Atlas of abundance and distribution patterns of ichthyoplankton from the Northeast Pacific Ocean and Bering Sea ecosystems: based on research conducted by the Alaska Fisheries Science Center (1972–1996)

This regional atlas summarizes and illustrates the distribution and abundance patterns of fish eggs and larvae of 102 taxa within 34 families found in the Northeast Pacific Ocean including the Bering Sea, Gulf of Alaska, and U.S. west coast ecosystems. Data were collected over a 20+ year period (1972–1996) by the Recruitment Processes Program of the Alaska Fisheries Science Center (AFSC). Ichthyoplankton catch records used in this atlas were generated from 11,379 tows taken during 100 cruises. For each taxon, general life history data are briefly summarized from the literature. Published information on distribution patterns of eggs and larvae are reviewed for the study area. Data from AFSC ichthyoplankton collections were combined to produce an average spatial distribution for each taxon. These data were also used to estimate mean abundance and percent occurrence by year and month, and relative abundance by larval length and season. Abundance from each tow was measured as catch per 10 m2 surface area. A larval distribution and abundance map was produced with a geographic information system using ArcInfo software. For taxa with identifiable pelagic eggs, distribution maps showing presence or absence of eggs are presented. Presence or absence of adults in the study area is mapped based on recent literature and data from AFSC groundfish surveys. Distributional records for adults and early life history stages revealed several new range extensions. (PDF file contains 288 pages.

Atlas of Wetlands in the Principal Coal Surface Mining Region of Western Kentucky

This atlas contains maps of wetlands and surface mining activity in the Western Kentucky Coal Field, and focuses on a 3960 km2 (1530 mi2) region where approximately 90 percent of surface mining in the Coal field occures. Some present and potential competition exists between surface coal mining and wetland protection. A wetland classification, based on the recent FWS classification, includes six types of palustrine systems and one each of riverine and laucstrine systems. Wetlands and surface mines are located on twenty-seven 7.5 minute USGS quadrangles that define the study region. A total of 460 km2 (177 mi2) of wetlands are identified. Approximately 84 percent are broad-leaved deciduous forested wetlands, mostly as periodically-flooded riparian hardwood forests along broad alluvial bottom-lands. Also, several significant persistent emergent wetlands, shrub-scrub wetlands, and needle-leaved deciduous forested wetlands (bald cypress swamps) are identified in the study region. Summaries of geology and coal mining, hydrology, water quality, wetland vegetation and unique fish and wildlife species are presented for each quadrangle. Effects of existing and potential future surface mining of coal on wetland structure, function, and value are discussed. Species lists for vegetation and fish and wildlife and recent water quality data for the study region are given in the Appendices

A genome-wide study of Hardy–Weinberg equilibrium with next generation sequence data

Statistical tests for Hardy–Weinberg equilibrium have been an important tool for detecting genotyping errors in the past, and remain important in the quality control of next generation sequence data. In this paper, we analyze complete chromosomes of the 1000 genomes project by using exact test procedures for autosomal and X-chromosomal variants. We find that the rate of disequilibrium largely exceeds what might be expected by chance alone for all chromosomes. Observed disequilibrium is, in about 60% of the cases, due to heterozygote excess. We suggest that most excess disequilibrium can be explained by sequencing problems, and hypothesize mechanisms that can explain exceptional heterozygosities. We report higher rates of disequilibrium for the MHC region on chromosome 6, regions flanking centromeres and p-arms of acrocentric chromosomes. We also detected long-range haplotypes and areas with incidental high disequilibrium. We report disequilibrium to be related to read depth, with variants having extreme read depths being more likely to be out of equilibrium. Disequilibrium rates were found to be 11 times higher in segmental duplications and simple tandem repeat regions. The variants with significant disequilibrium are seen to be concentrated in these areas. For next generation sequence data, Hardy–Weinberg disequilibrium seems to be a major indicator for copy number variation.Peer ReviewedPostprint (published version

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Appraisal of health care: from patient value to societal benefit

Aim: This paper summarizes the deficiencies and weaknesses of the most frequently used methods for the allocation of health-care resources. New, more transparent and practical methods for optimizing the allocation of these resources are proposed. Method: The examples of quality-adjusted life years (QALYs) and efficiency frontier (EF) are analyzed to describe weaknesses and problems in decisions regulating health-care provision. After conducting a literature search and discussions with an international group of professionals, three groups of professionals were formed to discuss the assessment and appraisal of health-care services and allocation of available resources. Results: At least seven essential variables were identified that should be heeded when applying the concept of QALYs for decisions concerning health-care provision. The efficiency frontier (EF) concept can be used to set a ceiling price and perform a cost-benefit analysis of provision, but different stakeholders—a biostatistician (efficacy), an economist (costs), a clinician (effectiveness), and the patient (value)—could provide a fairer appraisal of health-care services. Efficacy and costs are often based on falsifiable data. Effectiveness and value depend on the success with which a particular clinical problem has been solved. These data cannot be falsified. The societal perspective is generated by an informal cost-benefit analysis including appraisals by the above-mentioned stakeholders and carried out by an authorized institution. Conclusion: Our analysis suggests that study results expressed in QALYs or as EF cannot be compared unless the variables included in the calculation are specified. It would be far more objective and comprehensive if an authorized institution made an informal decision based on formal assessments of the effectiveness of health-care services evaluated by health-care providers, of the value assessed by consumers, of efficacy described by biostatisticians, and of costs calculated by economists

US Cosmic Visions: New Ideas in Dark Matter 2017: Community Report

This white paper summarizes the workshop "U.S. Cosmic Visions: New Ideas in Dark Matter" held at University of Maryland on March 23-25, 2017.Comment: 102 pages + reference

Improved results of lung transplantation for patients with cystic fibrosis

AbstractPatients with cystic fibrosis pose particular challenges for lung transplantation surgeons. Earlier reports from North America centers suggested that patients with cystic fibrosis were greater risk for heart-lung or isolated lung transplantation than other patients with end-stage pulmonary disease. During a 3 ½ year period, 44 patients with end-stage lung disease resulting from cystic fibrosis underwent double lung transplantation at this institution. During the same interval, 18 patients with cystic fibrosis, died while waiting for a double lung transplantation. The ages of the recipients ranged from 8 to 45 years, and mean forced expiratory volume in 1 second was 21% predicted. Seven patients had Pseudomonas cepacia bacteria before transplantation. Bilateral sequential implantation with omentopexy was used in all patients. There were no operative deaths, although two patients required urgent retransplantation because of graft failure. Cardiopulmonary bypass was necessary in six procedures in five patients and was associated with an increased blood transfusion requirement, longer postoperative ventilation, and longer hospital stay. Actuarial survival rate was 85% at 1 year and 67% at 2 years. Infection was the most common cause of death within 6 months of transplantation ( Pseudomonas cepacia pneumonia was the cause of death in two patients), and bronchitis obliterans was the most common cause of death after 6 months. Actuarial freedom form development of clinically significant bronchiolitis obliterans was 59% at 2 years. Results of pulmonary function tests improved substantially in survivors, with forced expiratory volume in 1 second averaging 78% predicted 2 years after transplantation. Double lung transplantation can be accomplished with acceptable morbidity and mortality in patients with cystic fibrosis. (J THORAC CARDIOVAS SURG 1995;109-:204-35