Seasonal occurrence of fin whale song off Juan Fernandez, Chile

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Buchan, S. J., Gutierrez, L., Balcazar-Cabrera, N., & Stafford, K. M. Seasonal occurrence of fin whale song off Juan Fernandez, Chile. Endangered Species Research, 39, (2019): 135-145, doi:10.3354/esr00956.Fin whales Balaenoptera physalus were the species of baleen whale most widely caught by commercial whaling fleets off the Chilean coast and are globally classified as Endangered. However, very little is known about the present distribution and seasonal movements of fin whales off the coast of Chile. Passive acoustic data collected at the HA03 station of the Preparatory Commission for the Comprehensive Nuclear Test Ban Treaty Organization off the Juan Fernandez Archipelago (JFA) between 2007 and 2016 were analyzed. The temporal occurrence of fin whale song was examined using automatic detection via spectrogram cross-correlation of song notes and by calculating the average acoustic power in the frequency bands of fin whale song. Fin whale song off JFA was composed of regular 17 Hz notes associated with high-frequency components at 85 Hz, with singlet phrasing at a dominant primary inter-note interval of 14.4 s and a secondary interval of 30.8 s. There was a clear seasonal pattern in acoustic presence that was consistent across all years: low or no song during the austral summer and a peak in song occurrence in austral winter. A propagation loss model estimated the detection range at this site to be 186 km. Where the fin whales that are heard off JFA spend the summer months remains an open question. Possible locations include the Western Antarctic Peninsula and/or off northern-central mainland Chile. Further studies should be pursued to better understand the distribution and seasonal movements and to support the conservation of this Endangered species.We thank the Preparatory Commission for the Comprehensive Nuclear Test Ban Treaty Organization and the Chilean Commission of Nuclear Energy for proving the data used in this study. S.J.B. and N.B.C. were supported by the Center for Oceanographic Research COPAS Sur-Austral, CONICYT PIA PFB31. S.J.B. was also supported during analysis and writing by the Office of Naval Research Global (awards N62909-16-2214 and N00014-17-2606), and a grant to the Centro de Estudios Avanzados enZonas Áridas (CEAZA) ‘Proyecto CEAZA, 3er Fortalec-imiento de Centros Regionales, Programa Regional CONI-CYT R16A10003’. Our greatest thanks to John Hodgson MSc, Technical Director at Ocean Acoustic Developments and Adrian Brown of the Defence Science and Technology Laboratory (UK) for carrying out the propagation modelling free of charge. Many thanks to Rex Andrew for his help with PSD figure preparation in R. Thanks also go to Nathan Merchant for his kind help with PAMGuide. Many thanks to Michael Pitzrick for his guidance with XBAT. Many thanks to the members of the Southern Ocean Research Partnership Blue and Fin Whale Acoustic Trends Working group for useful discussions that improved the quality of this study

Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

Ductal carcinoma in situ; Tumor microenvironment; Whole genome sequencingCarcinoma ductal in situ; Microambiente tumoral; Secuenciación del genoma completoCarcinoma ductal in situ; Microambient tumoral; Seqüenciació del genoma completDuctal carcinoma in situ (DCIS) is the most common precursor of invasive breast cancer (IBC), with variable propensity for progression. We perform multiscale, integrated molecular profiling of DCIS with clinical outcomes by analyzing 774 DCIS samples from 542 patients with 7.3 years median follow-up from the Translational Breast Cancer Research Consortium 038 study and the Resource of Archival Breast Tissue cohorts. We identify 812 genes associated with ipsilateral recurrence within 5 years from treatment and develop a classifier that predicts DCIS or IBC recurrence in both cohorts. Pathways associated with recurrence include proliferation, immune response, and metabolism. Distinct stromal expression patterns and immune cell compositions are identified. Our multiscale approach employed in situ methods to generate a spatially resolved atlas of breast precancers, where complementary modalities can be directly compared and correlated with conventional pathology findings, disease states, and clinical outcome.This publication is part of the HTAN (Human Tumor Atlas Network) Consortium paper package. A list of HTAN members is available at humantumoratlas.org/htan-authors/. R01 CA185138-01 (E.S.H.); U2C CA-17-035 Pre-Cancer Atlas (PCA) Research Centers (E.S.H., R.B.W., C.M., K.P., G.A.C., K.O.); UO1 CA214183 (J.R.M.); DOD BC132057 (E.S.H., C.M.); BCRF 19-074 (E.S.H.); BCRF 19-028 (G.A.C.); PRECISION CRUK Grand Challenge (E.S.H.); R01CA193694 (R.B.W., G.A.C.), BCRF PPI-18-006 (R.B.W.). AEI RYC2019- 026576-I, "LaCaixa" Foundation LCF/PR/PR17/51120011 (J.A.S.). S.H.S. was supported by the Lundbeck Foundation (R288-2018-35) and the Danish Cancer Society (R229-A13616). K.E.H. was supported by a CIHR Banting Postdoctoral Fellowship. TBCRC 038 was conducted by the TBCRC, which receives major funding support from The Breast Cancer Research Foundation and Susan G. Komen. Some results in this paper are based upon data generated by the TCGA Research Network

The experience of taking methotrexate for juvenile idiopathic arthritis: results of a cross-sectional survey with children and young people

Background: Children and young people (CYP) with juvenile idiopathic arthritis (JIA) are known to have impaired health-related quality of life (HRQoL), which is improved significantly for many by treatment with methotrexate (MTX). However, a significant proportion of CYP experience difficulties in taking MTX, which may reduce its potential benefits for HRQoL. The aim of this research was to examine how CYP with JIA perceive MTX treatment and how this relates to HRQoL. Methods: CYP aged 8-16 years taking MTX for JIA completed an adapted Parent Adherence Report Questionnaire, which contains 100mm visual analogue scales, to assess difficulty taking MTX, adherence, frequency of negative reactions and helpfulness of MTX. They also completed the Pediatric Quality of Life Inventory (PedsQL) Generic and Rheumatology scales. We collected data on age, gender, JIA course, disease duration, MTX duration of use, route and dose. Number of inflamed and limited joints were indicators of disease severity. Results: 116 CYP participated. Most considered MTX helpful (median 87; interquartile range (IQR) 50.75–98) and reported adherence was high (median 98; IQR 90–100). There was greater variability on scores for difficulty (median 22; IQR 2–69) and frequency of negative reactions (median 14.5; IQR 1.25–80). Mean (S.D.) scores on the PedsQL Physical and Psychosocial subscales were 71.63 (24.02) and 71.78 (19.59) respectively, indicating poorer HRQoL than that reported by healthy children. After controlling for demographic and disease variables, poorer physical HRQoL was significantly accounted for by greater difficulty in taking MTX. Poorer psychosocial HRQoL was significantly accounted for by subcutaneous MTX administration, a lower rating of MTX helpfulness and a greater reported difficulty in taking MTX. Conclusions: Taking MTX for JIA was viewed as helpful by most CYP but HRQoL was poorer in those who reported greater difficulty in taking MTX

Will Patients Benefit from Regionalization of Gynecologic Cancer Care?

OBJECTIVE: Patient chances for cure and palliation for a variety of malignancies may be greatly affected by the care provided by a treating hospital. We sought to determine the effect of volume and teaching status on patient outcomes for five gynecologic malignancies: endometrial, cervical, ovarian and vulvar carcinoma and uterine sarcoma. METHODS: The Florida Cancer Data System dataset was queried for all patients undergoing treatment for gynecologic cancers from 1990-2000. RESULTS: Overall, 48,981 patients with gynecologic malignancies were identified. Endometrial tumors were the most common, representing 43.2% of the entire cohort, followed by ovarian cancer (30.9%), cervical cancer (20.8%), vulvar cancer (4.6%), and uterine sarcoma (0.5%). By univariate analysis, although patients treated at high volume centers (HVC) were significantly younger, they benefited from an improved short-term (30-day and/or 90-day) survival for cervical, ovarian and endometrial cancers. Multivariate analysis (MVA), however, failed to demonstrate significant survival benefit for gynecologic cancer patients treated at teaching facilities (TF) or HVC. Significant prognostic factors at presentation by MVA were age over 65 (HR = 2.6, p<0.01), African-American race (HR = 1.36, p<0.01), and advanced stage (regional HR = 2.08, p<0.01; advanced HR = 3.82, p<0.01, respectively). Surgery and use of chemotherapy were each significantly associated with improved survival. CONCLUSION: No difference in patient survival was observed for any gynecologic malignancy based upon treating hospital teaching or volume status. Although instances of improved outcomes may occur, overall further regionalization would not appear to significantly improve patient survival

International Coercion, Emulation and Policy Diffusion: Market-Oriented Infrastructure Reforms, 1977-1999

Why do some countries adopt market-oriented reforms such as deregulation, privatization and liberalization of competition in their infrastructure industries while others do not? Why did the pace of adoption accelerate in the 1990s? Building on neo-institutional theory in sociology, we argue that the domestic adoption of market-oriented reforms is strongly influenced by international pressures of coercion and emulation. We find robust support for these arguments with an event-history analysis of the determinants of reform in the telecommunications and electricity sectors of as many as 205 countries and territories between 1977 and 1999. Our results also suggest that the coercive effect of multilateral lending from the IMF, the World Bank or Regional Development Banks is increasing over time, a finding that is consistent with anecdotal evidence that multilateral organizations have broadened the scope of the “conditionality” terms specifying market-oriented reforms imposed on borrowing countries. We discuss the possibility that, by pressuring countries into policy reform, cross-national coercion and emulation may not produce ideal outcomes.http://deepblue.lib.umich.edu/bitstream/2027.42/40099/3/wp713.pd

Sex-related differences in aging rate are associated with sex chromosome system in amphibians

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture-recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the "unguarded X/Z effect") or repeat-rich Y/W chromosome (the "toxic Y/W effect") could accelerate aging in the heterogametic sex in some vertebrate clades.Peer reviewe

Submicron Structures Technology and Research

Contains table of contents for Part I, table of contents for Section 1 and reports on thirteen research projects.Joint Services Electronics Program Contract DAAL03-89-C-0001National Science Foundation Grant ECS 87-09806Semiconductor Research Corporation Contract 87-SP-080Hampshire Instruments CorporationNational Science Foundation Grant ECS-85-03443U.S. Air Force - Office of Scientific Research Grant AFOSR-88-0304U.S. Air Force - Office of Scientific Research Grant AFOSR-85-0154X-Opt., IncorporatedNational Aeronautics and Space Administration Contract NAS8-36748AT&T Bell Laboratorie

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations.

The prevalence and spectrum of germline mutations in BRCA1 and BRCA2 have been reported in single populations, with the majority of reports focused on White in Europe and North America. The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) has assembled data on 18,435 families with BRCA1 mutations and 11,351 families with BRCA2 mutations ascertained from 69 centers in 49 countries on six continents. This study comprehensively describes the characteristics of the 1,650 unique BRCA1 and 1,731 unique BRCA2 deleterious (disease-associated) mutations identified in the CIMBA database. We observed substantial variation in mutation type and frequency by geographical region and race/ethnicity. In addition to known founder mutations, mutations of relatively high frequency were identified in specific racial/ethnic or geographic groups that may reflect founder mutations and which could be used in targeted (panel) first pass genotyping for specific populations. Knowledge of the population-specific mutational spectrum in BRCA1 and BRCA2 could inform efficient strategies for genetic testing and may justify a more broad-based oncogenetic testing in some populations

The drivers and impacts of Amazon forest degradation

BACKGROUND: Most analyses of land-use and land-cover change in the Amazon forest have focused on the causes and effects of deforestation. However, anthropogenic disturbances cause degradation of the remaining Amazon forest and threaten their future. Among such disturbances, the most important are edge effects (due to deforestation and the resulting habitat fragmentation), timber extraction, fire, and extreme droughts that have been intensified by human-induced climate change. We synthesize knowledge on these disturbances that lead to Amazon forest degradation, including their causes and impacts, possible future extents, and some of the interventions required to curb them. ADVANCES: Analysis of existing data on the extent of fire, edge effects, and timber extraction between 2001 and 2018 reveals that 0.36 ×106 km2 (5.5%) of the Amazon forest is under some form of degradation, which corresponds to 112% of the total area deforested in that period. Adding data on extreme droughts increases the estimate of total degraded area to 2.5 ×106 km2, or 38% of the remaining Amazonian forests. Estimated carbon loss from these forest disturbances ranges from 0.05 to 0.20 Pg C year−1 and is comparable to carbon loss from deforestation (0.06 to 0.21 Pg C year−1). Disturbances can bring about as much biodiversity loss as deforestation itself, and forests degraded by fire and timber extraction can have a 2 to 34% reduction in dry-season evapotranspiration. The underlying drivers of disturbances (e.g., agricultural expansion or demand for timber) generate material benefits for a restricted group of regional and global actors, whereas the burdens permeate across a broad range of scales and social groups ranging from nearby forest dwellers to urban residents of Andean countries. First-order 2050 projections indicate that the four main disturbances will remain a major threat and source of carbon fluxes to the atmosphere, independent of deforestation trajectories. OUTLOOK: Whereas some disturbances such as edge effects can be tackled by curbing deforestation, others, like constraining the increase in extreme droughts, require additional measures, including global efforts to reduce greenhouse gas emissions. Curbing degradation will also require engaging with the diverse set of actors that promote it, operationalizing effective monitoring of different disturbances, and refining policy frameworks such as REDD+. These will all be supported by rapid and multidisciplinary advances in our socioenvironmental understanding of tropical forest degradation, providing a robust platform on which to co-construct appropriate policies and programs to curb it