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59 results for “SIB”
CINECA synthetic cohort Europe CH SIB [CC-BY-NC-SA]
<p>The “CINECA synthetic cohort EUROPE CH SIB” dataset consists of 6,733 synthetic samples with phenotypic and genotypic information. The synthetic phenotypic data were created from the CoLaus and PsyColaus cohort and the synthetic genetic data from the 1000 Genomes project. This dataset was created within the context of the CINECA project. More information about the creation of this dataset can be found in the included documentation. The phenotypic synthetic data is available under the Creative Commons Attribution (https://creativecommons.org/licenses/by/4.0/) and the genotypic data is available under the Creative Commons Attribution Non-Commercial Share-Alike license.To view a copy of the license, please visit: <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">https://creativecommons.org/licenses/by-nc-sa/4.0/</a>.</p> <p> </p>
High genetic gains in wood volume and fecundity can be both achieved by direct selection in half-sib families of Pinus yunnanensis Franch.
<p><strong><span>Experiment background</span></strong></p> <p><span>This study focused on characterizing phenotypic variation among and within provenances of <em>Pinus yunnanensis</em><span> Franch. aged 16 years in </span></span><span>a common garden</span><span>, with an emphasis on key traits such as cone production, trunk straightness, and crown health, as well as their relationships with traditional growth traits like tree height, diameter at breast height, and wood volume. Specifically, the objectives were to (1) characterize the variation of each trait within and among provenances; (2) assess inter-trait relationships, exploring patterns of co-variation and potential trade-offs; and (3) evaluate the feasibility of multi-trait selection strategies that aim for simultaneous improvements in growth, trunk straightness, and fecundity, contributing valuable insights for advancing <em>P. yunnanensis</em><span> </span>breeding efforts.</span></p> <p><strong><span>Experimental Design</span></strong></p> <p><span>This study was conducted in a common garden for <em>P. yunnanensis</em> located in Lufeng County, central Yunnan Province (102°12' E, 25°13' N) at an altitude of 1860 meters. The site lies in the transition zone between the subtropical humid climate of eastern Yunnan and the sub-humid climate of southwest Yunnan. The climate is characterized by warm and dry winters, humid and hot summers, with a mean annual temperature of 15.5°C and annual precipitation ranging between 900–1000 mm. The dry season extends from November to April, accounting for 6%-17% of the total annual precipitation.</span></p> <p><span>The common garden was established in 2006, with progeny from 179 superior trees selected from six provenance regions, including Anning County (AN), Qujing City (QJ), Yongren County (YR), Yulong County (YL), Tengchong County (TC), and Ninglang County (NL). Each provenance includes 30 families, except for one provenance with 29 families. </span></p> <p><span>The common garden has an area of about 3 ha, with a random block design, and a planting scheme of 2 m × 3 m</span><span>. </span><a name="_Hlk181695359"></a><span>To minimize environmental variation across the study site, a horizontal banding method was used for land preparation prior to planting.</span><span> </span><span>To reduce environmental variation across the study site, a horizontal banding method was used during land preparation. In each block, six provenances were randomly arranged, and families were randomly assigned within each provenance. Five plants from each family were planted in rows, and the design was replicated four times. A total of 3467 progeny from 179 superior trees across six provenances were included in the trial.</span></p> <p><strong><span>Experimental Variables</span></strong></p> <p><span>The study measured nine phenotypic traits, which included both quantitative and qualitative traits, as outlined below:</span></p> <p><span>Tree Height (H): Measured directly with a Vertex Laser instrument (DZH-30, Harbin, China) in meters (m).</span></p> <p><span>Diameter at Breast Height (D): Measured using a circumference tape in centimeters (cm).</span></p> <p><span>Crown Diameter (LCD, SCD): Long crown diameter (LCD) and short crown diameter (SCD), representing the maximum and minimum tree crown diameter, respectively, measured in meters (m) using a tower ruler.</span></p> <p><span>Height Under the Branch (TH): Measured in meters (m) using a tower ruler.</span></p> <p><span>Wood Volume (V): Estimated using the formula based on the forestry industry standard for <em>P. yunnanensis</em> (Agriculture and Forestry Ministry of China, 1977), with units in cubic meters (m³).</span></p> <p><span>Cone Production (CP): The number of open and closed cones in the canopy, including both serotinous and non-serotinous cones, recorded in counts to assess fecundity.</span></p> <p><span>Trunk Straightness (ST): A subjective visual assessment using a classification system: 1 for a highly twisted stem, 5 for a perfectly straight stem.</span></p> <p><span>Crown Health (CH): Visual assessment of the tree's crown, considering damage from abiotic and biotic stresses, with a grading scale from 1 (severely damaged) to 5 (perfectly healthy).</span></p> <p><strong><span>Data Analysis Methods</span></strong></p> <p><span>Data analysis was performed using R (version 3.6.3). The following statistical methods were employed:</span></p> <p><span>Variance Analysis: Nested variance analysis was used to evaluate the significance of differences and partition phenotypic variation among and within provenances. </span></p> <p><span>Principal Component Analysis (PCA): PCA was performed on the standardized matrix of nine phenotypic traits to reveal the dimensional structure and patterns of the data.</span></p> <p><span>Structural Equation Modeling (SEM): SEM was used to examine the direct and indirect relationships among traits, such as growth (H, D, V), crown size (LCD, SCD, TH), fecundity (CP), trunk straightness (ST), and crown health (CH). This analysis helped identify the causal pathways between the traits.</span></p> <p><span>Random Forest Analysis (RF): RF analysis was conducted to assess the importance of specific traits in predicting fecundity (CP) and trunk straightness (ST). Regression and classification methods were used for these analyses, with 1000 decision trees to ensure stable importance measures.</span></p> <p><strong><span>Dataset Description</span></strong></p> <p><span>The excel file (Raw Data) includes the following sheets: 1- Variables: Details on all the variables. 2- </span><span>Values of phenotypic traits</span><span>. 3- </span><span>Variance components </span><span>of phenotypic traits among and within provenances</span><span>. 4-</span><span> </span><span>Coefficient of variance</span><span> for phenotypic traits</span><span>. 5-</span><span> <span>The</span> <span>average membership function values (SFM) and </span>comprehensive weight of each principal component (PCA)<span> of </span></span><span>phenotypic traits</span><span>.</span></p>
Sib-mating enhances fitness in a haplodiploid beetle
<p>Inbreeding is generally avoided in animals due to the risk of inbreeding depression following an increase in homozygous deleterious alleles and loss of heterozygosity. Species that regularly inbreed challenge our understanding of the fitness effects of these risks. We investigated fitness consequences of extended inbreeding in the haplodiploid date-stone beetle, Coccotrypes dactyliperda. We hypothesized that continuous inbreeding could result in reduced fitness, while outbreeding would either increase fitness due to heterosis or lower fitness if co-adapted gene complexes are disrupted. We established three breeding treatments with beetles from two geographically separated populations: Sib-mating (inbreeding), and outbreeding within- and between-populations. Between-population outbreeding groups of both populations had lower fecundity and collapsed before the experiment ended, while sib-mated and within-population breeding groups persisted for ten generations. Sib-mated females had higher fecundity than within- and between-population outbreeding females. Inbreeding coefficients of sib-mated groups were higher than the other treatment groups, yet sib-mated beetles remained genetically polymorphic at the population level. Thus, there was no inbreeding depression, while crossing between distant populations led to outbreeding depression. Our findings are consistent with the life history of C. dactyliperda, in which sib-mating predominates within the date seed, but occasional within-population outbreeding may occur following local dispersal.</p>
Ablative Radiosurgery vs Stereotactic RT in 5 Fractions With SIB for Oligometastatic Bone Lesions
ClinicalTrials.gov study NCT05679427. IPD Sharing: YES. Countries: 1. Publications: 20.
5 fr Ultrahypofractionated WBI and SIB for Breast Cancer With Unfavorable Characteristics
ClinicalTrials.gov study NCT07020780. IPD Sharing: YES. Countries: 1. Publications: 45.
Sib-mating enhances fitness in a haplodiploid beetle
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Data from: Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens
Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population. Our study investigates the efficiency of sib-ship reconstruction in an advanced breeding population of Eucalyptus nitens with only partially tracked pedigree. The sib-ship reconstruction allowed the identification of selfs (4% of the sample) and the exploration of their potential effect on inbreeding depression in the traits studied. We detected signs of inbreeding depression in diameter at breast height and growth strain while no indications were observed in wood density, wood stiffness and tangential air-dry shrinkage. After the application of a corrected sib-ship relationship matrix, additive genetic variance and heritability were observed to increase where signs of inbreeding depression were initially detected. Conversely, the same genetic parameters for traits that appeared to be free of inbreeding depression decreased in size. It therefore appeared that greater genetic variance may be due, at least in part, to contributions from inbreeding in these studied populations rather than a removal of inbreeding as is traditionally thought.
Data from: Effects of sample size and full sibs on genetic diversity characterization: a case study of three syntopic Iberian pond-breeding amphibians
Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Bufo calamita, and Pelophylax perezi. We studied 17–21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77–96 individuals). As expected, FIS and tests for Hardy–Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses.
Intensity-modulated Radiotherapy (IMRT) With Simultaneous Integrated Boost (SIB) for Inoperable Non-small-cell Lung Cancer
ClinicalTrials.gov study NCT02841228. IPD Sharing: Not stated. Countries: 1. Publications: 1.
SIBS-Intervention for Siblings and Parents of Children With Chronic Illness
ClinicalTrials.gov study NCT04056884. IPD Sharing: NO. Countries: 1. Publications: 3.
IMRT-SIB and Capecitabine in Preoperative Rectal Cancer Treatment
ClinicalTrials.gov study NCT02268006. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Twice-daily SIB Radiotherapy Versus Standard Radiotherapy for Patients With SCLC
ClinicalTrials.gov study NCT03214003. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
HA-WBRT-SIB for Brain Metastasis of Lung Cancer
ClinicalTrials.gov study NCT06289023. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Phase 2 Trial in Multiple Brain Metastases Outcomes With HA-SIB-WBRT
ClinicalTrials.gov study NCT04452084. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Simultaneous Integrated Boost (SIB) in Esophageal Cancer
ClinicalTrials.gov study NCT01102088. IPD Sharing: Not stated. Countries: 1. Publications: 1.
High-Dose Lymph Node Intensity Modulated Radiation Therapy and Hypofractionated Prostate (SIB)
ClinicalTrials.gov study NCT02177292. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Effects of sample size and full sibs on genetic diversity characterization: a case study of three syntopic Iberian pond-breeding amphibians
Open the record for dataset details and reuse information.
Data from: Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens
Open the record for dataset details and reuse information.
Data from: QST FST comparisons with unbalanced half-sib designs
QST, a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between QST and FST, but that method is limited to balanced data sets with offspring related as half-sibs through shared fathers. We extend this approach to (1) allow for a model more suitable for some plant populations or breeding designs in which offspring are related through mothers (assuming independent fathers for each offspring; half-sibs by dam), and (2) by explicitly allowing for unbalanced data sets. The resulting approach is made available through the R package QstFstComp.
SIB-Time Web-application Tool for Typically Developing Siblings
ClinicalTrials.gov study NCT04633473. IPD Sharing: NO. Countries: 1. Publications: 0.
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