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Real-Time Clinical Genomics
Eligible cancer patients treated at St. Jude Children's Research Hospital are offered three-platform next-generation sequencing testing. This testing generally includes whole-genome sequencing (WGS) and whole-exome sequencing (WES) of tumor and normal tissue, as well as RNA sequencing (RNA Sequencing) of their tumor. Many of those patients consent to research data sharing so that their information can be leveraged to find cures for future patients. The Clinical Genomics dataset is comprised of data from these samples and is broken down into three distinct project phases. The Clinical Pilot project was a retrospective study that evaluated the accuracy and demonstrated the feasibility of three-platform sequencing in a CAP/CLIA setting. The findings of this project were published in Nature Communications. The Genomes 4 Kids (G4K) followed the Clinical Pilot. The goal of this prospective study was to determine whether the three-platform sequencing protocol laid out in the Clinical Pilot project could generate results on a clinical timeline in practice and to evaluate the prevalence of actionable findings. The study concluded with just over 300 patients, and the publication is currently in review. After the completion of G4K, clinical genomics became a standard service. Real-time Clinical Genomics (RTCG) is a first of its kind initiative, whereby St. Jude began releasing data from the clinical NGS service consented for research use to St. Jude Cloud in monthly batches to give researchers access to valuable data as quickly as possible. Subsequent publications are expected in the future.
Dataset related to article "Morphometric vertebral fractures in patients with castration-resistant prostate cancer undergoing treatment with radium-223: a longitudinal study in the real-life clinical practice"
<p>This record contains data related to article "Morphometric vertebral fractures in patients with castration-resistant prostate cancer undergoing treatment with radium-223: a longitudinal study in the real-life clinical practice"</p> <p><strong>Abstract</strong></p> <p><strong>Purpose: </strong>Radium-223 was associated with high incidence of non-vertebral fractures in patients with castration-resistant prostate cancer (CRPC). However, it is still unclear whether radium-223 may induce skeletal fragility regardless of other therapies for CRPC. We aimed at evaluating the prevalence, incidence, and determinants of vertebral fractures (VFs), i.e., the most frequent complication of skeletal fragility, in CRCP patients undergoing radium-223 therapy in the real-life clinical practice.</p> <p><strong>Methods: </strong>We retrospectively reviewed 49 CRPC patients with symptomatic bone metastases treated with radium-223. Patients received median number of four radium-223 doses (range: 2-6) and were followed-up for a median period of 11 months (range: 6-44). VFs were assessed by a quantitative morphometry using lateral images of spine 11C-Choline PET/CT, excluding from the analysis the vertebral bodies affected by bone metastases.</p> <p><strong>Results: </strong>Before radium-223 administration, 24 patients (49%) had VFs significantly associated with duration of androgen deprivation therapy (ADT; odds ratio 1.29) and previous abiraterone therapy (odds ratio 3.80). During radium-223 therapy, incident VFs occurred in 25% of patients, in relationship with prevalent VFs (hazard ratio 6.89) and change in serum total alkaline phosphatase values (hazard ratio 0.97), whereas the correlations with ADT and abiraterone therapy were lost. Noteworthy, the risk of VFs did not correlate with the therapeutic end points of radium-223.</p> <p><strong>Conclusions: </strong>This study provides a first evidence that in real-life clinical practice, radium-223 therapy may induce skeletal fragility with high risk of VFs, likely by inhibition of bone formation and independently of ADT and abiraterone therapy.</p>
G-REx: A Real-World Dataset of Group Emotion Experiences based on Physiological Data
<p>G-REx is a dataset for real-world affective computing. We collected physiological data (photoplethysmography and electrodermal activity) using a wrist-worn device during long-duration movie sessions. Emotion annotations were retrospectively performed on segments with elevated physiological responses. The dataset includes over 31 movie sessions, totaling 380 h+ of data from 190+ subjects. The data were collected in a group setting, which can give further context to emotion recognition systems.</p> <p> </p> <p><strong>TO HAVE ACCESS PLEASE FILL OUT: <a href="https://forms.gle/nhBRW2S2JrE5QB878" target="_blank" rel="noopener">https://forms.gle/nhBRW2S2JrE5QB878</a></strong></p>
Time series of simulated ionospheric fountain effect along with real-data TEC map and station-pair ionospheric gradients
<p>This dataset was used to generate a simulated Total Electron Content (TEC) distribution due to the Fountain Effect in equatorial and low-latitude regions. It is in Figure 6 from the article "Ground-Based Augmentation System Operation in Low Latitudes - Part 2: Space Weather, Ionospheric Behavior and Challenges" currently <em>in press</em> by the <em>Journal of Aerospace Technology and Management</em> (JATM).</p> <p>The same dataset also contains a TEC map over Brazil and station-pair ionospheric gradients measured from two stations in São José dos Campos/SP Brazil. Both data are from the night between November 21 and 22, 2014, and are part of Figure 10 of the same article cited above.</p>
Dataset related to article "Real-life Effectiveness and Safety of Risankizumab in Moderateto- severe Plaque Psoriasis: A 40-week Multicentric Retrospective Study"
<p>This record contains data related to article "Real-life Effectiveness and Safety of Risankizumab in Moderateto- severe Plaque Psoriasis: A 40-week Multicentric Retrospective Study"</p> <p>Risankizumab is a humanized monoclonal antibody that binds the p19 subunit of interleukin-23. It is approved for treatment of moderate-severe chronic plaque psoriasis. This retrospective study included 66 consecutive adults with moderate-to-severe psoriasis vulgaris treated with risankizumab in monotherapy up to week 40 in a “real-life” setting. At week 40, 98.7%, 85.7% and 62.3% of patients achieved a Psoriasis Area and Severity Index (PASI) reduction ≥ 75% (PASI 75), PASI 90 and PASI 100, respectively. Patients who had not responded to 2 or more previous biologic treatments were significantly less likely to achieve PASI 75/90 at week 16 and PASI 90/100 at week 40 compared<br> with those who had been previously treated with<br> only 1 biologic, and compared with those treated with risankizumab as a first-line biologic. Increasing body mass index decreased the chances of reaching PASI 90 at week 40. No significant safety findings were recorded throughout the study, and none of the patients had to interrupt the treatment. These data suggest that the efficacy of risankizumab for plaque psoriasis in “real-life” clinical practice could differ from pivotal clinical trials data.</p>
Dataset related to article "Biologic therapies for plaque type psoriasis in patients with previous malignant cancer: longterm safety in a single- center real-life population"
<p>This record contains data related to article "Biologic therapies for plaque type psoriasis in patients with previous malignant cancer: longterm safety in a single- center real-life population"</p> <p>ABSTRACT</p> <p>Introduction: This is an Italian single-center retrospective study evaluating safety and efficacy of biologic agents in psoriatic patients with a previous diagnosis of malignant cancer.</p> <p>Aim: Management of moderate and severe psoriasis patients with a past medical history of malignancies could be difficult because biologic agents are historically associated with a presumptive increased risk of neoplastic reactivation or of a new incoming cancer. The aim of this study is to assess the safety of biologics in patients with a previous cancer diagnosis.</p> <p>Material and methods: The study analyzed 16 moderate to severe psoriasis patients with a diagnosis of malignant cancer in the previous 10 years treated with biologic agents for up to at least 96 weeks. In five of these patients, cancer was diagnosed in the previous 5 years.</p> <p>Results: We observed a rapid decrease in PASI (psoriasis area severity index) reaching a 90% improvement in 100% of patients. Oncologic follow up did not show any worsening or reactivation of cancer during the entire observation period. No new malignancies were observed in the analyzed sample.</p> <p>Conclusions: Biologic agents in our experience have demonstrated to be safe and effective in psoriatic patients with a past medical history of malignant cancer.</p>
Dataset related to article "Impact of delay in follow-up due to COVID-19 pandemic on skin cancer progression: a real-life experience from an Italian hub hospital "
<p>This record contains data related to article "Impact of delay in follow-up due to COVID-19 pandemic on skin cancer progression: a real-life experience from an Italian hub hospital "</p> <p>Abstract</p> <p><strong>Background: </strong> The COVID-19 pandemic required the setting of a national lockdown in Italy from March 9, 2020, until May 18, 2020; therefore, most of the non-COVID-19 activities were postponed. As a consequence, many follow-up visits in patients with previously excised skin cancers were delayed. The aim of this retrospective real-life case-control study is demonstrating that delay in follow-up led to an increased incidence of advanced melanoma and keratinocyte cancers on the total of surgically excised skin cancers.</p> <p><strong>Methods: </strong> The incidence of excised advanced melanoma and keratinocyte cancers in our dermato-surgery division in the period May 18 to November 18, 2020, was compared to the same time span of 2019. All data were collected from the electronic database of our department. Odds ratio with 95% confidence interval was used to assess the risk of excised advanced skin cancers in 2020 compared to 2019.</p> <p><strong>Results: </strong> From May to November 2019, we performed 265 surgical excisions, while during the pandemic in 2020, we completed 280 surgeries. The number of advanced skin cancers excised between May 18 and November 18, 2020, was significantly higher compared with the same period in 2019 (54 vs. 22, OR: 2.64; 95% CI: 1.56-4.47; P = 0.0003). Significant differences were also observed regarding the number of surgically removed advanced BCCs (OR 2.15; 95% CI 1.14-4.07; P = 0.0187) and advanced SCCs (OR 4.60; 95% CI 1.31-16.18; P = 0.0175).</p> <p><strong>Conclusion: </strong> These results confirm that delay in follow-up and, consequently, postponed surgical excisions are related to an increased incidence of advanced skin tumors, resulting in poorer prognosis lifelong. Follow-up visits should be carried on even during COVID-19 pandemic, avoiding significant delays as much as possible. </p>
Deep Learning for Real Time 3D Multi-Object Detection, Localization, and Tracking : Application to Smart Mobility
<p>In core computer vision tasks, we have witnessed significant advances in object detection, localisation and tracking. However, there are currently no methods to detect, localize and track objects in road environments, and taking into account real-time constraints. In this paper, our objective is to develop a deep learning multi object detection and tracking technique applied to road smart mobility. Firstly, we propose an effective detector-based on YOLOV3 [1] which we adapt to our context. Subsequently, to localize successfully the detected objects, we put forward an adaptive method aiming to extract 3D information, i.e., depth maps. To do so, a comparative study is carried out taking into account two approaches: Monodepth2 [2,3] for monocular vision and MADNEt [4] for stereoscopic vision. These approaches are then evaluated over datasets containing depth information in order to discern the best solution that performs better in real-time condition. Object tracking is necessary in order to mitigate the risks of collisions. Unlike, traditional tracking approaches which requires target initialization beforehand, our approach consists of using information from object detection and distance estimation to initialize targets and to track them later. Expressly, we propose here to improve SORT [5] approach for 3D object tracking. We introduce an extended Kalman filter [6] to better estimate the position of objects. Extensive experiments carried out on KITTI dataset [7] prove that our proposal outperforms state-of-the-art approches. </p>
LLAMAFUZZ real-world programs supplementary experiment data
<div> <p>This is the raw experimental data of LLAMAFUZZ and AFL++ on a set of real-world programs. We choose FuzzBench as running framework to ensure the fairness.</p> </div>
ACPAS dataset: Aligned Classical Piano Audio and Score (real recording subset)
<p><strong>ACPAS</strong> is a dataset with aligned audio and scores for classical piano music containing 497 distinct music scores aligned with 2189 performances, in total 179.77 hours. For each performance, we provide the corresponding performance audio (real recording or synthesized recording), performance MIDI, and MIDI score, together with rhythm and key annotations.</p> <p>This is the <strong>Real recording subset</strong> of the ACPAS dataset. To download the full dataset and for dataset details, please refer to the dataset webpage at <a href="https://cheriell.github.io/research/ACPAS_dataset">https://cheriell.github.io/research/ACPAS_dataset</a></p> <p>For any questions, suggestions, or comments, please do not hesitate to contact <a href="mailto:lele.liu@qmul.ac.uk">lele.liu@qmul.ac.uk</a></p> <p><strong>How to cite:</strong></p> <p>- Lele Liu, Veronica Morfi, and Emmanouil Benetos, "ACPAS: A Dataset of Aligned Classical Piano Audio and Scores for Audio-to-Score Transcription," in ISMIR Late-breaking Demo, 2021.</p> <p><strong>Funding:</strong></p> <p>L. Liu is a research student at the UKRI Centre for Doctoral Training in Artificial Intelligence and Music, supported jointly by the China Scholarship Council and Queen Mary University of London.</p> <p> </p>
Dataset related to article "Real-Life Effectiveness and Safety of Risankizumab in 131 Patients Affected by Moderate-to-Severe Plaque Psoriasis: A 52-Week Retrospective Study"
<p>This record contains raw data related to article “Real-Life Effectiveness and Safety of Risankizumab in 131 Patients Affected by Moderate-to-Severe Plaque Psoriasis: A 52-Week Retrospective Study"</p> <p>Abstract</p> <p><strong>Introduction: </strong> Risankizumab is a humanized monoclonal antibody that selectively targets interleukin-23. It is approved for treatment of moderate-to-severe plaque psoriasis. We conducted a 52-week monocentric retrospective study to evaluate the effectiveness and safety of risankizumab in a real-life setting.</p> <p><strong>Methods: </strong> Our study included 131 adults with moderate-to-severe plaque psoriasis all treated with risankizumab for at least 52 weeks. Patient characteristics and PASI (Psoriasis Area and Severity Index) at each visit were recorded. The percentages of patients achieving 75%/90%/100% (PASI 75/90/100) improvement in PASI with respect to baseline were registered.</p> <p><strong>Results: </strong> At week 52, 93.9%, 78.6%, and 61.1% of patients achieved PASI 75/90/100, respectively. An absolute PASI ≤ 2 was reached by 90.8% at week 52. The higher body mass index and the presence of cardio-metabolic comorbidities did not interfere with the odds of reaching PASI 75/90/100 at each time-point. At week 52, comparable percentages of patients achieved PASI 100, regardless of the involvement of difficult-to-treat-areas. No significant safety findings were recorded and none of the patients had to interrupt the treatment because of adverse events.</p> <p><strong>Conclusions: </strong> Our findings confirmed that risankizumab is a safe and effective therapeutic option for the treatment of a wide "real-life" cohort of patients with psoriasis.</p>
Dataset related to article "Implementing Pre-Therapeutic UGT1A1 Genotyping in Clinical Practice: A Real-Life Study"
<p>This record contains raw data related to article “Implementing Pre-Therapeutic<em> UGT1A1</em> Genotyping in Clinical Practice: A Real-Life Study"</p> <p>Current guidelines recommend pre-therapeutic <em>UGT1A1</em> genotyping to guide irinotecan dosing, but the usefulness of this approach remains to be clarified. In 247 patients with advanced gastrointestinal cancers undergoing irinotecan-based chemotherapy, we prospectively performed <em>UGT1A1*28</em> genotyping and we analyzed the incidence of severe neutropenia according to genotype-guided dose reductions. Overall, 28 (11.3%) and 92 (37.2%) patients were homozygous or heterozygous <em>UGT1A1*28</em> carriers, respectively. Grade ≥ 3 neutropenia was reported in 39% of homozygous patients receiving an upfront dose reduction of irinotecan (median 40%, range 22-58%), in 20% of heterozygous or wild-type patients receiving full dose (OR<sub>vs*28/*28 genotype</sub> = 0.38; 95% CI: 0.14-1.03; <em>p</em> = 0.058), and in 15.3% of those receiving a reduced dose for clinical reasons (OR <sub>vs*28/*28 genotype</sub> = 0.28, 95% IC: 0.12-0.67; <em>p</em> = 0.004). Occurrence of severe neutropenia was inversely associated with dose reduction in <em>UGT1A1*28</em> homozygous carriers (OR<sub>x10 unit</sub> = 0.62, 95% CI: 0.27-1.40, <em>p</em> = 0.249) and <em>UGT1A1</em> heterozygous or wild-type patients (OR<sub>x10 unit</sub> = 0.87, 95% CI: 0.59-1.28, <em>p</em> = 0.478). Incidence of severe neutropenia was related to irinotecan doses and <em>UGT1A1</em> polymorphisms. Upfront irinotecan dose reductions do not reduce the burden of grade ≥ 3 neutropenia in <em>UGT1A1*28</em> homozygous carriers.</p>
Revisiting Ion-Pair Interactions in Phase Transfer Catalysis: From Ionic Compounds to Real Catalyst Systems
<p>Supporting information for the paper: Revisiting Ion-Pair Interactions in Phase Transfer Catalysis: From Ionic Compounds to Real Catalyst Systems</p>
Case Analysis on Real Life Incidence of Photodynamic Therapy (PDT) Safety Outcomes
ClinicalTrials.gov study NCT01203163. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Real-time quantitative PCR analysis of human adipose derived stem cells microvesicles
GEO Series GSE59811. Homo sapiens. 4 samples. Type: Other.
Real-time quantitative PCR analysis of the expression of neurotransmitter receptor and regulator genes in 4 week old male MeCP2 A140V mutant mouse brain cortex
GEO Series GSE35772. Mus musculus. 6 samples. Type: Expression profiling by RT-PCR.
Real-time quantitative PCR analysis of the expression of cytoskeleton regulator genes in 4 week old male MeCP2 A140V mutant mouse brain cortex
GEO Series GSE35770. Mus musculus. 6 samples. Type: Expression profiling by RT-PCR.
Real-time quantitative PCR analysis of human colon cancer cells for autophagy related genes
GEO Series GSE51141. Homo sapiens. 2 samples. Type: Expression profiling by RT-PCR.
Real-time quantitative PCR analysis of Chromatin-associated snoRNA in human NB4 cells using Arraystar_384 platform
GEO Series GSE173730. Homo sapiens. 8 samples. Type: Other.
Real-time microRNA quantitative PCR array of serum exosomes II
GEO Series GSE167162. Mus musculus. 6 samples. Type: Other.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.