79 research outputs found
Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms
<p>Abstract</p> <p>Background</p> <p>A central aim for studying runs of homozygosity (ROHs) in genome-wide SNP data is to detect the effects of autozygosity (stretches of the two homologous chromosomes within the same individual that are identical by descent) on phenotypes. However, it is unknown which current ROH detection program, and which set of parameters within a given program, is optimal for differentiating ROHs that are truly autozygous from ROHs that are homozygous at the marker level but vary at unmeasured variants between the markers.</p> <p>Method</p> <p>We simulated 120 Mb of sequence data in order to know the true state of autozygosity. We then extracted common variants from this sequence to mimic the properties of SNP platforms and performed ROH analyses using three popular ROH detection programs, PLINK, GERMLINE, and BEAGLE. We varied detection thresholds for each program (e.g., prior probabilities, lengths of ROHs) to understand their effects on detecting known autozygosity.</p> <p>Results</p> <p>Within the optimal thresholds for each program, PLINK outperformed GERMLINE and BEAGLE in detecting autozygosity from distant common ancestors. PLINK's sliding window algorithm worked best when using SNP data pruned for linkage disequilibrium (LD).</p> <p>Conclusion</p> <p>Our results provide both general and specific recommendations for maximizing autozygosity detection in genome-wide SNP data, and should apply equally well to research on whole-genome autozygosity burden or to research on whether specific autozygous regions are predictive using association mapping methods.</p
Herpesvírus bovino tipo 1 (HVB 1): inquérito soro-epidemiológico no rebanho leiteiro do estado do Rio Grande do Sul, Brasil
Changes in seed dormancy of Rosa multibracteata Hemsl. & E. H. Wilson with increasing elevation in an arid valley in the eastern Tibetan Plateau
HTLV-1 Evades Type I Interferon Antiviral Signaling by Inducing the Suppressor of Cytokine Signaling 1 (SOCS1)
Human T cell leukemia virus type 1 (HTLV-1) is the etiologic agent of Adult T cell Leukemia (ATL) and the neurological disorder HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Although the majority of HTLV-1–infected individuals remain asymptomatic carriers (AC) during their lifetime, 2–5% will develop either ATL or HAM/TSP, but never both. To better understand the gene expression changes in HTLV-1-associated diseases, we examined the mRNA profiles of CD4+ T cells isolated from 7 ATL, 12 HAM/TSP, 11 AC and 8 non-infected controls. Using genomic approaches followed by bioinformatic analysis, we identified gene expression pattern characteristic of HTLV-1 infected individuals and particular disease states. Of particular interest, the suppressor of cytokine signaling 1—SOCS1—was upregulated in HAM/TSP and AC patients but not in ATL. Moreover, SOCS1 was positively correlated with the expression of HTLV-1 mRNA in HAM/TSP patient samples. In primary PBMCs transfected with a HTLV-1 proviral clone and in HTLV-1-transformed MT-2 cells, HTLV-1 replication correlated with induction of SOCS1 and inhibition of IFN-α/β and IFN-stimulated gene expression. Targeting SOCS1 with siRNA restored type I IFN production and reduced HTLV-1 replication in MT-2 cells. Conversely, exogenous expression of SOCS1 resulted in enhanced HTLV-1 mRNA synthesis. In addition to inhibiting signaling downstream of the IFN receptor, SOCS1 inhibited IFN-β production by targeting IRF3 for ubiquitination and proteasomal degradation. These observations identify a novel SOCS1 driven mechanism of evasion of the type I IFN antiviral response against HTLV-1
Evaluation of a new virtual-reality training simulator for hysteroscopy
BACKGROUND: To determine realism and training capacity of HystSim, a new virtual-reality simulator for the training of hysteroscopic interventions. METHODS: Sixty-two gynaecological surgeons with various levels of expertise were interviewed at the 13(th) Practical Course in Gynaecologic Endoscopy in Davos, Switzerland. All participants received a 20-min hands-on training on the simulator and filled out a four-page questionnaire. Twenty-three questions with respect to the realism of the simulation and the training capacity were answered on a seven-point Likert scale along with 11 agree-disagree statements concerning the HystSim training in general. RESULTS: Twenty-six participants had performed more than 50 hysteroscopies ("experts") and 36 equal to or fewer than 50 ("novices"). Four of 60 (6.6%) responding participants judged the overall impression as "7 - absolutely realistic", 40 (66.6%) as "6 - realistic", and 16 (26.6%) as "5 - somewhat realistic". Novices (6.48; 95% confidence interval [CI] 6.28-6.7) rated the overall training capacity significantly higher than experts (6.08; 95% CI 5.85-6.3), however, high-grade acceptance was found in both groups. In response to the statements, 95.2% believe that HystSim allows procedural training of diagnostic and therapeutic hysteroscopy, and 85.5% suggest that HystSim training should be offered to all novices before performing surgery on real patients. CONCLUSION: Face validity has been established for a new hysteroscopic surgery simulator. Potential trainees and trainers assess it to be a realistic and useful tool for the training of hysteroscopy. Further systematic validation studies are needed to clarify how this system can be optimally integrated into the gynaecological curriculum
Genetic diversity of three ornamental reef fishes (Families Pomacanthidae and Chaetodontidae) from the Brazilian coast
Varying constants, Gravitation and Cosmology
Fundamental constants are a cornerstone of our physical laws. Any constant
varying in space and/or time would reflect the existence of an almost massless
field that couples to matter. This will induce a violation of the universality
of free fall. It is thus of utmost importance for our understanding of gravity
and of the domain of validity of general relativity to test for their
constancy. We thus detail the relations between the constants, the tests of the
local position invariance and of the universality of free fall. We then review
the main experimental and observational constraints that have been obtained
from atomic clocks, the Oklo phenomenon, Solar system observations, meteorites
dating, quasar absorption spectra, stellar physics, pulsar timing, the cosmic
microwave background and big bang nucleosynthesis. At each step we describe the
basics of each system, its dependence with respect to the constants, the known
systematic effects and the most recent constraints that have been obtained. We
then describe the main theoretical frameworks in which the low-energy constants
may actually be varying and we focus on the unification mechanisms and the
relations between the variation of different constants. To finish, we discuss
the more speculative possibility of understanding their numerical values and
the apparent fine-tuning that they confront us with.Comment: 145 pages, 10 figures, Review for Living Reviews in Relativit
- …