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34,558 results for “therapy”
Machine Learning Features from Proton Therapy Treatment Simulations with the Bergen DTC Prototype for Range Verification
<p>Extracted features from the simulation data found at DOI: <a href="https://doi.org/10.5281/zenodo.8192778">10.5281/zenodo.8192778</a></p> <p>Each simulation constitutes a single data sample. The following features were extracted.</p> <p>Detector features:</p> <ul> <li>Total number of active pixels</li> <li>Total number of clusters (hits)</li> <li>Number of clusters over threshold (5, 20 pixels)</li> <li>Mean and standard deviation of cluster sizes</li> <li>The number of clusters of any given size (1–72)</li> <li>Mean and standard deviation of x- and y-coordinates over each layer (0–42), and the entire detector</li> <li>Number of active pixels in each layer (0–42)</li> <li>Number of clusters (hits) in each layer (0–42)</li> <li>Total energy deposition of the hits in each layer (0–42)</li> </ul> <p>Higher-level detector features, i.e., function fits (linear, cubic, exponential) with their mean squared residuals over the following quantities:</p> <ul> <li>Active pixels over layer</li> <li>Number of clusters over layer</li> <li>Total deposited energy over layer</li> </ul> <p>201 RSP features extracted from the beam spot, the phantom rotation, and its 3D RSP image.</p> <p>Two datasets are included in two separate archive files:</p> <ul> <li><strong>features.tar.gz:</strong> 715-HN phantom by CIRS Inc. (Norfolk, VA, United States), digitized by Giacometti et al. (2017).</li> <li><strong>features-vhf.tar.gz:</strong> The Visible Human Female (VHF) Head phantom (Ackermann et al. 1995), courtesy of the U.S. National Library of Medicine, resampled to 1 mm voxels and scaled down to 80% size in the simulation.</li> </ul> <p>After extracting features, some outliers were removed from the datasets: 14 samples for 715-HN and 3 samples for VHF. The rest of the samples were split into train (70%), validation (10%), and test (20%) sets, for both phantoms separately, which can be found in separate CSV files: features_train.csv, features_val.csv, features_test.csv (715-HN) and features-vhf_train.csv, features-vhf_val.csv, features-vhf_test.csv (VHF).</p> <p>The last file (features_shifted_test.csv (715-HN) and features-vhf_shifted_test.csv (VHF)) contains 40 additional samples for each data point in the respective test set, representing a simulated lateral shift between 1 mm and 10 mm in 1 mm intervals in all directions along the x- and y-axis of the beam.</p>
Proton Therapy Treatment Simulations with the Bergen DTC Prototype for Range Verification
<p>This dataset contains proton therapy Monte Carlo simulations using GATE (Jan et al. 2004) version 9.2 and Geant4 (Agostinelli et al. 2003; Allison et al. 2006; Allison et al. 2016) version 11.0.0. The treatment targets are the pediatric head phantom 715-HN by CIRS Inc. (Norfolk, VA, United States), digitized by Giacometti et al. (2017), and The Visible Human Female (VHF) head, courtesy of the U.S. National Library of Medicine, resampled to 1 mm voxels and scaled down to 80%. Distal to the phantom, is a simplified geometry of the digital tracking calorimeter designed by the <a href="https://www.uib.no/en/ift/142356/medical-physics-bergen-pct-project">Bergen pCT collaboration</a> for proton computed tomography (Alme et al. 2020).</p> <ul> <li><strong>treatment_simulations.tar.gz:</strong> 36258 simulations with the 715-HN phantom</li> <li><strong>treatment_simulations_vhf.tar.gz:</strong> 35673 simulations with the VHF phantom</li> </ul> <p>Each simulation is a single pencil beam with <span class="math-tex">\(10^7\)</span> primary protons. To determine valid spots to use, probing simulations with <span class="math-tex">\(10^5\)</span> primaries were conducted, where the beam position, energy, and phantom rotation were varied: 10 mm interval in the xy-plane for the beam position, 3 mm water range interval for the beam energy, and 30° rotations of the phantom. If no primary was found in the detecter after the probing simulation, it is a valid spot for the dataset.</p> <p>Resulting hit files, containing simulated detector readout, can be found in the archive files for the respective phantom. Each simulation is accompanied by a metafile in JSON format, specifying all parameters used to produce the output. E.g., beam position and energy can be found in "parameters" -> "beam_spot_x", "beam_spot_y", "beam_energy" and the phantom rotation can be found in "parameters" -> "phantom_rotation_angle".</p> <p>Simulation data has been pre-processed with two steps. First, hits for the same track in the same layer are binned together into a single entry by averaging the positions (posX, posY, posZ) and summing the energy depositions (edep). Second, the energy deposition values are discretized into a cluster size and back into MeV, to represent the energy resolution of the ALPIDE chip (Alme et al. 2020). Clusters of size 0 are removed. Additionally, some of the unused GATE output columns are removed and a column specifying the detector layer is created through the formula layer = 2*volumeID[2] + volumeID[3]. Details about the meaning of the other output columns can be found in the <a href="https://opengate.readthedocs.io/en/latest/data_output_management.html">GATE documentation</a>.</p>
Data from Comparative effectiveness of common therapies for Wilson disease: A systematic review and meta‐analysis of controlled studies
<p>This dataset contains three text files in RIS format. They represent the screening process during study selection for "Comparative effectiveness of common therapies for Wilson disease: A systematic review and meta‐analysis of controlled studies" (<a href="https://doi.org/10.1111/liv.14179">https://doi.org/10.1111/liv.14179</a>). The file DOKU_All TiAb-Screening_20200116_cap contains all 3453 records (merged from original and update search) that were subjected to title-abstract screening. The file DOKU_All FT-Screening_20200116_cap contains all 174 records that were subjected to full-text screening. The file DOKU_All Included_20200116_cap contains all 26 records that were included into the final review.</p> <p>In addition, a PRISMA flow diagram (Fig. 1 in the paper) is available in TIF format.</p>
In silico prediction of ARB resistance: A first step in creating personalized ARB therapy
<p><strong>AT1R Model preparation</strong><br> The crystal structure of human AT1R bound to olmesartan (PDB: 4ZUD) was downloaded from the RCSB Protein Data Bank. 4ZUD contains apocytochrome b562RIL fused to the amino terminus, and many of the flexible regions, as well as helix 8, are not resolved. In order to generate an appropriate starting structure, olmesartan and the apocytochrome b562RIL fusion were removed from 4ZUD, and the missing regions were added to the protein with MOE software (Chemical Computing Group ULC, Montreal, Canada). Specifically, the N-Terminus (residues 1 to 25), intracellular loop 2 (residues 134 to 140), extracellular loop 2 (residues 186 to 188), intracellular loop 3 (residues 223 to 234), and helix 8 (residues 305 to 316) were added to the AT1R in accordance to the human AT1R sequence and PDB:4YAY. The remaining carboxyl-tail of the AT1R (residues 317 to 359) was not modeled. The AT1R model then underwent an energy minimization within MOE using the Amber10:Extended Huckel Theory (EHT) force field.</p> <p><strong>Molecular dynamic (MD) simulations and analysis</strong><br> The MOE minimized AT1R was loaded into CHARMM-GUI. An 80 Å by 80 Å lipid bi-layer composed of 13% cholesterol and 87% Phosphatidylcholine (POPC) was generated around the receptor. Water was packed 17.5 Å above and below the lipid bi-layer, and 150 mM Na+ and Cl- ions were added to the system via Monte-Carlo ion placing. The all-atom CHARMM C36 force field for proteins and ions, and the CHARMM TIP3P force field for water were selected. A hard non-bonded cutoff of 8.0 angstroms was utilized. All molecular dynamics simulations were performed using the PMEMD module of the AMBER16 package with support for MPI multi-process control and GPU acceleration code. Orthorhombic periodic boundary conditions with a constant pressure of 1 atm was set via the NPT ensemble and temperature was set to 310.15°K (37°C) using Langevin dynamics. The SHAKE algorithm was used to constrain bonds containing hydrogens. The dynamics were propagated using Langevin dynamics with Langevin damping coefficient of 1 ps-1 and a time step of 2 fs. Before the production run, the AT1R model was minimized for 5000 steps using the steepest descent method and then equilibrated for 600 ps. The protein coordinates were saved in 10 ps intervals. The production run lasted 150 ns, at which point all three replicas were stable for at least the last 20 ns.</p>
Plasmodium falciparum infection in febrile Congolese children: prevalence of clinical malaria ten years after introduction of Artemisinin-combination therapies
<p>dataset used in the paper.</p>
Dataset of the scientific paper "A Comparative Analysis of 2D and 3D Tasks for Virtual Reality Therapies Based on Robotic-Assisted Neurorehabilitation for Post-stroke Patients" (Front. Aging Neurosci.)
<p> There are three files with the following information:<br> - data_2d.bin, binary file with information of the different parameters of the nine subjects during 2d tasks<br> - data_3d.bin, binary file with information of the different parameters of the nine subjects during 3d tasks<br> - survey.bin, binary file with the score of the System Usability Scale (SUS) survey of each subject</p>
Research data supporting "Enzyme Prodrug Therapy Engineered into Electrospun Fibers with Embedded Liposomes for Controlled, Localized Synthesis of Therapeutics"
<p>Research data supporting the publication: Chandrawati R. et al., 2017, Enzyme Prodrug Therapy Engineered into Electrospun Fibers with Embedded Liposomes for Controlled, Localized Synthesis of Therapeutics, Advanced Healthcare Materials. DOI: 10.1002/adhm.201700385</p>
Single-cell mouse and PC9 data for "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability"
<p>This repository includes the processed data (including copy number profiles and related analysis) for the E/EP mouse tumors and for the PC9 resistance cell lines for all the analyses of the manuscript "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability".</p><p>The code for the related analyses is available in GitHub at https://github.com/zaccaria-lab/TP53loss_WGD</p>
Different components of cognitive-behavioural therapy affect specific cognitive mechanisms: supporting data
<p>This repository holds data associated with the manuscript "Different components of cognitive-behavioural therapy affect specific cognitive mechanisms" (<a href="https://osf.io/preprints/psyarxiv/ydct5">https://osf.io/preprints/psyarxiv/ydct5</a>).</p><ul><li>rew-eff-planningX .csv files represent data from experiments testing effects of a planning/goal-setting intervention on reward-effort decision-making (X=1, initial discovery sample, X=2, replication sample)</li><li>causal-attr-X .csv files represent data from experiments testing the effects of a cognitive restructuring intervention on causal attribution tendencies (X=1, initial discovery sample, X=2, replication sample)</li><li>crossover-study-X .csv files represent data from the crossover-design study (data saved separately for participants randomly allocated to complete the reward-effort vs causal attribution tasks).</li></ul><p>Data-generating task code and full analysis code can be found at <a href="https://github.com/agnesnorbury/cognitive-mechanisms-psychotherapy">https://github.com/agnesnorbury/cognitive-mechanisms-psychotherapy</a>.</p>
THE ROLE OF HOMOCYSTEINE AS A BIOMARKER OF CYTOKINE STORM IN IMMUNOONCOLOGY AND THERAPY OF COVID-19
<p>Homocysteine is a sulfur-containing amino acid that can act as an important biomarker of inflammatory processes, including cytokine storm, observed in various pathological conditions such as cancer and COVID-19. In the conditions of the cytokine storm characteristic of severe forms of COVID-19 and progressive stages of cancer, elevated homocysteine levels can increase oxidative stress and inflammatory reactions, which, in turn, exacerbates tissue and organ damage. Studies show that homocysteine can play a significant role in the pathogenesis of these conditions, affecting the vascular and immune systems. Thus, monitoring of homocysteine levels is important for the diagnosis, prognosis and development of new therapeutic strategies in the field of immuno-oncology and treatment of COVID-19.</p>
Safety and Efficacy of Mesenchymal Stromal Cells Mitochondria Transplantation as a Cell-Free Therapy for Osteoarthritis
<p><strong><span>Abstract</span></strong></p> <p><strong><span>Objective</span></strong></p> <p><span>The inflammatory responses from synovial fibroblasts and macrophages</span><span> and the mitochondrial dysfunction in chondrocytes<span> leading to oxidative stress, disrupt extracellular matrix (ECM) homeostasis</span> and accelerate the deterioration process of articular cartilage<span> in osteoarthritis (OA).<span> </span>In the last years, it has been proposed that mesenchymal stromal cells (MSC) transfer their functional mitochondria to damaged cells in response to cellular stress, becoming one of the mechanisms underpinning their therapeutic effects. </span>Therefore, we hypothesize that a novel cell-free treatment for OA could involve direct mitochondria transplantation, leading to the restoration of both cellular and mitochondrial homeostasis.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>Mitochondria<span> were isolated from Umbilical Cord (UC)-MSC (Mito-MSC) and characterized based on their morphology, phenotype, functions, and their ability to be </span>internalized by <span>different articular cells. Furthermore, </span>the transcriptional changes following mitochondrial uptake by chondrocytes were evaluated using an Affymetrix analysis, Lastly, <span>the dose dependance therapeutic efficacy, biodistribution and immunogenicity of Mito-MSC w</span>ere assessed<span> in vivo, </span>through an intra-articular injection <span>in male C57BL6 mice in a </span>collagenase-induced OA <span>(CIOA) </span>model.</span></p> <p><strong><span>Results</span></strong></p> <p><span>Our findings demonstrate the functional integrity of Mito-MSC and their ability to be efficiently <span>transferred into chondrocytes, synovial macrophages, and synovial fibroblasts. </span>Moreover, the transcriptomic analysis showed the upregulation of genes involved in stress such as DNA reparative machinery and<span> inflammatory antiviral responses</span>.<span> </span>Finally, <span>Mito-MSC transplantation </span>yielded significant reductions<span> in joint mineralization, </span>a hallmark of OA progression<span>, </span>as well as improvements in OA-related histological signs, with the lower dose exhibiting better therapeutic efficacy. <span><span> </span></span>Furthermore, Mito-MSC were detected within the knee joint for up to 24 hours post-injection without eliciting an inflammatory response in CIOA mice. </span></p> <p><strong><span>Conclusion</span></strong></p> <p><span><span> </span>Collectively, our results reveal that mitochondria derived from MSC are transferred to key articular cells and are retained in the joint without generating an inflammatory immune response mitigating articular cartilage degradation in OA, probably through a restorative effect trigger by the stress antiviral response within OA chondrocytes.</span></p>
Topical-siRNA-therapy-1: Source data
<p>This repository contains the source data for the scientific article:</p> <p>article title: "Topical siRNA Therapy of Diabetic-Like Wound Healing"</p> <p>author: "Eva Neuhoferova & Marek Kindermann et al"</p> <p>date: "2024-19-12"</p> <p>description: "Functional and biocompatible wound dressing developed to enable a controlled release of a traceable vector loaded with the antisense siRNA against MMP-9 in the wound"</p> <ul> <li>primary data source: <a href="https://github.com/KindermannMarek/Topical-siRNA-therapy-1">https://github.com/KindermannMarek/Topical-siRNA-therapy-1</a></li> <li>the "README.md" file contains a description of the files stored in the repository</li> </ul>
Dataset accompanying the journal article: Bouldering psychotherapy is not inferior to cognitive behavioural therapy in the group treatment of depression: A randomized controlled trial
<p>SPSS-Dataset containing the (not-imputed) raw data for the non-inferiority trial on BPT vs. CBT. All personal data removed. Only data of participants of the CBT or BPT group included.</p>
Associated code and data for "Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization (doi: 10.3389/fcell.2021.74635)"
<p>This deposit contains the data, code, and analysis to reproduce the results in the manuscript - Lai X, Keller C, Santos-Rosales G, Schaft N, Dörrie J, Vera J. Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization. Frontiers in Cell and Developmental Biolology. 2022; 9:746359; <a href="https://www.researchgate.net/publication/358461035_Multi-Level_Computational_Modeling_of_Anti-Cancer_Dendritic_Cell_Vaccination_Utilized_to_Select_Molecular_Targets_for_Therapy_Optimization">doi:10.3389/fcell.2021.746359</a>.</p> <p>If you have used the code for your research, please cite the original publication. Thank you very much.</p> <p> </p>
Development of a machine learning model to predict non- durable response to anti-TNF therapy in Crohn's disease using transcriptome imputed from genotypes
<p>This is the expression value predicted using PrediXcan version 7 to find a gene feature that can distinguish between patients with and without effect on infliximab.</p> <p>Among the various tissue models provided by PrediXcan v7, three models were selected and used: whole blood, Colon transverse, and terminal ileum of small intestine, and the predicted gene counts of each model were 6,294, 5,612 and 3,107.</p> <p>For each of the three models, predicted gene expression values and phenotype information per sample were submitted.</p>
Fig. 3 in The Wolbachia endosymbiont of Brugia malayi has an active phosphoglycerate mutase: a candidate target for anti-filarial therapies
Fig. 3 Activity of recombinant wBm–iPGM. Conversion of 3-PG to 2-PG by MBP–wBm–iPGM (filled circle) is measured indirectly by a decrease in NADH concentration, determined spectrophotometrically at 340 nm. Consumption of NADH is directly proportional to PGM activity. A baseline control lacking wBm–iPGM (open circle) is shown
Fig. 1 in The Wolbachia endosymbiont of Brugia malayi has an active phosphoglycerate mutase: a candidate target for anti-filarial therapies
Fig. 1 Alignment of the deduced amino acid sequences of various iPGM enzymes. The sequence of iPGM from the Wolbachia endosymbiont of Brugia malayi (wBm; GenBank accession no. AAW70991) is aligned with the extensively studied and structurally characterized iPGM from Bacillus stearothermophilus (Bs; GenBank accession no. Q9X519; Jedrzejas et al. 2000a,b) and the characterized iPGM from Brugia malayi (Bm; GenBank accession no. AAQ97626; Zhang et al. 2004; Raverdy et al. 2007). Residues that are identical in at least two of the three sequences are shaded in black, while conserved amino acid changes are grey. The catalytic serine (@) and 13 other residues (*) involved in catalysis (Jedrzejas 2000) are conserved in all three enzymes. Alignment generated with ClustalW and displayed with BOXSHADE (www.ch.embnet.org/software/ BOX_form.html)
Fig. 2 in The Wolbachia endosymbiont of Brugia malayi has an active phosphoglycerate mutase: a candidate target for anti-filarial therapies
Fig. 2 Purification of MBP–wBm–iPGM expressed intracellularly in the yeast K. lactis. Fractions from the purification were analyzed by SDS-PAGE and the gel stained with Coomassie Blue. Lane 1 Protein Ladder (New England Biolabs), lane 2 K. lactis lysate, lane 3 supernatant of K. lactis lysate, lane 4 pellet of K. lactis lysate, lane 5 flow-through from amylose column, lane 6 column wash, lanes 7, 8, and 9, elution fractions. The arrowhead indicates the protein band corresponding to recombinant MBP–wBm–iPGM
Conserved angio-immune subtypes of the cancer microenvironment predict response to immune checkpoint blockade therapy
<p>Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment. However, only a fraction of the patients respond to ICB therapy. Accurate prediction of patients to likely respond to ICB would maximize the efficacy of ICB therapy. The tumor microenvironment (TME) dictates tumor progression and therapy outcome. Here, we classify the TME by analyzing the transcriptome from 11,069 cancer patients based on angiogenesis and T-cell activity. We find three distinct angio-immune TME subtypes conserved across 30 non-hematological cancers. There is a clear inverse relationship between angiogenesis and anti-tumor immunity in TME. Remarkably, patients displaying TME with low angiogenesis with strong anti-tumor immunity show the most significant responses to ICB therapy in four cancers. Re-evaluation of the renal cell carcinoma clinical trials provides compelling evidence that the baseline angio-immune state is robustly predictive of ICB responses. This study offers a rationale for incorporating baseline angio-immune scores for future ICB treatment strategies.</p>
Intravenous Versus Oral Transition Therapy for the Treatment of Viridans Group Streptococcal Bloodstream Infections
<p><strong>Background: </strong><em>Streptococcus</em> are amongst the most common pathogens implicated in bloodstream infections (BSI). Within the genus, S. <em>pneumoniae</em> and beta-hemolytic <em>Streptococcus</em> are the most frequently reported organisms. Viridans Group <em>Streptococcus</em> (VGS) have emerged as a more common cause and are associated with more severe complications. IV antibiotics have long been considered the standard of care, but recent studies have shown similar efficacy between IV and oral antibiotics. This is important because switching to oral antibiotics is associated with benefits like a shorter length of stay, decreased patient and hospital expenses, and a lower rate of adverse events. <strong>Objective</strong>: To determine if oral (PO) transition therapy is non-inferior to intravenous (IV)-only therapy for the treatment of uncomplicated Viridians Group <em>Streptococcus</em> (VGS) bloodstream infections (BSI). <strong>Design</strong>: Retrospective, non-inferiority cohort study. <strong>Setting</strong>: St. Luke’s University Health Network, a non-profit, academic health network. <strong>Patients</strong>: Adult inpatients with a diagnosis of VGS BSI between January 1, 2018, and December 31, 2022. <strong>Methods</strong>: Patients with VGS BSI were categorized on whether they received IV therapy for their entire treatment course or transitioned to PO therapy. The primary outcome of treatment failure was defined as a composite of all-cause mortality, hospital readmission due to infectious process, or recurrent BSI within 90 days. Secondary outcomes included the individual components of the primary outcome, adverse events, and length of stay. Non-inferiority threshold was set at 10% in the 95% CI for the difference in the proportion of patients with treatment failure between the oral transition and intravenous-only groups. <strong>Results</strong>: The primary composite outcome occurred in 20.8% of the IV group and 11.5% of the PO transition group (RR, 0.55 [95% CI 0.18 to 1.72]). Hospital length of stay was significantly longer in the IV-only group. There were no significant differences in the other outcomes. Notably, 12 of the 16 treatment-related adverse events observed in the IV-only group were associated with use of an indwelling IV catheter. <strong>Conclusions</strong>: Although the risk ratio for the composite outcome of treatment failure favors a transition to oral therapy, statistical non-inferiority could not be established.</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
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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.
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