Stock assessment of Pacific sardine for 1998 with management recommendations for 1999

The primary goal of sardine management as directed by the California Fish and Game Code is rehabilitation of the resource with an added objective of maximizing sustained harvest. Accordingly, the Code states that the annual sardine quota can be set at an amount greater than 1,000 tons, providing that the level of take allows for continued increase in the spawning population. We estimated the sardine population size within the range of the fishery and survey data (Ensenada, Baja California to San Francisco, California) to have been 1,182,881 short tons on July 1, 1998. Our estimate was based on output from a modified version of the integrated stock assessment model called CANSAR (Deriso et al. 1996). CANSAR is a forward-casting, age-structured analysis using fishery-dependent and fishery-independent data to obtain annual estimates of sardine abundance, year-class strength and age-specific fishing mortality for 1983 through the first semester of 1998. Non-linear least-squares criteria are used to find the best fit between model estimates and input data. Questions about stock structure and range extent remain major sources of uncertainty in assessing current sardine population biomass. Recent survey results and anecdotal evidence suggest increased sardine abundance in the Pacific Northwest and areas offshore from central and southern California. It is difficult to determine if those fish were part of the stock available to the California fishery. Last year, in an attempt to address this problem, the original CANSAR model was reconfigured into a Two-Area Migration Model (CANSAR-TAM; Hill et al. 1998) which accounted for sardine lost to the areas of the fishery and abundance surveys due to population expansion and net emigration. While the model includes guesses and major assumptions about net emigration and recruitment, it provides an estimate which is likely closer to biological reality than original CANSAR assessments. Corroborative results from a new, preliminary sardine stock assessment model, 'SAM', are also presented in this report. Based on the 1998 estimate of age 1+ biomass within the range of the fishery and survey data, and a proposed harvest formula in the draft Coastal Pelagic Species Fishery Management Plan (Amendment 8), we recommend a 1999 sardine harvest quota of 132,800 tons for the California fishery. The 1999 quota is a significant increase from the final 1998 sardine harvest quota for California of 48,000 tons. (93pp.

Measurement errors in body size of sea scallops (Placopecten magellanicus) and their effect on stock assessment models

Body-size measurement errors are usually ignored in stock assessments, but may be important when body-size data (e.g., from visual sur veys) are imprecise. We used experiments and models to quantify measurement errors and their effects on assessment models for sea scallops (Placopecten magellanicus). Errors in size data obscured modes from strong year classes and increased frequency and size of the largest and smallest sizes, potentially biasing growth, mortality, and biomass estimates. Modeling techniques for errors in age data proved useful for errors in size data. In terms of a goodness of model fit to the assessment data, it was more important to accommodate variance than bias. Models that accommodated size errors fitted size data substantially better. We recommend experimental quantification of errors along with a modeling approach that accommodates measurement errors because a direct algebraic approach was not robust and because error parameters were diff icult to estimate in our assessment model. The importance of measurement errors depends on many factors and should be evaluated on a case by case basis

The Grizzly, November 13, 1981

Suspicious Visitor Causes Alarm • Whistle Blowing: The Problem of Ethics in Business • Two Students Caught In Breaking and Entering • Pledging Discussion • Student Teachers Putting in Their Hours • Powlette Speaks on Values • USGA Notes • Students Attend Orchestra Concert in Philadelphia • Ursinus Represented at PCCA Choir Festival • Winterfest Brings Culture Shock to UC • Study Abroad Series: Gidget Goes to Rome • UC Attempts \u27World\u27s Largest Sandcastle\u27 • Davis Selected All-American • Dickinson vs Bears in ECAC Championship • Student Plays for Peru in Pan Am Games • Swimmers Enthusiastic About New Season • Fencing Foils F&M • Bears End Disappointing Season With Loss • Grapplers Anxious To Begin • U.C. Harriers MAC Champs... Againhttps://digitalcommons.ursinus.edu/grizzlynews/1067/thumbnail.jp

Re-examining the relationship between audiometric profile and tinnitus pitch

Objective: We explored the relationship between audiogram shape and tinnitus pitch to answer questions arising from neurophysiological models of tinnitus: ‘Is the dominant tinnitus pitch associated with the edge of hearing loss?’ and ‘Is such a relationship more robust in people with narrow tinnitus bandwidth or steep sloping hearing loss?’ Design: A broken-stick fitting objectively quantified slope, degree and edge of hearing loss up to 16 kHz. Tinnitus pitch was characterized up to 12 kHz. We used correlation and multiple regression analyses for examining relationships with many potentially predictive audiometric variables. Study Sample: 67 people with chronic bilateral tinnitus (43 men and 24 women, aged from 22 to 81 years). Results: In this ample of 67 subjects correlation failed to reveal any relationship between the tinnitus pitch and the edge frequency. The tinnitus pitch generally fell within the area of hearing loss. The pitch of the tinnitus in a subset of subjects with a narrow tinnitus bandwidth (n = 23) was associated with the audiometric edge. Conclusions: Our findings concerning subjects with narrow tinnitus bandwidth suggest that this can be used as an a priori inclusion criterion. A large group of such subjects should be tested to confirm these results

Topoisomerase II alpha gene copy loss has adverse prognostic significance in ERBB2-amplified breast cancer: a retrospective study of paraffin-embedded tumor specimens and medical charts

<p>Abstract</p> <p>Background</p> <p>Amplification of the <it>ERBB2 </it>(<it>Her-2/neu</it>) oncogene, which occurs in approximately 25% of breast carcinomas, is a known negative prognostic factor. Available data indicate that a variable number of nearby genes on chromosome 17q may be co-amplified or deleted, forming a continuous amplicon of variable size. In approximately 25% of these patients, the amplicon extends to the gene for <it>topoisomerase II alpha </it>(<it>TOP2A</it>), a target for anthracyclines. We sought to understand the significance of these associated genomic changes for breast cancer prognosis and predicting response to therapy.</p> <p>Methods and patients</p> <p>Archival tissue samples from 63 breast cancer patients with <it>ERBB2 </it>amplification, stages 0–IV, were previously analyzed with FISH probes for genes located near <it>ERBB2</it>. In the present study, the clinical outcome data were determined for all patients presenting at stages I–III for whom adequate clinical follow up was available.</p> <p>Results</p> <p>Four amplicon patterns (Classes) were identified. These were significantly associated with the clinical outcome, specifically, recurrence of breast cancer. The Amplicon class IV with deleted <it>TOP2A </it>had 67% (6/9) cases with recurrence, whereas the other three classes combined had only 12% (3/25) cases (p-value = 0.004) at the time of last follow-up. <it>TOP2A </it>deletion was also significantly associated with time to recurrence (p-value = 0.0002). After adjusting for age in Cox regression analysis, the association between <it>TOP2A </it>deletion and time to recurrence remains strongly significant (p-value = 0.002) whereas the association with survival is marginally significant (p-value = 0.06).</p> <p>Conclusion</p> <p><it>TOP2A </it>deletion is associated with poor prognosis in <it>ERBB2</it>-amplified breast carcinomas. Clarification of the mechanism of this association will require additional study.</p

Dynamic Responsiveness in the U.S. Senate

I develop a theory of dynamic responsiveness that suggests that parties that win elections choose candidates who are more extreme and parties that lose elections choose candidates who are more moderate. Moreover, the size of past victories matters. Close elections yield little change, but landslides yield larger changes in the candidates offered by both parties. I test this theory by analyzing the relationship between Republican vote share in U.S. Senate elections and the ideology of candidates offered in the subsequent election. The results show that Republican (Democratic) victories in past elections yield candidates who are more (less) conservative in subsequent elections, and the effect is proportional to the margin of victory. This suggests that parties or candidates pay attention to past election returns. One major implication is that parties may remain polarized in spite of their responsiveness to the median voter

Impacts of 21st century climate change on global air pollution-related premature mortality

Climate change modulates surface concentrations of fine particulate matter (PM2.5) and ozone (O-3), indirectly affecting premature mortality attributed to air pollution. We estimate the change in global premature mortality and years of life lost (YLL) associated with changes in surface O-3 and PM2.5 over the 21st century as a result of climate change. We use a global coupled chemistry-climate model to simulate current and future climate and the effect of changing climate on air quality. Epidemiological concentration-response relationships are applied to estimate resulting changes in premature mortality and YLL. The effect of climate change on air quality is isolated by holding emissions of air pollutants constant while allowing climate to evolve over the 21st century according to a moderate projection of greenhouse gas emissions (A1B scenario). Resulting changes in 21st century climate alone lead to an increase in simulated PM2.5 concentrations globally, and to higher (lower) O-3 concentrations over populated (remote) regions. Global annual premature mortality associated with chronic exposure to PM2.5 increases by approximately 100 thousand deaths (95 % confidence interval, CI, of 66-130 thousand) with corresponding YLL increasing by nearly 900 thousand (95 % CI, 576-1,128 thousand) years. The annual premature mortality due to respiratory disease associated with chronic O-3 exposure increases by +6,300 deaths (95 % CI, 1,600-10,400). This climate penalty indicates that stronger emission controls will be needed in the future to meet current air quality standards and to avoid higher health risks associated with climate change induced worsening of air quality over populated regions.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326944000011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Environmental SciencesMeteorology &amp; Atmospheric SciencesSCI(E)EI17ARTICLE2239-25312

DOP-PCR amplification of whole genomic DNA and microchip-based capillary electrophoresis.

Universal or whole genome amplification by polymerase chain reaction (PCR) is a rapid and efficient method to generate fragments representing the target sequence, as well as to increase a limited amount of template. One of the most common PCR protocols for total genome amplification is the interspersed repetitive sequence-PCR (IRS-PCR) in which primers specific for human repeat-rich regions are used to generate PCR products between adjacent repeated sequences (1). However, although IRS-PCR across regions such as Alu families of human repeat has been demonstrated to be useful, the nonuniform distribution of repeat-rich region within the human genome has been a limitation. Alternative strategies have been proposed. In the primer-extension preamplification (PEP), multiple rounds of extensions with Taq DNA polymerase and a random mixture of 15-base oligonucleotides as primers produce multiple copies of the template present in the sample (2–5). In a more demanding protocol, called linker adaptor-PCR, RsaI restricted genomic DNA fragments are ligated to SmaI-cut pUC plasmid. Subsequently, the inserts are amplified by PCR using the universal M13/pUC sequencing and reverse sequencing primers and then released by EcoRI digestion (6). The tagged random primer PCR (T-PCR) is a two-step PCR strategy which consists of a pool of all possible 3'-sequences for binding to the target DNA and a constant 5'-region for the detection of incorporated primers (7). Recently, degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) was developed to allow random amplification of DNA from any source (8–10). DOP-PCR uses a partially degenerate sequence in a PCR protocol with two different annealing temperatures. It has been successfully applied for amplifying entire genomes such as human, mouse, and fruit fly, as well as isolated human chromosomes and cosmids (11). The technique has also been used to prepare whole chromosome paint probes (11,12) for micro-FISH assays (13–15), comparative genomic hybridization (16), to increase the amount of sample for genotyping (17), and genomic fingerprinting (18). The DOP-PCR primer consists of three regions. The 5'-end carries a recognition sequence for XhoI (C•TCGAG), a restriction endonuclease that cuts rarely within the human genome. This sequence can be used for cloning, if desired. The sequence is then followed by a middle portion containing six nucleotides of degenerate sequence (NNNNNN, where N = A, C, G, or T in approximately equal proportions) and a 3'-end sequence containing six specific bases (ATGTGG) which primes the reaction approximately every 4 kb (8,9). The principle of the technique is that at a sufficiently low annealing temperature only the six specific nucleotides included in the 3'-end of the degenerate oligonucleotide will anneal to the genomic strand allowing the primer to initiate PCR. The PCR fragments are then generated which contain the full length of the oligoprimer at one end and its complementary sequence at the other end. Subsequently, the temperature is increased to the level required for the full length of the degenerate primer to anneal. For additional details, we direct the reader to the original papers (8,9). We have adapted the DOP-PCR technique to a three-microchip format (19). DOP-PCR amplified genomic DNA produced in a first silicon-glass chip is transferred to a second chip for a locus-specific, multiplex PCR of the dystrophin gene exons in order to detect deletions causing Duchenne/Becker muscular dystrophy (DMD/BMD). Amplicons from the multiplex-PCR are then analyzed by electrophoresis in a third microchip. The analytical performance of the microchip capillary electrophoresis (MCE) is also compared to conventional capillary electrophoresis (CE)