cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1588559
title: Plant height on insect abundance as measured by quadrats in York University's Pond Rd grasslands

description: Quadrat samples were randomly taken at the grassland area of York University's Pond Rd on October 13th and October 20th, 2015. Plant height was measured using transect tape and the average plant height of each quadrat was calculated using the principle of mean data values. Insect abundance was a visual count of all insect individuals regardless of the species that were found in the area. The concrete ecosystem was that which had no grass on it and was found on the road near the grasslands. The short grass ecosystem consisted of grass 2 to 5 inches in length found in patches at the grassland. The tall grass ecosystem consisted of tall species of grass anywhere from 5-35 inches in height found in patches near the grasslands.
DOI: 10.6084/m9.figshare.1588555.v1
title: Genome-wide Identification and Characterisation of Tissue-specific RNA Editing Events in <i>D. melanogaster</i> and their Potential Role in Regulating Alternative Splicing

description: RNA editing is a widespread mechanism that plays a crucial role in diversifying gene products. Its abundance and importance in regulating cellular processes were revealed using new sequencing technologies. The majority of these editing events, however, cannot be associated with regulatory mechanisms. We use tissue-specific high-throughput libraries of <i>D. melanogaster</i> to study RNA editing. We introduce an analysis pipeline that utilises large input data and explicitly captures ADAR's requirement for double-stranded regions. It combines probabilistic and deterministic filters and can identify RNA editing events with a low estimated false positive rate. Analysing ten different tissue types, we predict 2879 editing sites and provide their detailed characterisation. Our analysis pipeline accurately distinguishes genuine editing sites from SNPs and sequencing and mapping artefacts. Our editing sites are three times more likely to occur in exons with multiple splicing acceptor/donor sites than in exons with unique splice sites (p-value &lt; 2 10–15). Furthermore, we identify 244 edited regions where RNA editing and alternative splicing are likely to influence each other. For 96 out of these 244 regions, we find evolutionary evidence for conserved RNA secondary-structures near splice sites suggesting a potential regulatory mechanism where RNA editing may alter splicing patterns via changes in local RNA structure.
DOI: 10.6084/m9.figshare.1588552
title: Circadian regulation gene polymorphisms are associated with sleep disruption and duration, and circadian phase and rhythm in adults with HIV

description: Genes involved in circadian regulation, such as circadian locomotor output cycles kaput [CLOCK], cryptochrome [CRY1] and period [PER], have been associated with sleep outcomes in prior animal and human research. However, it is unclear whether polymorphisms in these genes are associated with the sleep disturbances commonly experienced by adults living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS). Thus, the purpose of this study was to describe polymorphisms in selected circadian genes that are associated with sleep duration or disruption as well as the sleep–wake rhythm strength and phase timing among adults living with HIV/AIDS. A convenience sample of 289 adults with HIV/AIDS was recruited from HIV clinics and community sites in the San Francisco Bay Area. A wrist actigraph was worn for 72 h on weekdays to estimate sleep duration or total sleep time (TST), sleep disruption or percentage of wake after sleep onset (WASO) and several circadian rhythm parameters: mesor, amplitude, the ratio of mesor to amplitude (circadian quotient), and 24-h autocorrelation. Circadian phase measures included clock time for peak activity (acrophase) from actigraphy movement data, and bed time and final wake time from actigraphy and self-report. Genotyping was conducted for polymorphisms in five candidate genes involved in circadian regulation: CLOCK, CRY1, PER1, PER2 and PER3. Demographic and clinical variables were evaluated as potential covariates. Interactions between genotype and HIV variables (i.e. viral load, years since HIV diagnosis) were also evaluated. Controlling for potentially confounding variables (e.g. race, gender, CD4+ T-cell count, waist circumference, medication use, smoking and depressive symptoms), CLOCK was associated with WASO, 24-h autocorrelation and objectively-measured bed time; CRY1 was associated with circadian quotient; PER1 was associated with mesor and self-reported habitual wake time; PER2 was associated with TST, mesor, circadian quotient, 24-h autocorrelation and bed and wake times; PER3 was associated with amplitude, 24-h autocorrelation, acrophase and bed and wake times. Most of the observed associations involved a significant interaction between genotype and HIV. In this chronic illness population, polymorphisms in several circadian genes were associated with measures of sleep disruption and timing. These findings extend the evidence for an association between genetic variability in circadian regulation and sleep outcomes to include the sleep–wake patterns experienced by adults living with HIV/AIDS. These results provide direction for future intervention research related to circadian sleep–wake behavior patterns.
DOI: 10.6084/m9.figshare.1588556.v1
title: Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome)

description: ABSTRACTWe describe here a platform for high-throughput protein expression and interaction analysis aimed at identifying the RNA-interacting domainome. This approach combines the selection of a phage library displaying “filtered” open reading frames with next-generation DNA sequencing. The method was validated using an RNA bait corresponding to the AU-rich element of α-prothymosin, an RNA motif that promotes mRNA stability and translation through its interaction with the RNA-binding protein ELAVL1. With this strategy, we not only confirmed known RNA-binding proteins that specifically interact with the target RNA (such as ELAVL1/HuR and RBM38) but also identified proteins not previously known to be ARE-binding (R3HDM2 and RALY). We propose this technology as a novel approach for studying the RNA-binding proteome.
DOI: 10.6084/m9.figshare.1588541
title: Noise_sensitivity

description: Livi et al.
DOI: 10.6084/m9.figshare.1588541.v1
title: Noise_sensitivity

description: Livi et al.
DOI: 10.6084/m9.figshare.1588542
title: Renal impairment in patients with chronic hepatitis C treated with first generation protease inhibitors

description: <b><i>Background</i></b>: The incidence, course and risk factors associated with renal impairment (RI) in patients treated with triple therapy (TT) with pegylated interferon, ribavirin and telaprevir/boceprevir (PR/TVR/BOC) vs. dual therapy (DT) with PR were analyzed in this study. The association between RI and the decline of hemoglobin (Hb) was also examined.<b><i>Methods</i></b>: Retrospective analysis included 110 patients with genotype 1b chronic HCV infection, aged 18 – 80 years, who underwent TT (48TVR/14BOC) or DT (48 patients). The estimated glomerular filtration rate (eGFR), serum creatinine concentration (SCr) and Hb were measured at baseline, at weeks 4, 12, 24, 48 of treatment, and post-treatment week 24.<b><i>Results</i></b>: RI occurred in 9/62 (14.5%) patients who underwent TT, eight of whom were treated with TVR, one with BOC, and none treated with DT. The risk factors associated with RI were the following: TT (p = 0.0078), usage of nephrotoxic drugs (p = 0.0288), and older age (p <b><i>Conclusions</i></b>: RI is not a rare but a reversible complication of TT. It is necessary to monitor SCr and eGFR, especially in patients with a potential risk factor of RI occurrence. The Hb drop is more severe in patients with RI than in those without it.
DOI: 10.6084/m9.figshare.1588552.v2
title: Circadian regulation gene polymorphisms are associated with sleep disruption and duration, and circadian phase and rhythm in adults with HIV

description: Genes involved in circadian regulation, such as circadian locomotor output cycles kaput [CLOCK], cryptochrome [CRY1] and period [PER], have been associated with sleep outcomes in prior animal and human research. However, it is unclear whether polymorphisms in these genes are associated with the sleep disturbances commonly experienced by adults living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS). Thus, the purpose of this study was to describe polymorphisms in selected circadian genes that are associated with sleep duration or disruption as well as the sleep–wake rhythm strength and phase timing among adults living with HIV/AIDS. A convenience sample of 289 adults with HIV/AIDS was recruited from HIV clinics and community sites in the San Francisco Bay Area. A wrist actigraph was worn for 72 h on weekdays to estimate sleep duration or total sleep time (TST), sleep disruption or percentage of wake after sleep onset (WASO) and several circadian rhythm parameters: mesor, amplitude, the ratio of mesor to amplitude (circadian quotient), and 24-h autocorrelation. Circadian phase measures included clock time for peak activity (acrophase) from actigraphy movement data, and bed time and final wake time from actigraphy and self-report. Genotyping was conducted for polymorphisms in five candidate genes involved in circadian regulation: CLOCK, CRY1, PER1, PER2 and PER3. Demographic and clinical variables were evaluated as potential covariates. Interactions between genotype and HIV variables (i.e. viral load, years since HIV diagnosis) were also evaluated. Controlling for potentially confounding variables (e.g. race, gender, CD4+ T-cell count, waist circumference, medication use, smoking and depressive symptoms), CLOCK was associated with WASO, 24-h autocorrelation and objectively-measured bed time; CRY1 was associated with circadian quotient; PER1 was associated with mesor and self-reported habitual wake time; PER2 was associated with TST, mesor, circadian quotient, 24-h autocorrelation and bed and wake times; PER3 was associated with amplitude, 24-h autocorrelation, acrophase and bed and wake times. Most of the observed associations involved a significant interaction between genotype and HIV. In this chronic illness population, polymorphisms in several circadian genes were associated with measures of sleep disruption and timing. These findings extend the evidence for an association between genetic variability in circadian regulation and sleep outcomes to include the sleep–wake patterns experienced by adults living with HIV/AIDS. These results provide direction for future intervention research related to circadian sleep–wake behavior patterns.
DOI: 10.6084/m9.figshare.1588539
title: Generation of gradients on a microfluidic device: toward a high-throughput investigation of spermatozoa chemotaxis

description: _
DOI: 10.6084/m9.figshare.1588542.v1
title: Renal impairment in patients with chronic hepatitis C treated with first generation protease inhibitors

description: <b><i>Background</i></b>: The incidence, course and risk factors associated with renal impairment (RI) in patients treated with triple therapy (TT) with pegylated interferon, ribavirin and telaprevir/boceprevir (PR/TVR/BOC) vs. dual therapy (DT) with PR were analyzed in this study. The association between RI and the decline of hemoglobin (Hb) was also examined.<b><i>Methods</i></b>: Retrospective analysis included 110 patients with genotype 1b chronic HCV infection, aged 18 – 80 years, who underwent TT (48TVR/14BOC) or DT (48 patients). The estimated glomerular filtration rate (eGFR), serum creatinine concentration (SCr) and Hb were measured at baseline, at weeks 4, 12, 24, 48 of treatment, and post-treatment week 24.<b><i>Results</i></b>: RI occurred in 9/62 (14.5%) patients who underwent TT, eight of whom were treated with TVR, one with BOC, and none treated with DT. The risk factors associated with RI were the following: TT (p = 0.0078), usage of nephrotoxic drugs (p = 0.0288), and older age (p <b><i>Conclusions</i></b>: RI is not a rare but a reversible complication of TT. It is necessary to monitor SCr and eGFR, especially in patients with a potential risk factor of RI occurrence. The Hb drop is more severe in patients with RI than in those without it.
DOI: 10.6084/m9.figshare.1588552.v1
title: Circadian regulation gene polymorphisms are associated with sleep disruption and duration, and circadian phase and rhythm in adults with HIV

description: Genes involved in circadian regulation, such as circadian locomotor output cycles kaput [CLOCK], cryptochrome [CRY1] and period [PER], have been associated with sleep outcomes in prior animal and human research. However, it is unclear whether polymorphisms in these genes are associated with the sleep disturbances commonly experienced by adults living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS). Thus, the purpose of this study was to describe polymorphisms in selected circadian genes that are associated with sleep duration or disruption as well as the sleep–wake rhythm strength and phase timing among adults living with HIV/AIDS. A convenience sample of 289 adults with HIV/AIDS was recruited from HIV clinics and community sites in the San Francisco Bay Area. A wrist actigraph was worn for 72 h on weekdays to estimate sleep duration or total sleep time (TST), sleep disruption or percentage of wake after sleep onset (WASO) and several circadian rhythm parameters: mesor, amplitude, the ratio of mesor to amplitude (circadian quotient), and 24-h autocorrelation. Circadian phase measures included clock time for peak activity (acrophase) from actigraphy movement data, and bed time and final wake time from actigraphy and self-report. Genotyping was conducted for polymorphisms in five candidate genes involved in circadian regulation: CLOCK, CRY1, PER1, PER2 and PER3. Demographic and clinical variables were evaluated as potential covariates. Interactions between genotype and HIV variables (i.e. viral load, years since HIV diagnosis) were also evaluated. Controlling for potentially confounding variables (e.g. race, gender, CD4+ T-cell count, waist circumference, medication use, smoking and depressive symptoms), CLOCK was associated with WASO, 24-h autocorrelation and objectively-measured bed time; CRY1 was associated with circadian quotient; PER1 was associated with mesor and self-reported habitual wake time; PER2 was associated with TST, mesor, circadian quotient, 24-h autocorrelation and bed and wake times; PER3 was associated with amplitude, 24-h autocorrelation, acrophase and bed and wake times. Most of the observed associations involved a significant interaction between genotype and HIV. In this chronic illness population, polymorphisms in several circadian genes were associated with measures of sleep disruption and timing. These findings extend the evidence for an association between genetic variability in circadian regulation and sleep outcomes to include the sleep–wake patterns experienced by adults living with HIV/AIDS. These results provide direction for future intervention research related to circadian sleep–wake behavior patterns.
DOI: 10.6084/m9.figshare.1588513
title: Face-noise ERP onsets from 194 recording sessions

description: This data package contains ERP onsets estimated from 120 participants, 74 of whom were tested twice. Stimuli were face images and noise textures. Onsets were estimated using ERP data low-pass filtered or not, using t-tests on means or 20% trimmed-means. We corrected for multiple comparisons using cluster based statistics in conjunction with a percentile-t bootstrap procedure. The results were reported in this paper accepted for publication: <strong>A robust and representative lower bound on object processing speed in humans</strong><br>Magdalena Bieniek, Patrick Bennett, Allison Sekuler & Guillaume Rousselet<br><em>European Journal of Neuroscience</em>
DOI: 10.6084/m9.figshare.1588513.v1
title: Face-noise ERP onsets from 194 recording sessions

description: This data package contains ERP onsets estimated from 120 participants, 74 of whom were tested twice. Stimuli were face images and noise textures. Onsets were estimated using ERP data low-pass filtered or not, using t-tests on means or 20% trimmed-means. We corrected for multiple comparisons using cluster based statistics in conjunction with a percentile-t bootstrap procedure. The results were reported in this paper accepted for publication: <strong>A robust and representative lower bound on object processing speed in humans</strong><br>Magdalena Bieniek, Patrick Bennett, Allison Sekuler & Guillaume Rousselet<br><em>European Journal of Neuroscience</em>
DOI: 10.6084/m9.figshare.1588414
title: Characterization of 14 novel microsatellite loci in the Argentine black and white tegu (Salvator merianae) via 454 pyrosequencing

description: We have developed 14 novel microsatellite loci for the Argentine black and white tegu (<em>Salvator merianae</em>), using samples from invasive populations from the US state of Florida. Pyrosequencing was used to identify 3154 potentially amplifiable microsatellite loci and to subsequently develop 14 informative markers. These 14 markers were screened for variation in 40 individuals from Miami-Dade County, Florida. All loci were polymorphic and contained between 2 and 4 alleles per locus (mean ± SE = 2.71 ± 0.24), with observed heterozygosity ranging from 0.00 to 0.88 (mean ± SE = 0.38 ± 0.07). Four of the loci (Teg4, Teg5, Teg17, Teg19) significantly deviated from Hardy-Weinberg proportions and three of these loci (Teg4, Teg5, Teg19) showed evidence of null alleles. In addition, there was statistical evidence for genotypic disequilibrium between Teg14 and Teg19. BLASTn searches of NCBI’s ‘nr/nt’ database using microsatellite containing 454 fragments as queries were largely uninformative; however, it is likely that some of these markers will be of utility in <em>S. merinae</em>’s native range. <strong>Supplementary Data File 1:</strong> Zip archive containing FASTA files of the 454 sequences generated during the course of our study.<br><strong>Supplementary Data File 2:</strong> Excel spreadsheet containing the primers associated with the potentially amplifiable loci identified during the course of our study.
DOI: 10.6084/m9.figshare.1588384
title: Appendix-E1

description: data and scripts as example of use of MGKit
DOI: 10.6084/m9.figshare.1588414.v1
title: Characterization of 14 novel microsatellite loci in the Argentine black and white tegu (Salvator merianae) via 454 pyrosequencing

description: We have developed 14 novel microsatellite loci for the Argentine black and white tegu (<em>Salvator merianae</em>), using samples from invasive populations from the US state of Florida. Pyrosequencing was used to identify 3154 potentially amplifiable microsatellite loci and to subsequently develop 14 informative markers. These 14 markers were screened for variation in 40 individuals from Miami-Dade County, Florida. All loci were polymorphic and contained between 2 and 4 alleles per locus (mean ± SE = 2.71 ± 0.24), with observed heterozygosity ranging from 0.00 to 0.88 (mean ± SE = 0.38 ± 0.07). Four of the loci (Teg4, Teg5, Teg17, Teg19) significantly deviated from Hardy-Weinberg proportions and three of these loci (Teg4, Teg5, Teg19) showed evidence of null alleles. In addition, there was statistical evidence for genotypic disequilibrium between Teg14 and Teg19. BLASTn searches of NCBI’s ‘nr/nt’ database using microsatellite containing 454 fragments as queries were largely uninformative; however, it is likely that some of these markers will be of utility in <em>S. merinae</em>’s native range. <strong>Supplementary Data File 1:</strong> Zip archive containing FASTA files of the 454 sequences generated during the course of our study.<br><strong>Supplementary Data File 2:</strong> Excel spreadsheet containing the primers associated with the potentially amplifiable loci identified during the course of our study.
DOI: 10.6084/m9.figshare.1588337
title: 新建文件夹.zip

description: <b>File 1.</b> Raw data of the EEM results <b>File 2</b>. Raw data of the HRTEM results <b>File 3.</b> Raw data of the FTIR results <b>File 4.</b> Raw data of the HRTEM-EDS results
DOI: 10.6084/m9.figshare.1588384.v1
title: Appendix-E1

description: data and scripts as example of use of MGKit
DOI: 10.6084/m9.figshare.1588337.v1
title: 新建文件夹.zip

description: <b>File 1.</b> Raw data of the EEM results <b>File 2</b>. Raw data of the HRTEM results <b>File 3.</b> Raw data of the FTIR results <b>File 4.</b> Raw data of the HRTEM-EDS results
DOI: 10.6084/m9.figshare.1587276
title: The Effect of the Amount of Light and the Abundance of Buckthorn on Native Saplings

description: The data for this lab was collected at York University's woodlot on Ocober 14, 2015 from 3:11 - 5:00 P.M and October 21, 2015 from 3:05 - 4:09 by Reena, Ratiba, Farka, Huda and Olivia. The temperature for both days were around 10 degrees celcius and was cold with a slight breeze. The second day however had more fallen leaves on the ground than the first day. The sampling began by starting at the edge of the woodlot (station 0) and walking 5 meters along a 120 meter transect towards the centre of the woodlot. At this point, a 2x2 meter measuring tape was used to form a quadrat. Three quadrats were placed to the right of the transect tape at the 5 meter mark, adjacent to it, and 3 quadrats were placed on the other side (left side) of the transect, also adjacent to it. The abundance of the native sapling (Acer) and the Buckthorn plant within each quadrat were recorded by counting each one individually. In addition, the percentage of light reaching each quadrat was recorded. To determine the percent light, an individual's hands are used to form a box. Then standing in the centre of each quadrat and looking up towards the sky, one's judgement was used in order to determine the amound of light penetrating through the canapy above, only looking though the area formed by one's hands. The percentage of light was recorded as continuous data whereas the number of quadrats and the abundance of plants and stations are discrete data. These steps were repeated every 5 meters for a total of 21 times (21 stations - every 5 meters counts as 1 station) for an overall distance of 100 meters into the centre of the woodlot. On the fist day, 0 - 50 meters were completed and on the second day, 55 - 100 meters were completed. This allowed for 126 quadrats to be sampled. The importance performing such an experiment was to observe the effect of of the abundance of Buckthorn, an invasive species, and the percentage of light available on the abundance of of the native plants (saplings) in the woodlot. The data also inspires further research into the effects of invasive species and how they are able to adapt and survive.