Morphometric analysis of ears in two families of pinnipeds

Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 2001Pinniped (seal and sea lion) auditory systems operate in two acoustically distinct environments, air and water. Piniped species differ in how much time they typically spend in water. They therefore offer an exceptional opportunity to investigate aquatic versus terrestrial hearing mechanisms. The Otariidae (sea lions and fur seals) generally divide their time evenly between land and water and have several adaptations; e.g. external pinnae, related to this lifestyle. Phocidae (true seals) spend the majority of their time in water; they lack external pinnae and have well developed ear canal valves. Differences in hearing ranges and sensitivities have been reported recently for members of both of these familes (Kastak, D., Schusterman, RJ., 1998. Low frequency amphibious hearing in pinnipeds. J. Acoust. Soc. Am. 1303,2216- 2228.; Moore, P.W.B., Schusterman, RJ., 1987. Audiometric assessment of northern fur seals, Callorhinus ursinus. Mar. Mamm. Sci. 3,31-53.). In this project, the ear anatomy of three species of pinnipeds: an otariid, the California sea lion (Zalophus californianus), and two phocids, the northern elephant seal (Mirounga angustirostris) and the harbor seal (Phoca vitulina), was examined using computerized tomography (CT scans) and gross dissection. Thee-dimensional reconstructions of the heads and ears from CT data were used to determine interaural dimensions and ossicular chain morphometrics. Ossicular weights and densities were measured conventionally. Results strongly support a canalcentric system for pinniped sound reception and localization. Further, true seals show adaptations for aquatic high frequency specialization.I was supported by an NDSEG fellowship from ONR

The Regency novel and the British constitution: Austen, Brunton, Shelley, and the culture of Romantic decline

During the Regency period (1811-1820), Britons were faced at home with daunting political problems: a scandal-plagued royal family; ongoing war with France; a weak postwar economy; a complicated and relatively new union of Scotland with England and Wales; and an enormous new empire abroad that few understood and none knew how to manage. As a hedge against this apparent national decline, Britons made frequent recourse to an ideal of national cohesion they called the British constitution: in medicine, the constitution (or health) of British bodies; in domestic matters, the constitution of the British family; in science, the constitution of the British atmosphere and landscape; in politics, the constitution of the British polity out of the English, the Welsh, and the Scottish; in government, the constitutional monarchy comprising the House of Lords, the House of Commons, and the king; in jurisprudence, the body of parliamentary law known as the British Constitution. Constitution was for Britons a multivalent and extremely powerful term that emphasized the interrelatedness of political, legal, social, environmental, and medical understandings of lived experience. And yet, as the nineteenth century moved into its second decade, Britons were nevertheless convinced that theirs was a national constitution on the verge of ruin. This dissertation assesses the interaction of British constitutions--physiological, legal, and national--with genre in the Regency-era novels of Jane Austen, Mary Brunton, and Mary Shelley. These novels are no exception to the larger trend of Regency-era declinism; what makes these women's fictive appraisals of Britain's ruin so remarkable is how they use gender and genre categories to unsettle the seemingly stable idea of a British constitution. The novel was primed for this political work because it was the principal conduit through which Britons indulged their obsession with constitutional decline: eighteenth-century sentimental and gothic fictions almost universally feature as a plotline the constitutional ruin of heroines. In their Regency-era novels, Austen, Brunton, and Shelley seized upon this older tradition to level its sexual double standard: constitutional decline, they insist, inheres not in women's bodies (as the sentimental and gothic traditions held), but in a social order--and a literary tradition--that maintained women and other disenfranchised groups in positions of precarious constitutional legitimacy. Taken together, the Regency-era novels of Austen, Brunton, and Shelley demonstrate that the British constitution--that old ideal of national cohesion--might be nothing more (and certainly nothing less) than Britain's greatest national fiction.Doctor of Philosoph

The water quality of the River Enborne, UK: observations from high-frequency Monitoring in a rural, lowland river system

This paper reports the results of a 2-year study of water quality in the River Enborne, a rural river in lowland England. Concentrations of nitrogen and phosphorus species and other chemical determinands were monitored both at high-frequency (hourly), using automated in situ instrumentation, and by manual weekly sampling and laboratory analysis. The catchment land use is largely agricultural, with a population density of 123 persons km−2. The river water is largely derived from calcareous groundwater, and there are high nitrogen and phosphorus concentrations. Agricultural fertiliser is the dominant source of annual loads of both nitrogen and phosphorus. However, the data show that sewage effluent discharges have a disproportionate effect on the river nitrogen and phosphorus dynamics. At least 38% of the catchment population use septic tank systems, but the effects are hard to quantify as only 6% are officially registered, and the characteristics of the others are unknown. Only 4% of the phosphorus input and 9% of the nitrogen input is exported from the catchment by the river, highlighting the importance of catchment process understanding in predicting nutrient concentrations. High-frequency monitoring will be a key to developing this vital process understanding

Donor KIR B Genotype Improves Progression-Free Survival of Non-Hodgkin Lymphoma Patients Receiving Unrelated Donor Transplantation

Donor killer immunoglobulin-like receptor (KIR) genotypes are associated with relapse protection and survival after allotransplantation for acute myelogenous leukemia. We examined the possibility of a similar effect in a cohort of 614 non-Hodgkin lymphoma (NHL) patients receiving unrelated donor (URD) T cell-replete marrow or peripheral blood grafts. Sixty-four percent (n = 396) of donor-recipient pairs were 10/10 allele HLA matched and 26% were 9/10 allele matched. Seventy percent of donors had KIR B/x genotype; the others had KIR A/A genotype. NHL patients receiving 10/10 HLA-matched URD grafts with KIR B/x donors experienced significantly lower relapse at 5 years (26%; 95% confidence interval [CI], 21% to 32% versus 37%; 95% CI, 27% to 46%; P = .05) compared with KIR A/A donors, resulting in improved 5-year progression-free survival (PFS) (35%; 95% CI, 26% to 44% versus 22%; 95% CI, 11% to 35%; P = .007). In multivariate analysis, use of KIR B/x donors was associated with significantly reduced relapse risk (relative risk [RR], .63, P = .02) and improved PFS (RR, .71, P = .008). The relapse protection afforded by KIR B/x donors was not observed in HLA-mismatched transplantations and was not specific to any particular KIR-B gene. Selecting 10/10 HLA-matched and KIR B/x donors should benefit patients with NHL receiving URD allogeneic transplantation

Southeastern Association of Law Libraries Annual Meeting

The 2009 SEAALL Annual Meeting was held in Athens Georgia, April 16-18, 2009

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

BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology

Background Identified as an Alzheimer’s disease (AD) susceptibility gene by genome wide-association studies, BIN1 has 10 isoforms that are expressed in the Central Nervous System (CNS). The distribution of these isoforms in different cell types, as well as their role in AD pathology still remains unclear. Methods Utilizing antibodies targeting specific BIN1 epitopes in human post-mortem tissue and analyzing mRNA expression data from purified microglia, we identified three isoforms expressed in neurons and astrocytes (isoforms 1, 2 and 3) and four isoforms expressed in microglia (isoforms 6, 9, 10 and 12). The abundance of selected peptides, which correspond to groups of BIN1 protein isoforms, was measured in dorsolateral prefrontal cortex, and their relation to neuropathological features of AD was assessed. Results Peptides contained in exon 7 of BIN1’s N-BAR domain were found to be significantly associated with AD-related traits and, particularly, tau tangles. Decreased expression of BIN1 isoforms containing exon 7 is associated with greater accumulation of tangles and subsequent cognitive decline, with astrocytic rather than neuronal BIN1 being the more likely culprit. These effects are independent of the BIN1 AD risk variant. Conclusions Exploring the molecular mechanisms of specific BIN1 isoforms expressed by astrocytes may open new avenues for modulating the accumulation of Tau pathology in AD

Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine

Communities, birth attendants and health facilities: a continuum of emergency maternal and newborn care (the global network's EmONC trial)

<p>Abstract</p> <p>Background</p> <p>Maternal and newborn mortality rates remain unacceptably high, especially where the majority of births occur in home settings or in facilities with inadequate resources. The introduction of emergency obstetric and newborn care services has been proposed by several organizations in order to improve pregnancy outcomes. However, the effectiveness of emergency obstetric and neonatal care services has never been proven. Also unproven is the effectiveness of community mobilization and community birth attendant training to improve pregnancy outcomes.</p> <p><b>Methods/Design</b></p> <p>We have developed a cluster-randomized controlled trial to evaluate the impact of a comprehensive intervention of community mobilization, birth attendant training and improvement of quality of care in health facilities on perinatal mortality in low and middle-income countries where the majority of births take place in homes or first level care facilities. This trial will take place in 106 clusters (300-500 deliveries per year each) across 7 sites of the Global Network for Women's and Children's Health Research in Argentina, Guatemala, India, Kenya, Pakistan and Zambia. The trial intervention has three key elements, community mobilization, home-based life saving skills for communities and birth attendants, and training of providers at obstetric facilities to improve quality of care. The primary outcome of the trial is perinatal mortality. Secondary outcomes include rates of stillbirth, 7-day neonatal mortality, maternal death or severe morbidity (including obstetric fistula, eclampsia and obstetrical sepsis) and 28-day neonatal mortality.</p> <p>Discussion</p> <p>In this trial, we are evaluating a combination of interventions including community mobilization and facility training in an attempt to improve pregnancy outcomes. If successful, the results of this trial will provide important information for policy makers and clinicians as they attempt to improve delivery services for pregnant women and newborns in low-income countries.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov NCT01073488</p