and soil moisture on plant abundance

description: This experiement and data collection was carried out with 3 of my lab group members, Khaula Sahi, Alexandra Nushis and Kathy Chan. Data collection took place at York Universty Campus in the grasslands or woodlots. Data collection began at approximately 3pm, and lasted 2 hours, till 5pm. Weather on day 1 of data collection consisted of cloudiness and no sun, with winds. Day 2 of data collection had rainy and windy weather. The purpose of this experiment was to observe how sunlight exposure and soil moisture affects plant abundance. The experiment was carried out by randomly placing quadrats in certain areas of grassland and woodlot, and counting approximately how many plants were present, recording amount of sunlight on a scale of 0-3 and soil moisture on a scale of 0-2. 80 replicates were recorded for both grassland and woodlot.
DOI: 10.6084/m9.figshare.1590962.v2
title: A Textual-based Technique for Code and Test Smell Detection

description: Bad smells are symptoms of poor design or imple- mentation choices that may affect both production and test code. Previous studies demonstrated the huge impact of these smells on change- and fault-proneness, comprehensibility and, more in general, on maintainability. For these reasons researchers have spent a lot of effort on the definition of methods and tools aimed at detecting smells in production and test code. Existing detection techniques are largely based on using structural information extracted from source code without considering the textual content of the code, which can be a useful source of information to detect design flaws. In this paper, we present TACO (Textual Analysis for Code Smell Detection), a technique that exploits textual analysis to detect smells in both production code and test code. We run TACO on 20 open source projects, comparing its performance with existing state-of-the-art smell detectors purely based on structural analysis. Our findings indicate that TACO’s precision ranges between 57% and 75%, while its recall ranges between 68% and 85%. Moreover, we observed that TACO often outperforms alternative structural approaches confirming, once again, the usefulness of information that can be derived from the textual part of source code components.
DOI: 10.6084/m9.figshare.1590045.v2
title: Influence of treatment of vulvovaginal atrophy with intravaginal prasterone on the male partner

description: ABSTRACT<i>Objective</i> The aim was to analyze the opinion of the male partner of women treated for vulvovaginal atrophy (VVA) with intravaginal 0.50% DHEA (prasterone), thus providing information on both members of the couple.<i>Methods</i> On a voluntary basis, in a prospective, randomized, double-blind and placebo-controlled phase-III clinical trial, the male partner filled a questionnaire at baseline and at 12 weeks stating his observations related to his penis and intercourse before and after VVA treatment.<i>Results</i> Sixty-six men having a partner treated with intravaginal DHEA and 34 others having a partner treated with placebo answered the questionnaires. Concerning the feeling of vaginal dryness of their female partner, the severity score following DHEA treatment improved by 81% (0.76 units) over placebo (<i>p</i> = 0.0347). Thirty-six percent of men having a partner treated with DHEA did not feel the vaginal dryness of the partner at the end of treatment compared to 7.8% in the placebo group. When analyzing the situation at 12 weeks compared to baseline, an improved score of 1.09 units was the difference found for the DHEA group compared to 0.76 for the placebo group (<i>p</i> = 0.05 vs. placebo). In the DHEA group, 38% of men scored very improved compared to 18% in the placebo group. No adverse event has been reported.<i>Conclusion</i> The male partner had a very positive evaluation of the treatment received by his female partner.
DOI: 10.6084/m9.figshare.1590047.v1
title: Sunlight exposure and soil moisture on plant abundance

description: This experiement and data collection was carried out with 3 of my lab group members, Khaula Sahi, Alexandra Nushis and Kathy Chan. Data collection took place at York Universty Campus in the grasslands or woodlots. Data collection began at approximately 3pm, and lasted 2 hours, till 5pm. Weather on day 1 of data collection consisted of cloudiness and no sun, with winds. Day 2 of data collection had rainy and windy weather. The purpose of this experiment was to observe how sunlight exposure and soil moisture affects plant abundance. The experiment was carried out by randomly placing quadrats in certain areas of grassland and woodlot, and counting approximately how many plants were present, recording amount of sunlight on a scale of 0-3 and soil moisture on a scale of 0-2. 80 replicates were recorded for both grassland and woodlot.
DOI: 10.6084/m9.figshare.1590040
title: New distinct compartments in the G<sub>2</sub> phase of the cell cycle defined by the levels of γH2AX.

description: Induction of DNA double strand breaks leads to phosphorylation and focus-formation of H2AX. However, foci of phosphorylated H2AX (γH2AX) appear during DNA replication also in the absence of exogenously applied injury. We measured the amount and the number of foci of γH2AX in different phases of the cell cycle by flow cytometry, sorting and microscopy in 4 malignant B-lymphocyte cell lines. There were no detectable γH2AX and no γH2AX-foci in G<sub>1</sub> cells in exponentially growing cells and cells treated with PARP inhibitor (PARPi) for 24 h to create damage and reduce DNA repair. The amount of γH2AX increased immediately upon S phase entry, and about 10 and 30 γH2AX foci were found in mid-S phase control and PARPi-treated cells, respectively. The γH2AX-labeled damage caused by DNA replication was not fully repaired before entry into G<sub>2</sub>. Intriguingly, G<sub>2</sub> cells populated a continuous distribution of γH2AX levels, from cells with a high content of γH2AX and the same number of foci as S phase cells (termed “G<sub>2</sub>H” compartment), to cells that there were almost negative and had about 2 foci (termed “G<sub>2</sub>L” compartment). EdU-labeling of S phase cells revealed that G<sub>2</sub>H was directly populated from S phase, while G<sub>2</sub>L was populated from G<sub>2</sub>H, but in control cells also directly from S phase. The length of G<sub>2</sub>H in particular increased after PARPi treatment, compatible with longer DNA-repair times. Our results show that cells repair replication-induced damage in G<sub>2</sub>H, and enter mitosis after a 2–3 h delay in G<sub>2</sub>L.
DOI: 10.6084/m9.figshare.1590045.v1
title: Influence of treatment of vulvovaginal atrophy with intravaginal prasterone on the male partner

description: ABSTRACT<i>Objective</i> The aim was to analyze the opinion of the male partner of women treated for vulvovaginal atrophy (VVA) with intravaginal 0.50% DHEA (prasterone), thus providing information on both members of the couple.<i>Methods</i> On a voluntary basis, in a prospective, randomized, double-blind and placebo-controlled phase-III clinical trial, the male partner filled a questionnaire at baseline and at 12 weeks stating his observations related to his penis and intercourse before and after VVA treatment.<i>Results</i> Sixty-six men having a partner treated with intravaginal DHEA and 34 others having a partner treated with placebo answered the questionnaires. Concerning the feeling of vaginal dryness of their female partner, the severity score following DHEA treatment improved by 81% (0.76 units) over placebo (<i>p</i> = 0.0347). Thirty-six percent of men having a partner treated with DHEA did not feel the vaginal dryness of the partner at the end of treatment compared to 7.8% in the placebo group. When analyzing the situation at 12 weeks compared to baseline, an improved score of 1.09 units was the difference found for the DHEA group compared to 0.76 for the placebo group (<i>p</i> = 0.05 vs. placebo). In the DHEA group, 38% of men scored very improved compared to 18% in the placebo group. No adverse event has been reported.<i>Conclusion</i> The male partner had a very positive evaluation of the treatment received by his female partner.
DOI: 10.6084/m9.figshare.1590962.v3
title: A Textual-based Technique for Code and Test Smell Detection

description: Bad smells are symptoms of poor design or imple- mentation choices that may affect both production and test code. Previous studies demonstrated the huge impact of these smells on change- and fault-proneness, comprehensibility and, more in general, on maintainability. For these reasons researchers have spent a lot of effort on the definition of methods and tools aimed at detecting smells in production and test code. Existing detection techniques are largely based on using structural information extracted from source code without considering the textual content of the code, which can be a useful source of information to detect design flaws. In this paper, we present TACO (Textual Analysis for Code Smell Detection), a technique that exploits textual analysis to detect smells in both production code and test code. We run TACO on 20 open source projects, comparing its performance with existing state-of-the-art smell detectors purely based on structural analysis. Our findings indicate that TACO’s precision ranges between 57% and 75%, while its recall ranges between 68% and 85%. Moreover, we observed that TACO often outperforms alternative structural approaches confirming, once again, the usefulness of information that can be derived from the textual part of source code components.
DOI: 10.6084/m9.figshare.1590040.v2
title: New distinct compartments in the G<sub>2</sub> phase of the cell cycle defined by the levels of γH2AX.

description: Induction of DNA double strand breaks leads to phosphorylation and focus-formation of H2AX. However, foci of phosphorylated H2AX (γH2AX) appear during DNA replication also in the absence of exogenously applied injury. We measured the amount and the number of foci of γH2AX in different phases of the cell cycle by flow cytometry, sorting and microscopy in 4 malignant B-lymphocyte cell lines. There were no detectable γH2AX and no γH2AX-foci in G<sub>1</sub> cells in exponentially growing cells and cells treated with PARP inhibitor (PARPi) for 24 h to create damage and reduce DNA repair. The amount of γH2AX increased immediately upon S phase entry, and about 10 and 30 γH2AX foci were found in mid-S phase control and PARPi-treated cells, respectively. The γH2AX-labeled damage caused by DNA replication was not fully repaired before entry into G<sub>2</sub>. Intriguingly, G<sub>2</sub> cells populated a continuous distribution of γH2AX levels, from cells with a high content of γH2AX and the same number of foci as S phase cells (termed “G<sub>2</sub>H” compartment), to cells that there were almost negative and had about 2 foci (termed “G<sub>2</sub>L” compartment). EdU-labeling of S phase cells revealed that G<sub>2</sub>H was directly populated from S phase, while G<sub>2</sub>L was populated from G<sub>2</sub>H, but in control cells also directly from S phase. The length of G<sub>2</sub>H in particular increased after PARPi treatment, compatible with longer DNA-repair times. Our results show that cells repair replication-induced damage in G<sub>2</sub>H, and enter mitosis after a 2–3 h delay in G<sub>2</sub>L.