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34,558 results for “therapy”
Massively parallel sequencing data of the HIV-1 pol region generated from the plasma of therapy-naïve chronically infected Brazilian blood donors
<p>The submitted massively parallel sequencing (MPS) data were partial data from the pol region of HIV-1 plasma viruses. Samples were obtained from 18 therapy-naive HIV-1 Brazilian blood donors with longstanding infection. Illumina ultra-deep sequencing technology (MiSeq platform) was used to generate the sequences. </p>
Beam properties within the momentum acceptance of a clinical gantry beamline for proton therapy
<p>Publicly accessible data associated with the publication: </p><p><strong>Beam properties within the momentum acceptance of aclinical gantry beamline for proton therapy</strong>. </p><p>AC Giovannelli, V Maradia, D Meer, S Safai, S Psoroulas, M Togno, C Bula, DC Weber, AJ Lomax, G Fattori. Med Phys 2022;49(3):1417-1431. <a href="https://doi.org/10.1002/mp.15449">https://doi.org/10.1002/mp.15449</a></p><p>Data generated within the project "New concept for adaptive real time tumour tracking" funded by the Swiss National Science Foundation (SNSF) under grant agreement 200021_185082: <a href="https://data.snf.ch/grants/grant/185082">https://data.snf.ch/grants/grant/185082</a> </p><p> </p>
Overcoming clinical resistance to EZH2 inhibition using rational epigenetic combination therapy
<p>Supplementary data for Kazansky et al, "Overcoming clinical resistance to EZH2 inhibition using rational epigenetic combination therapy" and "Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas." Raw RNA-seq data from G401 cells can be found at the Gene Expression Omnibus (GEO) repository, accession number GSE213845. RNA-seq data from patient tumor samples has been deposited to the Database of Genotypes and Phenotypes (dbGaP), accession number phs003188.v1.p1.</p> <p>All files are labeled with their corresponding figures.</p> <p>"DESeq_processing_FINAL.R" was used for analysis of patient RNA-seq data, using "20230131_SampleTable.csv" and all "*_htseq.txt" files as input.</p> <p>"Tumor_growth_analysis_FINAL_UPDATED" was used for analysis of tumor growth kinetics using the aucVardiTest function. This was used for both of the manuscripts desscribed above.</p>
Data from: Quantitative PCR as a marker for preemptive therapy and its role in therapeutic control in Trypanosoma cruzi/HIV coinfection
<p><strong>Background: </strong><em>Trypanosoma cruzi</em> and HIV coinfection can evolve with depression of cellular immunity and increased parasitemia. We applied quantitative PCR (qPCR) as a marker for preemptive antiparasitic treatment to avoid fatal Chagas disease reactivation and analyzed the outcome of treated cases.</p> <p><strong>Methodology:</strong> This mixed cross-sectional and longitudinal study included 171 Chagas disease patients, 60 coinfected with HIV. Of these 60 patients, ten showed Chagas disease reactivation, confirmed by parasites identified in the blood, cerebrospinal fluid, or tissues, 12 exhibited high parasitemia but no reactivation, and 38 had low parasitemia and no reactivation.</p> <p><strong>Results</strong>: We showed, for the first time, the success of the timely introduction of benznidazole in the non-reactivated group with high levels of parasitemia detected by qPCR and the absence of parasites in reactivated cases with at least 58 days of benznidazole. HIV+ and HIV+ without reactivation had a 4.0 – 5.1 higher chance of having parasitemia than HIV seronegative cases. A positive correlation was found between parasite and viral loads. Remarkably, treated <em>T. cruzi/</em>HIV-coinfected patients had 77.3% conversion from positive to negative parasitemia compared to 19.1% of untreated patients. Additionally, untreated patients showed ~13.6 times higher odds of having positive parasitemia in the follow-up period compared with treated patients. Treated and untreated patients showed no differences regarding the evolution of Chagas disease. The main factors associated with all-cause mortality were higher parasitemia, lower CD4 counts/µL, higher viral load, and absence of antiretroviral therapy.</p> <p><strong>Conclusion</strong>: We recommend qPCR prospective monitoring of <em>T. cruzi</em> parasitemia in HIV+ patients and point out the value of pre-emptive therapy for patients with temporary high parasitemia. In parallel, an early antiretroviral therapy introduction is advisable, aiming at viral load control, immune response restoration, and major survival. We also suggest an earlier antiparasitic treatment for all coinfected patients, followed by effectiveness analysis alongside antiretroviral therapy.</p>
Data for 'Simulating Photodynamic Therapy for the Treatment of Glioblastoma using Monte Carlo Radiative Transport'
<p>Files added include the data used to make each data plot within the paper.</p> <p>Figure 5:</p> <p>pen_depth_plot.py</p> <p>pen_depth_plot_y.py</p> <p>pen_depth_plot_z.py</p> <p>jmean_run2NB.dat</p> <p>o21_full_run2NB.dat</p> <p>rhokap_run2NB.dat</p> <p>tumour.dat</p> <p> </p> <p>Figure 6:</p> <p>tumour_percentage.py</p> <p>tumkill_full_994.dat</p> <p>tumkill_full_1.dat</p> <p> </p> <p>Figure 7:</p> <p>temp_run2NB.dat</p> <p>max_temp_timeNB.dat</p> <p> </p> <p>Figure 8:</p> <p>power_run2NB.dat</p> <p>s0_slice_run2NB.dat</p> <p>o23_slice_run2NB.dat</p> <p>o21_slice_run2NB.dat</p> <p>temp_slice_run2NB.dat</p> <p> </p> <p>Figure 9:</p> <p>percent_left_run2NB.dat</p> <p>percent_left_run11NB.dat</p> <p>percent_left_run12NB.dat</p> <p>percent_left_run13NB.dat</p> <p> </p> <p>Figure 10:</p> <p>percent_left_run1NB.dat</p> <p>percent_left_run2NB.dat</p> <p>percent_left_run3NB.dat</p> <p>percent_left_run4NB.dat</p> <p> </p> <p>Figure 11:</p> <p>max_temp_time_run1NB.dat</p> <p>max_temp_timeNB.dat</p> <p>percent_left_run1NB.dat</p> <p>percent_left_run2NB.dat</p> <p> </p> <p>Figure 12:</p> <p>percent_left_run2NB.dat</p> <p>percent_left_run10NB.dat</p> <p>max_temp_time_run10NB.dat</p> <p>max_temp_timeNB.dat</p> <p> </p> <p>Figure 13:</p> <p>percent_left_run2NB.dat</p> <p>max_temp_timeNB.dat</p> <p>percent_left_run9NB.dat</p> <p>max_temp_time_run9NB.dat</p> <p> </p> <p>Figure 14:</p> <p>percent_left_run2NB.dat</p> <p>percent_left_run14NB.dat</p> <p>percent_left_run15NB.dat</p> <p> </p> <p>Figure 15:</p> <p>percent_left_run2NB.dat</p> <p>percent_left_run56NB.dat</p> <p>percent_left_run62NB.dat</p> <p>max_temp_time_run56NB.dat</p> <p>max_temp_timeNB.dat</p> <p> </p>
Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms
<p>Single-cell RNA (scRNA) and single-cell TCR (scTCR)-sequencing data data for patients number 11, 12 and 14 from the article " Identification of clinically relevant T-cell receptors for personlized T-cell therapy". </p> <p>Each compressed file contains two subfolders. One is for the scRNA-seq (GEX-sequencing) and the other for the scTCR-seq (VDJ-sequencing). </p> <p>In the original article, scRNA-seq and scTCR-seq were aligned to the GRCh38 reference genome using <em>cellranger count </em>(10X Genomics, version 3.0.1) and <em>vdj </em>(10X Genomics, version 3.1.0) respectively. The subsequent data processing was performed using Seurat library (V.4.3.0) on R Statistical Software (V.4.0.3).</p>
Replication Data for: Precision Oncology, Cell Signaling and Targeted Therapy: A Holistic Approach to Molecular Cancer Therapeutics
<p>In recent decades, there has been a deluge in the large-scale production of anticancer agents, primarily due to advances in genomic technologies enabling precise targeting of oncogenic pathways involved in disease progression. This initiated a paradigm shift in cancer research and therapeutics based on the ability to study molecular changes throughout the genome. It provided a unique opportunity in the field of translational cancer research and have led to the concept of precision medicine in cancer therapy, raising hopes of developing better diagnostic and therapeutic means for the management of cancer. The purpose of this article is to briefly review the tools and techniques involved in precision oncology research and their applications in the field of cancer treatment. </p>
Evaluation of comparative Efficacy of two routes of administration of Carathmus Tinctorius (Medicated Enema and Nasal Administration) as an Adjuvant Therapy with Standard Care With Physiotherapy in the Rehabilitation of Thrombolytic Stroke (Pakshaghat): A Randomized Controlled Trial Protocol
Open the record for dataset details and reuse information.
Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplants: Spatial transcriptomic dataset and images
<p>The outputs of the NanoString GeoMx DSP platform were concatenated into three xlsx files, each illustrating a separate experiment along with their sample annotations. This technique analyzes protein or RNA abundance within regions of interest (ROIs) or specific cell segments selected based on histological features and immunofluorescence. In this repository, the concatenated GeoMx output files are presented, along with PowerPoint presentations for each biopsy that show immunofluorescence images of the selected ROIs and/or cell segments.</p> <ul> <li><strong>Protein_Full ROI:</strong> This experiment measured the abundance of 41 proteins in discrete regions of interest (ROIs) within transplant kidney biopsies.</li> <li><strong>Protein_Rare cell:</strong> This experiment measured the abundance of 40 proteins in specific cell segments, such as CD4+FoxP3- cells vs. CD4+FoxP3+ cells, within transplant kidney biopsies.</li> <li><strong>RNA:</strong> This experiment measured the abundance of 90 genes in discrete ROIs within transplant kidney biopsies.</li> </ul>
Supplementary Data for "Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance"
<p><strong>We performed functional genomic profiling of diverse leukemias using label tracing techniques. We identified AML stem cell quiescence is defined by distinct promoter-centered chromatin and gene expression dynamics, and controlled by a novel transcription factor network, which is associated with disease persistence and chemotherapy resistance in multiple patients. </strong></p>
Impact of New Developments in the Commissioning of Operational Radiation Protección in Compact Proton Therapy Centers (CPTC)
<p>Proton therapy is in continuous ever evolving to improve its performance. Some prominent current trends involve cutting-edge delivery methods or building compact proton centers. New developments have a direct impact in radiation protection of proton facilities and actions should be developed continuously with the aim that new centers meet all the requirements. The study of radiological protection in multi-room centers has been widely studied elsewhere, however, compact centers have specific features that pose a challenge in radiation protection, and the present work suggest different contributions to the body of knowledge in these compact facilities. Compact Proton Therapy Centers (CPTC) act out latest advances in particles: Usually have one single room, small footprint and a standard configuration, higher radiation density (Sv/m<sup>2</sup>), using the most advanced equipment and machinery to reduce their size, the delivery mode of protons is Pencil Beam Scanning (PBS), and there is a mix of professional exposed workers (clinical and technical staff) in these centers.</p> <p>The present work is framed into the project Contributions to operational radiation protection and neutron dosimetry in compact proton therapy centers (CPTC), which is focused on assessing the impact of these innovations on the operational radiation protection and commissioning of the compact facilities. Thus, several tasks have been carried out over the last three years, as checking and evaluation of shielding, comparing ambient dose equivalent of several CPTC, analyzing activation with different types of concrete, and activation in machinery, air and water of the facility, characterizing wide range rem-meters and neutron area monitors to measure neutron fields, studying new proton delivery techniques and their neutron fields, or assessing personal dosemeters, among others. The aim of the work is to present outcomes achieved in the aforementioned areas. As a result, a commissioning process of the operational radiation protection in compact centers will be suggested, lined up with the requirements by the Spanish Regulatory Body.</p> <p>Considering topics as new methods of application of dose in development (proton arc therapy, flash-therapy with protons), new materials for barriers and shielding or recent radiation monitoring equipment, future works must be carried out to study their impact on operational radiation protection and recommendations such as ICRP Publication 127, Radiological Protection in Ion Beam Radiotherapy, should be updated periodically taking into account the new methods and technologies developed.</p>
Anti-TNF therapy for inflammatory bowel disease in patients with neurodegenerative Niemann-Pick disease Type C
<p>Abstract:</p> <p>Background: Blockade of tumour necrosis factor (anti-TNF) is effective in patients with Crohn’s Disease but has been associated with infection risk and neurological complications such as demyelination. Niemann-Pick disease Type C1 (NPC1) is a lysosomal storage disorder presenting in childhood with neurological deterioration, liver damage and respiratory infections. Some NPC1 patients develop severe Crohn’s disease. Our objective was to investigate the safety and effectiveness of anti-TNF in NPC1 patients with Crohn’s disease.</p> <p>Methods: Retrospective data on phenotype and therapy response were collected from patients with genetically confirmed NPC1 defects and intestinal inflammation. We investigated TNF secretion in peripheral blood mononuclear cells treated with NPC1 inhibitor in response to bacterial stimuli.</p> <p>Results: NPC1 inhibitor treated PBMCs show significantly increased TNF production after lipopolysaccharide or bacterial challenge providing a rationale for anti-TNF therapy. We identified 5 NPC1 patients with CD-like intestinal inflammation treated using anti-TNF therapy (mean age of onset 8.6 years, mean treatment length 27.2 months, overall treatment period 11.3 patient years). Anti-TNF therapy was associated with reduced gastrointestinal symptoms with no apparent adverse neurological events. Therapy improved intestinal inflammation in 4 patients.</p> <p>Conclusion: Anti-TNF therapy appears safe in patients with NPC1 and is an effective treatment strategy for the management of intestinal inflammation in these patients.</p>
Regulatory and Technical boundaries for phage therapy and FMT in animals - 17.10.2021 (Part B)
<p>Roundtable discussion on Fecal Microbiota Transplantation chaired by Klaus Helmann (KLIFOVET, DE).</p> <p>The roundtable participants enlisted below:</p> <ul> <li>Thomas Thymann (University of Copenhagen, DK)</li> <li>Mirja Huhtinen (Orion Pharma, FI)</li> <li>Jordi Torren (European Medicines Agency, NL)</li> <li>Alexandre Thibodeau (University of Montreal, CA)</li> <li>Lotte Dahl (Danish Medicines Agency, DK)</li> <li>Martin Bronislaw Oleksiewicz (Danish Medicines Agency, DK)</li> </ul> <p>The invited speakers and the attendees of the workshop have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679.</p> <p>The video is available on YouTube: <strong><a href="http://youtu.be/0fzARCNlDg8">https://youtu.be/0fzARCNlDg8</a></strong></p> <p>The presentations and opinions disclosed in this video are only for general information purpose and do not constitute a joint declaration on behalf of the beneficiaries of the AVANT project.</p> <p>For any further questions please contact us <strong><a href="avant@rtds-group.com">avant@rtds-group.com</a></strong></p>
Regulatory and Technical boundaries for phage therapy and FMT in animals - 17.10.2021 (Part A)
<p>Roundtable discussion on Phage Therapy chaired by Klaus Helmann (KLIFOVET, DE).</p> <p>The roundtable participants enlisted below:</p> <ul> <li>Michela Gambino (University of Copenhagen, DK)</li> <li>Frenk Smrekar (JAFRAL, SI)</li> <li>Javier Pozo Gonzalez (European Medicines Agency, NL)</li> <li>Lotte Dahl (Danish Medicines Agency, DK)</li> <li>Martin Bronislaw Oleksiewicz (Danish Medicines Agency, DK)</li> </ul> <p>The invited speakers and the attendees of the workshop have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679.</p> <p>The video is available on YouTube: <strong><a href="http://youtu.be/ySXKKC8CGf8">https://youtu.be/ySXKKC8CGf8</a></strong></p> <p>The presentations and opinions disclosed in this video are only for general information purpose and do not constitute a joint declaration on behalf of the beneficiaries of the AVANT project.</p> <p>For any further questions please contact us <strong><a href="avant@rtds-group.com">avant@rtds-group.com</a></strong></p>
Dataset related to article "Intracranial Sonodynamic Therapy With 5-Aminolevulinic Acid and Sodium Fluorescein Safety Study in a Porcine Model"
<p>pigs treatments</p>
Remodeling dental anatomy vs sham therapy for chronic temporomandibular disorders: A placebo-controlled randomized clinical trial
<div><em>Background</em></div> <div>Evidence regarding the etiology or effective treatments for chronic orofacial pain, the majority diagnosed as temporomandibular disorder (TMD), is limited.</div> <div> </div> <div><em>Purpose</em></div> <div>To investigate whether occlusal equilibration therapy (ET) and decreasing the (higher) angle of the lateral guidance on the nonworking-side leads to a reduction in chronic TMDs intensity.</div> <div> </div> <div><em>Methods</em></div> <div>It was conducted a randomized, explanatory, single blind with blinded assessment, placebo-controlled trial with strong protection against bias involving patients with chronic TMDs. Participants were randomly assigned to receive equilibration therapy or sham therapy. ET in this study consisted of minimal invasive occlusal remodeling to obtain balanced occlusion with reduction of the steeper angle of lateral mandibular movement with respect to the Frankfort plane. The primary outcome was a change in the pain intensity score (on a 0–10 point scale, with 0 indicating no pain and 10 the worst possible pain) at month 6. Secondary outcomes include maximum unassisted mouth opening and psychological distress.</div> <div> </div> <div><em>Results</em></div> <div>A total of 77 participants underwent randomization, 39 of whom received ET and 38 sham therapy. The trial was stopped early for efficacy, according to preestablished rules when 67 participants (n = 34, n = 33, respectively) had completed the analysis. At month 6, the mean unadjusted pain intensity score was 2.1 in the ET and 3.6 in the sham therapy group (adjusted mean difference, −1.54; 95% confidence interval [CI] −0.5 to −2.6; P = 0.004; ANCOVA model). The mean increase in maximum unassisted mouth opening (main secondary outcome) was significantly higher in the real therapy group (adjusted mean difference 3.1 mm, 95% CI 0.5–5.7, p = 0.02).</div> <div> </div> <div><em>Conclusion</em></div> <div>ET significantly reduced the intensity of facial pain associated with chronic TMDs and increased maximum unassisted mouth opening, as compared with sham therapy, over the course of 6 months. There were no serious adverse events.</div>
Hematopoietic Tumors in a Mouse Model of X-linked Chronic Granulomatous Disease after Lentiviral Vector-Mediated Gene Therapy
<p>Chronic granulomatous disease (CGD) is a rare inherited disorder due to loss-of-function mutations in genes encoding the NADPH oxidase subunits. Hematopoietic stem and progenitor cell (HSPC) gene therapy (GT) using regulated lentiviral vectors (LVs) has emerged as a promising therapeutic option for CGD patients. We performed non-clinical Good Laboratory Practice (GLP) and laboratory-grade studies to assess the safety and genotoxicity of LV targeting myeloid specific Gp91phox expression in X-linked chronic granulomatous disease (XCGD) mice. We found persistence of gene-corrected cells for up to 1 year, restoration of Gp91phox expression and NADPH oxidase activity in XCGD phagocytes, and reduced tissue inflammation after LV-mediated HSPC GT.<br> Although most of the mice showed no hematological or biochemical toxicity, a small subset of XCGD GT mice developed<br> T cell lymphoblastic lymphoma (2.94%) and myeloid leukemia (5.88%). No hematological malignancies were identified in C57BL/6 mice transplanted with transduced XCGD HSPCs. Integration pattern analysis revealed an oligoclonal composition with rare dominant clones harboring vector insertions near oncogenes in mice with tumors. Collectively, our data support the long-term efficacy of LV-mediated HSPC GT in XCGD mice and provide a safety warning because the chronic inflammatory XCGD background may contribute to oncogenesis.</p>
Data sets used to demonstrate the software MadHitter in the manuscript "The Landscape of Receptor-Mediated Precision Cancer Combination Therapy Via a Single-Cell Perspective"
<p>This is a zip archive of nine single-cell RNASeq data sets used in the manuscript entitled:</p> <p>"The Landscape of Receptor-Mediated Precision Cancer Combination Therapy Via A Single-Cell Perspective" by Saba Ahmadi, Pattara Sukprasert, Rahulsimham Vegesna, Sanju Sinha, Fiorella Schischlik, Natalie Artzi, Samir Khuller, Alejandro A. Schaffer, Eytan Ruppin,</p> <p>The README.txt describes the data sets in detail.</p> <p>The associated software can be found at https://github.com/ruppinlab/madhitter</p>
Quality of life in chronic pain treated through pulsed radiofrequency therapy: A retrospective study
<p>Anxiety and depression are often symptoms present in people who suffer from chronic pain, compromising the quality of life of these individuals. The objective of this study was to assess whether a pulsed radiofrequency (PRF) treatment, in addition to psychological support intervention, can decrease chronic pain, thereby improving quality of life and restoring psychological well-being.Fifty outpatients with a diagnosis of chronic pain, without any benefit from traditional drug therapies, were selected to perform a PRF treatment in combination with a psychological intervention. They were evaluated before and after the intervention through the Hamilton Anxiety Rating Scale and the Beck Depression Inventory-II for anxiety and depression symptomatology, respectively, the Short Form Health Survey 36 (SF-36) was used to assess the subject's quality of life, and the Numerical Rating Scale was used for pain assessment.The Wilcoxon signed-rank test showed a significant difference in Beck Depression Inventory-II (P < .001), Hamilton Anxiety Rating Scale (P < .01), and Numerical Rating Scale (P = .004). In the SF-36 scores, we observed a significant difference between T0 and T1 in both mental (P < .001) and physical (P < .001) dimensions.This study shows that a chronic pain reduction leads to a decrease of anxiety-depressive symptoms and an improvement in quality of life. PRF seems to be an appropriate method to reduce the chronic pain that influences psychological well-being and quality of life.</p>
miRNA profiling of human nasopharyngeal carcinoma cell lines HONE1 and CNE2 after X-ray therapy
<p>The package contains two file:</p> <p>Supplementary Table 1. Kruskal Wallis test for cell viability rate</p> <p>Supplementary Table 2. Kruskal Wallis test for apoptosis rate</p> <p>The HONE1 and CNE2 cells were irradiated with X-rays at doses of 4 Gy, 8 Gy, 16 Gy and 20 Gy for 24 h. The cell viability rate and apoptosis rate were compared.</p>
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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.