Pacific Hake, Merluccius productus, Autecology: A Timely Review

Pacific hake, Merluccius productus, the most abundant groundfish in the California Current Large Marine Ecosystem (CCLME), is a species of both commercial significance, supporting a large international fishery, and ecological importance, connecting other species as both predator and prey. Coastal Pacific hake migrations are characterized by movements between northern summer feeding areas and southern winter spawning areas, with variations in annual abundance, distribution, and the extent of these movements associated with varying climate-ocean conditions. In general, warm (cool) years with enhanced (reduced) stratification and poleward (equatorward) transport are often related to good (poor) recruitment, increased (decreased) northward distribution, and reduced (enhanced) growth. However, the classic periodic pattern of annual migration and distribution may no longer be fully representative. Based on recent advances in the understanding of climate-ocean variability off the U.S. west coast, we hypothesize that the annual movements of Pacific hake are more responsive to climate-ocean variability than previously thought, and further, that changes observed in Pacific hake distributions may reflect long-term changes in climate-ocean conditions in the CCLME. Therefore, an updated model of these relations is key to effective monitoring and management of this stock, as well as to devising scenarios of future change in the CCLME as a result of climate variations. The current state of knowledge of the relationship between the Pacific hake and its environment is reviewed, highlighting emerging ideas compared to those of the past, and priorities for future research are suggested

Star Formation, Radio Sources, Cooling X-ray Gas, and Galaxy Interactions in the Brightest Cluster Galaxy in 2A0335+096

We present deep emission-line imaging taken with the SOAR Optical Imaging Camera of the brightest cluster galaxy (BCG) in the nearby (z=0.035) X-ray cluster 2A0335+096. We analyze long-slit optical spectroscopy, archival VLA, Chandra X-ray, and XMM UV data. 2A0335+096 is a bright, cool-core X-ray cluster, once known as a cooling flow. Within the highly disturbed core revealed by Chandra X-ray observations, 2A0335+096 hosts a highly structured optical emission-line system. The redshift of the companion is within 100 km/s of the BCG and has certainly interacted with the BCG, and is likely bound to it. The comparison of optical and radio images shows curved filaments in H-alpha emission surrounding the resolved radio source. The velocity structure of the emission-line bar between the BCG nucleus and the companion galaxy provides strong evidence for an interaction between the two in the last ~50 Myrs. The age of the radio source is similar to the interaction time, so this interaction may have provoked an episode of radio activity. We estimate a star formation rate of >7 solar mass/yr based on the Halpha and archival UV data, a rate similar to, but somewhat lower than, the revised X-ray cooling rate of 10-30 solar masses/year estimated from XMM spectra by Peterson & workers. The Halpha nebula is limited to a region of high X-ray surface brightness and cool X-ray temperature. The detailed structures of H-alpha and X-ray gas differ. The peak of the X-ray emission is not the peak of H-alpha emission, nor does it lie in the BCG. The estimated age of the radio lobes and their interaction with the optical emission-line gas, the estimated timescale for depletion and accumulation of cold gas, and the dynamical time in the system are all similar, suggesting a common trigger mechanism.Comment: Accepted AJ, July 2007 publication. Vol 134, p. 14-2

Graft-versus-host disease of the skin: life and death on the epidermal edge

AbstractDespite impressive advances in the field of allogeneic hematopoietic transplantation, graft versus host disease (GVHD) remains a significant obstacle to be overcome; it would enhance the safety and efficacy of this life-saving therapy. This review provides a framework for understanding the molecular and cellular basis underlying GVHD. We propose a 3-phase model of GVHD that highlights the importance of the conditioning regimen on the recipient tissues administered prior to infusion of donor bone marrow inoculum. A novel skin explant model, designed to take into consideration the immunobiological consequences of conditioning regimens on resident host cells, is proposed to advance our understanding of GVHD and serve as a potential prognostic tool when allogeneic recipient/donor combinations are being contemplated in the clinic. Within this review, specific emphasis is placed on the importance of defining the apoptotic machinery engaged in epidermal keratinocytes triggered by both conditioning regimens, and by host resident and recruited immunocytes and soluble mediators produced at sites of injury. The review is completed with a working model for cutaneous GVHD. Although the skin is highlighted because of its accessibility for clinical observations and serial sampling opportunities, lessons learned from studies of cutaneous GVHD are likely to provide valuable insights into GVHD occurring in the gastrointestinal tract, lung, and liver. With new insights designed to better predict and prevent GVHD and novel agents designed to treat GVHD, overcoming this current impediment to successful bone marrow transplantation should become increasingly feasible

Patterns of substance use across the first year of college and associated risk factors

Starting college is a major life transition. This study aims to characterize patterns of substance use across a variety of substances across the first year of college and identify associated factors. We used data from the first cohort (N = 2056, 1240 females) of the “Spit for Science” sample, a study of incoming freshmen at a large urban university. Latent transition analysis was applied to alcohol, tobacco, cannabis, and other illicit drug uses measured at the beginning of the fall semester and midway through the spring semester. Covariates across multiple domains – including personality, drinking motivations and expectancy, high school delinquency, peer deviance, stressful events, and symptoms of depression and anxiety – were included to predict the patterns of substance use and transitions between patterns across the first year. At both the fall and spring semesters, we identified three subgroups of participants with patterns of substance use characterized as: (1) use of all four substances; (2) alcohol, tobacco, and cannabis use; and (3) overall low substance use. Patterns of substance use were highly stable across the first year of college: most students maintained their class membership from fall to spring, with just 7% of participants in the initial low substance users transitioning to spring alcohol, tobacco, and cannabis users. Most of the included covariates were predictive of the initial pattern of use, but covariates related to experiences across the first year of college were more predictive of the transition from the low to alcohol, tobacco, and cannabis user groups. Our results suggest that while there is an overall increase in alcohol use across all students, college students largely maintain their patterns of substance use across the first year. Risk factors experienced during the first year may be effective targets for preventing increases in substance use

Molecular Genetic Influences on Normative and Problematic Alcohol Use in a Population-Based Sample of College Students

Background: Genetic factors impact alcohol use behaviors and these factors may become increasingly evident during emerging adulthood. Examination of the effects of individual variants as well as aggregate genetic variation can clarify mechanisms underlying risk. Methods: We conducted genome-wide association studies (GWAS) in an ethnically diverse sample of college students for three quantitative outcomes including typical monthly alcohol consumption, alcohol problems, and maximum number of drinks in 24 h. Heritability based on common genetic variants (h2SNP) was assessed. We also evaluated whether risk variants in aggregate were associated with alcohol use outcomes in an independent sample of young adults. Results: Two genome-wide significant markers were observed: rs11201929 in GRID1 for maximum drinks in 24 h, with supportive evidence across all ancestry groups; and rs73317305 in SAMD12 (alcohol problems), tested only in the African ancestry group. The h2SNP estimate was 0.19 (SE = 0.11) for consumption, and was non-significant for other outcomes. Genome-wide polygenic scores were significantly associated with alcohol outcomes in an independent sample. Conclusions: These results robustly identify genetic risk for alcohol use outcomes at the variant level and in aggregate. We confirm prior evidence that genetic variation in GRID1impacts alcohol use, and identify novel loci of interest for multiple alcohol outcomes in emerging adults. These findings indicate that genetic variation influencing normative and problematic alcohol use is, to some extent, convergent across ancestry groups. Studying college populations represents a promising avenue by which to obtain large, diverse samples for gene identification

Accuracy of Digital Breast Tomosynthesis for Depicting Breast Cancer Subgroups in a UK Retrospective Reading Study (TOMMY Trial)

Purpose To compare the diagnostic performance of two-dimensional (2D) mammography, 2D mammography plus digital breast tomosynthesis (DBT), and synthetic 2D mammography plus DBT in depicting malignant radiographic features. Materials and Methods In this multicenter, multireader, retrospective reading study (the TOMMY trial), after written informed consent was obtained, 8869 women (age range, 29–85 years; mean, 56 years) were recruited from July 2011 to March 2013 in an ethically approved study. From these women, a reading dataset of 7060 cases was randomly allocated for independent blinded review of (a) 2D mammography images, (b) 2D mammography plus DBT images, and (c) synthetic 2D mammography plus DBT images. Reviewers had no access to results of previous examinations. Overall sensitivities and specificities were calculated for younger women and those with dense breasts. Results Overall sensitivity was 87% for 2D mammography, 89% for 2D mammography plus DBT, and 88% for synthetic 2D mammography plus DBT. The addition of DBT was associated with a 34% increase in the odds of depicting cancer (odds ratio [OR] = 1.34, P = .06); however, this level did not achieve significance. For patients aged 50–59 years old, sensitivity was significantly higher (P = .01) for 2D mammography plus DBT than it was for 2D mammography. For those with breast density of 50% or more, sensitivity was 86% for 2D mammography compared with 93% for 2D mammography plus DBT (P = .03). Specificity was 57% for 2D mammography, 70% for 2D mammography plus DBT, and 72% for synthetic 2D mammography plusmDBT. Specificity was significantly higher than 2D mammography (P < .001in both cases) and was observed for all subgroups (P < .001 for all cases). Conclusion The addition of DBT increased the sensitivity of 2D mammography in patients with dense breasts and the specificity of 2D mammography for all subgroups. The use of synthetic 2D DBT demonstrated performance similar to that of standard 2D mammography with DBT. DBT is of potential benefit to screening programs, particularly in younger women with dense breasts. © RSNA, 2015The TOMMY Trial (a comparison of digital breast tomosynthesis with mammography in the UK Breast Screening Programme) was supported by the NIHR Health Technology Assessment Programme.This is the final published version of the article. It was originally published in Radiology (Gilbert et al., Radiology, 2015, doi:10.1148/radiol.2015142566). The final version is available at http://dx.doi.org/10.1148/radiol.201514256

Accuracy of Digital Breast Tomosynthesis for Depicting Breast Cancer Subgroups in a UK Retrospective Reading Study (TOMMY Trial).

PURPOSE: To compare the diagnostic performance of two-dimensional (2D) mammography, 2D mammography plus digital breast tomosynthesis (DBT), and synthetic 2D mammography plus DBT in depicting malignant radiographic features. MATERIALS AND METHODS: In this multicenter, multireader, retrospective reading study (the TOMMY trial), after written informed consent was obtained, 8869 women (age range, 29-85 years; mean, 56 years) were recruited from July 2011 to March 2013 in an ethically approved study. From these women, a reading dataset of 7060 cases was randomly allocated for independent blinded review of (a) 2D mammography images, (b) 2D mammography plus DBT images, and (c) synthetic 2D mammography plus DBT images. Reviewers had no access to results of previous examinations. Overall sensitivities and specificities were calculated for younger women and those with dense breasts. RESULTS: Overall sensitivity was 87% for 2D mammography, 89% for 2D mammography plus DBT, and 88% for synthetic 2D mammography plus DBT. The addition of DBT was associated with a 34% increase in the odds of depicting cancer (odds ratio [OR] = 1.34, P = .06); however, this level did not achieve significance. For patients aged 50-59 years old, sensitivity was significantly higher (P = .01) for 2D mammography plus DBT than it was for 2D mammography. For those with breast density of 50% or more, sensitivity was 86% for 2D mammography compared with 93% for 2D mammography plus DBT (P = .03). Specificity was 57% for 2D mammography, 70% for 2D mammography plus DBT, and 72% for synthetic 2D mammography plusmDBT. Specificity was significantly higher than 2D mammography (P < .001in both cases) and was observed for all subgroups (P < .001 for all cases). CONCLUSION: The addition of DBT increased the sensitivity of 2D mammography in patients with dense breasts and the specificity of 2D mammography for all subgroups. The use of synthetic 2D DBT demonstrated performance similar to that of standard 2D mammography with DBT. DBT is of potential benefit to screening programs, particularly in younger women with dense breasts. (©) RSNA, 2015.The TOMMY Trial (a comparison of digital breast tomosynthesis with mammography in the UK Breast Screening Programme) was supported by the NIHR Health Technology Assessment Programme.This is the final published version of the article. It was originally published in Radiology (Gilbert et al., Radiology, 2015, doi:10.1148/radiol.2015142566). The final version is available at http://dx.doi.org/10.1148/radiol.201514256

Yeast:One cell, one reference sequence, many genomes?

The genome of Saccharomyces cerevisiae – brewer’s or baker’s yeast – was the first eukaryotic genome to be sequenced in 1996. The identity of that yeast genome has been not just a product of sequencing, but also of its use after sequencing and particularly of its mobilization in scientific literature. We ask “what is the yeast genome?” as an empirical question by investigating “the yeast genome” as a discursive entity. Analyzing publications that followed sequencing points to several “yeast genomes” existing side-by-side: genomes as physical molecules, digital texts, and a historic event. Resolving this unified-yet-multiple “genome” helps make sense of contemporary developments in yeast genomics such as the synthetic yeast project, in which apparently “the same” genome occupies multiple roles and locations, and points to the utility of examining specific non-human genomes independent of the Human Genome Project

Mammographic density and breast cancer risk in breast screening assessment cases and women with a family history of breast cancer.

BACKGROUND: Mammographic density has been shown to be a strong independent predictor of breast cancer and a causative factor in reducing the sensitivity of mammography. There remain questions as to the use of mammographic density information in the context of screening and risk management, and of the association with cancer in populations known to be at increased risk of breast cancer. AIM: To assess the association of breast density with presence of cancer by measuring mammographic density visually as a percentage, and with two automated volumetric methods, Quantra™ and VolparaDensity™. METHODS: The TOMosynthesis with digital MammographY (TOMMY) study of digital breast tomosynthesis in the Breast Screening Programme of the National Health Service (NHS) of the United Kingdom (UK) included 6020 breast screening assessment cases (of whom 1158 had breast cancer) and 1040 screened women with a family history of breast cancer (of whom two had breast cancer). We assessed the association of each measure with breast cancer risk in these populations at enhanced risk, using logistic regression adjusted for age and total breast volume as a surrogate for body mass index (BMI). RESULTS: All density measures showed a positive association with presence of cancer and all declined with age. The strongest effect was seen with Volpara absolute density, with a significant 3% (95% CI 1-5%) increase in risk per 10 cm3 of dense tissue. The effect of Volpara volumetric density on risk was stronger for large and grade 3 tumours. CONCLUSIONS: Automated absolute breast density is a predictor of breast cancer risk in populations at enhanced risk due to either positive mammographic findings or family history. In the screening context, density could be a trigger for more intensive imaging