228 research outputs found
High-resolution Ce 3d-edge resonant photoemission study of CeNi_2
Resonant photoemission (RPES) at the Ce 3d -> 4f threshold has been performed
for alpha-like compound CeNi_2 with extremely high energy resolution (full
width at half maximum < 0.2 eV) to obtain bulk-sensitive 4f spectral weight.
The on-resonance spectrum shows a sharp resolution-limited peak near the Fermi
energy which can be assigned to the tail of the Kondo resonance. However, the
spin-orbit side band around 0.3 eV binding energy corresponding to the f_{7/2}
peak is washed out, in contrast to the RPES spectrum at the Ce 3d -> 4f RPES
threshold. This is interpreted as due to the different surface sensitivity, and
the bulk-sensitive Ce 3d -> 4f RPES spectra are found to be consistent with
other electron spectroscopy and low energy properties for alpha-like
Ce-transition metal compounds, thus resolves controversy on the interpretation
of Ce compound photoemission. The 4f spectral weight over the whole valence
band can also be fitted fairly well with the Gunnarsson-Schoenhammer
calculation of the single impurity Anderson model, although the detailed
features show some dependence on the hybridization band shape and (possibly) Ce
5d emissions.Comment: 4 pages, 3 figur
Comparison of techniques used to count single-celled viable phytoplankton
Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Applied Phycology 24 (2012): 751-758, doi:10.1007/s10811-011-9694-z.Four methods commonly used to count phytoplankton were evaluated based upon the precision of concentration
estimates: Sedgewick Rafter and membrane filter direct counts, flow cytometry, and flow-based imaging cytometry
(FlowCAM). Counting methods were all able to estimate the cell concentrations, categorize cells into size classes,
and determine cell viability using fluorescent probes. These criteria are essential to determine whether discharged
ballast water complies with international standards that limit the concentration of viable planktonic organisms based
on size class. Samples containing unknown concentrations of live and UV-inactivated phytoflagellates (Tetraselmis
impellucida) were formulated to have low concentrations (<100 ml-1) of viable phytoplankton. All count methods
used chlorophyll a fluorescence to detect cells and SYTOX fluorescence to detect non-viable cells. With the
exception of one sample, the methods generated live and non-viable cell counts that were significantly different
from each other, although estimates were generally within 100% of the ensemble mean of all subsamples from all
methods. Overall, percent coefficient of variation (CV) among sample replicates was lowest in membrane filtration
sample replicates, and CVs for all four counting methods were usually lower than 30% (although instances of ~60%
were observed). Since all four methods were generally appropriate for monitoring discharged ballast water,
ancillary considerations (e.g., ease of analysis, sample processing rate, sample size, etc.) become critical factors for
choosing the optimal phytoplankton counting method.This study was supported by the U.S. Coast Guard Research and Development Center under contract HSCG32-07-
X-R00018. Partial research support to DMA and DMK was provided
through NSF International Contract 03/06/394, and Environmental Protection Agency Grant RD-83382801-0
The BRCA2 c.68-7T > A variant is not pathogenic : A model for clinical calibration of spliceogenicity
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44x10(-115). There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.Peer reviewe
The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity.
Although the spliceogenic nature of the BRCA2 c.68-7T>A variant has been demonstrated, its association with cancer risk remains ontroversial. In this study, we accurately quantified by real-time PCR and digital PCR the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636
individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T>A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 x 10-115. There was neither evidence for
increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24), nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the non-pathogenicity of the BRCA2 c.68-7T>A. Genetic and quantitative
transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants
Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1
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Breast Cancer Polygenic Risk Score and Contralateral Breast Cancer Risk.
Previous research has shown that polygenic risk scores (PRSs) can be used to stratify women according to their risk of developing primary invasive breast cancer. This study aimed to evaluate the association between a recently validated PRS of 313 germline variants (PRS313) and contralateral breast cancer (CBC) risk. We included 56,068 women of European ancestry diagnosed with first invasive breast cancer from 1990 onward with follow-up from the Breast Cancer Association Consortium. Metachronous CBC risk (N = 1,027) according to the distribution of PRS313 was quantified using Cox regression analyses. We assessed PRS313 interaction with age at first diagnosis, family history, morphology, ER status, PR status, and HER2 status, and (neo)adjuvant therapy. In studies of Asian women, with limited follow-up, CBC risk associated with PRS313 was assessed using logistic regression for 340 women with CBC compared with 12,133 women with unilateral breast cancer. Higher PRS313 was associated with increased CBC risk: hazard ratio per standard deviation (SD) = 1.25 (95%CI = 1.18-1.33) for Europeans, and an OR per SD = 1.15 (95%CI = 1.02-1.29) for Asians. The absolute lifetime risks of CBC, accounting for death as competing risk, were 12.4% for European women at the 10th percentile and 20.5% at the 90th percentile of PRS313. We found no evidence of confounding by or interaction with individual characteristics, characteristics of the primary tumor, or treatment. The C-index for the PRS313 alone was 0.563 (95%CI = 0.547-0.586). In conclusion, PRS313 is an independent factor associated with CBC risk and can be incorporated into CBC risk prediction models to help improve stratification and optimize surveillance and treatment strategies
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