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1,530 results for “treatment response”
Evaluating rose yield responses to compost treatments: Data from an 18-month field study in Kenya
<p>This dataset and these scripts supports the manuscript 'Modelling cut rose yield after compost amendment over an 18-month period using repeated sigmoidal Gompertz curve fitting' by Evy de Nijs, Roland Bol, Albert Tietema & Emiel van Loon. </p> <p>Roses are an important crop for the floricultural sector of Kenya. Roses are a perennial crop and under continuous production for six to ten years. To optimize rose production, it is essential to understand how different management practices impact yield over time. This dataset contains a detailed record of rose yield data collected in an 18-month large-scale field experiment. The aim of this experiment was to evaluate the effect of pre-planting compost amendment on the yield and quality of cut roses. It was conducted in a polythene greenhouse near lake Naivasha, Kenya. Yield data included the number of stems harvested per day per flowering bed. Data presented here offer a comprehensive view of the impacts of different compost treatments on the yield of cut roses. Combined with the offered scripts, this is the framework presented in the aforementioned manuscript. This approach allows to use repeated growth curves to analyze yields compared to a baseline General Additive Model. </p> <p> </p> <p>de Nijs, E. A., Tietema, A., Bol, R., & van Loon, E. E. (2025). Modeling Cut Rose Yield Over an 18‐Month Period After Compost Amendment Using Repeated Sigmoidal Gompertz Curve Fitting. <em>Plant‐Environment Interactions</em>, <em>6</em>(3), e70049.</p>
Oak litter decomposition parameters across 19 Nutrient Network grassland sites in response to NPK and herbivore exclusion treatments
These data are from a study examining how herbivory and nutrient supply affect long-term aboveground decomposition. A novel oak litter was decomposed across 19 grassland sites of the Nutrient Network distributed experiment. At each site, a full-factorial experiment of combined nitrogen, phosphorus, and potassium plus micronutrients ('control' or 'NPK') and mammalian herbivore exclusion ('fencing') was carried out in a randomized block design. The duration of the decomposition experiment varied by site but litter bags were harvested at approximately annual intervals for up to seven years. Litter decay parameters were calculated using four alternative statistical models of litter decomposition. Covariate data describing site and plot-level abiotic and biotic characteristics were also measured, including climate, atmospheric nitrogen deposition, live and dead aboveground biomass, and percent cover.
Genetic association analysis of anti-VEGF treatment response in neovascular age-related macular degeneration
<p>Summary statisics of an association study of 6,908,005 genetic variants with anti-VEGF nAMD treatment response in 179 treatment-naïve nAMD probands. This dataset supplements the publication "Genetic Association Analysis of Anti-VEGF Treatment Response in Neovascular Age-Related Macular Degeneration" (DOI: 10.3390/ijms23116094). Details regarding the methods and version numbers can be found in the corresponding manuscript.</p>
Bone metabolism gene variation and response to bisphosphonate treatment in women with postmenopausal osteoporosis
<p>This repository contains the raw and source data for the manuscript "Bone metabolism gene polymorphism and response to bisphosphonate treatment in women with postmenopausal osteoporosis" submitted to PLOS ONE.</p> <p><strong>Abstract: </strong></p> <p><em>Introduction:</em> Long-term treatment is used in patients with osteoporosis, and bisphosphonates (BPs) are the most commonly prescribed medications. However, in some patients this therapy is not effective, cause different side effects and complications. Unfortunately, at least one year is needed to identify and confirm an ineffectiveness of BPs therapy on bone mineral density (BMD). Among other factors, a response to BPs therapy may also be explained by genetic factors. The aim of this study was to analyze the influence of <em>SOST, PTH, FGF2, FDPS, GGPS1, </em>and<em> LRP5</em> gene polymorphisms on the response to treatment with BPs.</p> <p><em>Materials and methods: </em>Women with postmenopausal osteoporosis were included to this study if they used bisphosphonates for at least 12 months. Exclusion criteria were: persistence on BPs therapy less than 80%, bone metabolic diseases, diseases deemed to affect bone metabolism, malignant tumours, using of any medications influencing BMD. The study protocol was approved by the local ethics committee. The BMD at the lumbar spine and femoral neck were measured using dual x-ray absorptiometry (GE Lunar) before and at least 12 months after treatment with BPs. According to BMD change, patients were divided in two groups – responders and non-responders to BPs terapy. Polymorphic variants in <em>SOST, PTH, FGF2, FDPS, GGPS1, </em>and<em> LRP5</em> genes were determined using PCR analysis with TaqMan probes (Thermo Scientific).</p> <p><em>Results:</em> In total, 201 women with BPs therapy were included in the study. No statistically significant differences were observed in age, age at menopause, weight, height, BMI and baseline BMD levels between responders (122 subjects) and non-responders (79 subjects).</p> <p>As single markers, the <em>SOST </em>rs1234612 T/T (OR=2.3; P=0.02), <em>PTH</em> rs7125774 T/T (OR=2.8, P=0.0009), <em>FDPS</em> rs2297480 G/G (OR=29.3, P=2.2×10<sup>-7</sup>), and <em>GGPS1</em> rs10925503 C/C+C/T (OR=2.9; P=0.003) gene variants were over-represented in non-responders group. No significant association between <em>FGF2</em> rs6854081 and <em>LRP5</em> rs3736228 gene variants and response to BPs treatment was observed. The carriers of T-T-G-C allelic combination (constructed from rs1234612, rs7125774, rs2297480, and rs10925503) were predisposed to negative response to BPs treatment (OR = 4.9, 95% CI 1.7–14.6, P=0.005). The C-C-T-C combination was significantly over-represented in responders (OR = 0.1, 95% CI 0.1–0.5, P=0.006).</p> <p><em>Conclusions:</em> Our findings highlight the importance of identified single gene variants and their allelic combinations for pharmacogenetics of BPs therapy of osteoporosis. Complex screening of these genetic markers could be used as a new strategy for personalized antiresorptive therapy.</p>
Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors
<p>Data required to reproduce the results/figures of the "<strong>Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors</strong>" project. </p>
ACF database on the predictors of time to recovery and non-response to SAM treatment in the MANGO trial
<p>This database contains the variables used to analyse the predictors of time to recovery and non-response to treatment of SAM in Burkina Faso. These results are have been submitted to review in Plos One in November 2020.</p>
Caudal fin area: body length ratio (A:L 2; mean..) FIGURE 5 CF s S E measured from photographs of Salmo trutta parr at 20 and 32 weeks after exercise treatment initiation. A:L 2 values between the two CF s groups were significantly different (Welch's two sample t- test p <0.05) in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr
Caudal fin area: body length ratio (A:L 2; mean..) FIGURE 5 CF s S E measured from photographs of Salmo trutta parr at 20 and 32 weeks after exercise treatment initiation. A:L 2 values between the two CF s groups were significantly different (Welch's two sample t- test p <0.05)
Point-of-care monitoring of head and neck cancer treatment response and recurrence development using nanopore-based ctDNA consensus sequencing
<p>Circulating tumor DNA (ctDNA) in blood may become a generic biomarker for non-invasive cancer diagnosis and monitoring. However, detection of ctDNA is challenged by the presence of many circulating DNA molecules from healthy cells. We found that single ctDNA molecules can be sequenced with high accuracy by a three-step process consisting of capturing, copying and concatenation of the original double-stranded ctDNA molecules. This innovative approach - called CyclomicsSeq - is unparalleled by any other method in terms of cost-efficiency and speed, allowing point-of-care cancer diagnostics.</p> <p>Within this CPOC, subsidized by the Oncode institute, we have applied our CyclomicsSeq ctDNA test in patients with advanced head and neck cancer squamous cell carcinoma (HNSCC). Head and neck cancer (HNSCC) accounts for 380,000 cancer-related deaths worldwide. For these patients, determining whether a patient responds to the primary chemoradiation treatment is challenging, and non-responders are sometimes identified when other treatment options are no longer possible. By measuring the ctDNA levels in the blood of these patients prior to and during treatment, we aim to identify non-responders at an earlier stage.</p> <p>This dataset contains base calls of TP53 of 47 nanopore sequencing runs. We included 10 patients and 7 controls. For the patients, we have samples of multiple time points (0 = prior to treatment, 1 = 1 week after treatment initiation, etc).</p>
Dataset and Data treatment for Data mining Raman Microspectroscopic Responses of Cells to Drugs in Vitro using Multivariate Curve Resolution-Alternating Least Squares
<p><strong>Matlab scripts for the simulation and treatment of Raman datasets obtained from time dependent experiments Using MCR-ALS.</strong></p> <p> </p> <p><strong>- SIMULATED DATA: </strong>Simulated data is obtained by adding spectra of artificially generated responses (weighted considering artificially generated time profiles) to an experimental cell spectrum (Initial component) Three Different Scenarios are generated. </p> <p>Spectral and time profiles are obtained from here: </p> <p> </p> <p><strong>- EXPERIMENTAL DATA: </strong>DOX dataset obtained from here</p> <p>https://doi.org/10.1002/jbio.201800328</p> <p> </p> <p> </p> <p><strong>- DATA ANALYSIS INSTRUCTIONS</strong></p> <p>Run <em>datatreatment.m</em></p>
Phosphomapping of S. cerevisiae Pkc1 in response to hydroxyurea treatment
<p>We performed phosphorylation site mapping on of budding yeast Pkc1 applying a quantitative mass spectrometry (MS)-based proteomics approach based on stable isotope labeling with amino acids in cell culture (SILAC). We determined changes in the Pkc1 phosphorylation pattern in response to genotoxic stress induced by Hydroxyurea treatment. This dataset includes all MS RAW files.</p>
Efficacy, Safety and Tolerability of Cariprazine as an Adjunctive Treatment to Antidepressant Therapy (ADT) in Patients With Major Depressive Disorder (MDD) Who Have Had an Inadequate Response to Anti
ClinicalTrials.gov study NCT03738215. IPD Sharing: YES. Countries: 7. Publications: 1.
Study of Power Doppler Ultrasound (PDUS) to Measure Response of Secukinumab Treatment in Patients With Active Psoriatic Arthritis (PsA)
ClinicalTrials.gov study NCT02662985. IPD Sharing: UNDECIDED. Countries: 17. Publications: 1.
EValuating trEatment RESponses of Dupilumab Versus Omalizumab in Type 2 Patients
ClinicalTrials.gov study NCT04998604. IPD Sharing: YES. Countries: 17. Publications: 2.
Physiology of GERD and Treatment Response
ClinicalTrials.gov study NCT04292470. IPD Sharing: NO. Countries: 1. Publications: 2.
A Study to Assess the Ability of Eltrombopag to Induce Sustained Response Off Treatment in Subjects With ITP
ClinicalTrials.gov study NCT03524612. IPD Sharing: YES. Countries: 15. Publications: 1.
Immune repertoire sequencing reveals differences in treatment response to camrelizumab plus platinum-based chemotherapy in advanced ESCC
Open the record for dataset details and reuse information.
Data from: Social behavior mediates the microbiome response to antibiotic treatment in a wild mammal
Open the record for dataset details and reuse information.
Synthesizing community changes to global change treatments using the CoRRE (Community Responses to Resource Experiments) database - Data to accompany Avolio et al. 2021
These are the required data to do all subsequent analyses in Avolio et al. 2021 in Ecology Letters using the Community Responses to Resource Experiments database (corredata.weebly.com). Paper abstract: Global change is impacting plant community composition, but the mechanisms underlying these changes are unclear. Using a dataset of 58 global change experiments, we tested the five fundamental mechanisms of community change: changes in evenness and richness, re-ordering, species gains and losses. We found 71% communities were impacted by global change treatments, and 88% of communities that were exposed to two or more global change drivers were impacted. Further, all mechanisms of change were equally likely to be affected by global change treatments – species losses and changes in richness were just as common as species gains and re-ordering. We also found no evidence of a progression of community changes, e.g., re-ordering and changes in evenness did not precede species gains and losses. We demonstrate that all processes underlying plant community composition changes are equally affected by treatments and often occur simultaneously, necessitating a wholistic approach to quantifying community changes.
Foliar and sapwood nutritional and metabolic responses to Ca-treatment at the Hubbard Brook Experimental Forest, 2000 – 2015
Background Acidic deposition has caused a depletion of calcium (Ca) in the northeastern forest soils. One time application of wollastonite (CaSiO3 - 1.2 Mg ha-1 of Ca) was done at watershed 1 (WS1) of the Hubbard Brook Experimental Forest (HBEF) in 1999 to evaluate its effects on various functions of the HBEF ecosystem. This rate of application was intended to increase the existing base saturation of the soil from 10% to approximately 19%, and to increase the soil pH to the level that was estimated to exist ~50 years prior to treatment. More details on the treatment can be found at http://www.hubbardbrook.org/research/longterm/calcium/w1_overview/index.html. The overall objective of this study was to evaluate changes in foliar and sapwood metabolic parameters and microbial diversity as indicators of stress and overall health in trees exposed to Ca-supplementation. Raw data from Ca-treated WS1 are compared with WS3 (reference watershed) for cellular metabolites, exchangeable foliar chemistry (not totals) 2000-2015. These watersheds are in close proximity (less than 1.5 Km apart) with similar geology, temperature, soils, and overall climate. For more details see a list of references given below Ca-Supplementation-Metabolic Study (WS1 & along eastern edge of WS3) SUMMARY: The effects of Ca addition on foliar soluble (extractable in 5% HClO4) ions, chlorophyll, polyamines, and amino acids were studied in three hardwood species, namely sugar maple, yellow birch, and American beech. We further analyzed these effects in relation to elevation at Ca-supplemented WS1 and reference WS3 watersheds. During the earlier years foliar soluble Ca increased significantly in all species at mid and high elevations at Ca-supplemented WS1. This was accompanied by increases in soluble P, chlorophyll, and two amino acids, glutamate and glycine. A decrease in known metabolic indicators of physiological stress (i.e. the amino acids, arginine and γ-aminobutyric acid (GABA), and the diamine, pu
Data from: The 15-year post-treatment response of a mixed-conifer understory plant community to thinning and burning treatments
<p>Disturbance is central to maintaining diversity in forest ecosystems. In the dry forests of the western United States, over a century of fire exclusion has altered the fire regimes of these forests, resulting in high fuel loads and a loss of plant diversity. Mechanical thinning and prescribed fire are widely used to restore structural complexity and species diversity in many western U.S. forests. While studies have shown that the reintroduction of fire into these forests initially promotes plant diversity, there is limited information on the persistence of this effect. We evaluated the effects of thinning and burning treatments on the understory plant community fifteen years after treatment in an old-growth, Sierran mixed-conifer forest. Using a full-factorial design, including three levels of thinning and two levels of burning, we found mechanical thinning and prescribed fire reduced litter depths and increased the availability of bare ground, resulting in an initial increase in herb cover. However, fifteen years after treatment, litter depths and shrub cover increased, resulting in a more homogenous understory community and a loss of herb cover. Overall, our results suggest that while thinning and burning treatments initially promote herbaceous plant cover, these effects are short lived in the absence of a second disturbance.</p>
ScienceDex guides
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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.