Archeota, Fall 2015

https://scholarworks.sjsu.edu/saasc_archeota/1001/thumbnail.jp

Prevalence of age-related macular degeneration in Nakuru, Kenya: a cross-sectional population-based study.

BACKGROUND: Diseases of the posterior segment of the eye, including age-related macular degeneration (AMD), have recently been recognised as the leading or second leading cause of blindness in several African countries. However, prevalence of AMD alone has not been assessed. We hypothesized that AMD is an important cause of visual impairment among elderly people in Nakuru, Kenya, and therefore sought to assess the prevalence and predictors of AMD in a diverse adult Kenyan population. METHODS AND FINDINGS: In a population-based cross-sectional survey in the Nakuru District of Kenya, 100 clusters of 50 people 50 y of age or older were selected by probability-proportional-to-size sampling between 26 January 2007 and 11 November 2008. Households within clusters were selected through compact segment sampling. All participants underwent a standardised interview and comprehensive eye examination, including dilated slit lamp examination by an ophthalmologist and digital retinal photography. Images were graded for the presence and severity of AMD lesions following a modified version of the International Classification and Grading System for Age-Related Maculopathy. Comparison was made between slit lamp biomicroscopy (SLB) and photographic grading. Of 4,381 participants, fundus photographs were gradable for 3,304 persons (75.4%), and SLB was completed for 4,312 (98%). Early and late AMD prevalence were 11.2% and 1.2%, respectively, among participants graded on images. Prevalence of AMD by SLB was 6.7% and 0.7% for early and late AMD, respectively. SLB underdiagnosed AMD relative to photographic grading by a factor of 1.7. After controlling for age, women had a higher prevalence of early AMD than men (odds ratio 1.5; 95% CI, 1.2-1.9). Overall prevalence rose significantly with each decade of age. We estimate that, in Kenya, 283,900 to 362,800 people 50 y and older have early AMD and 25,200 to 50,500 have late AMD, based on population estimates in 2007. CONCLUSIONS: AMD is an important cause of visual impairment and blindness in Kenya. Greater availability of low vision services and ophthalmologist training in diagnosis and treatment of AMD would be appropriate next steps. Please see later in the article for the Editors' Summary

A Case of Highly Aggressive Extraskeletal Myxoid Chondrosarcoma

Extraskeletal myxoid chondrosarcoma (EMC) is a soft tissue malignancy characterized by specific chromosomal abnormalities involving the TEC gene. This disease has historically been considered largely indolent both histologically and clinically. Rarer subsets of EMC exist that demonstrate aggressive histopathologic features and clinical behavior, though it remains unclear whether or not aggressive histopathology is predictive of outcome. Herein we present a case of EMC with aggressive histopathologic features that underwent rapid clinical progression despite initial treatment with curative intent. This case provides the context for a discussion of the existing literature regarding treatment, prognosis, pathology, and genetic/molecular features of EMC in general and aggressive EMC specifically

Sympatric prey responses to lethal top-predator control: predator manipulation experiments

Introduction: Many prey species around the world are suffering declines due to a variety of interacting causes such as land use change, climate change, invasive species and novel disease. Recent studies on the ecological roles of top-predators have suggested that lethal top-predator control by humans (typically undertaken to protect livestock or managed game from predation) is an indirect additional cause of prey declines through trophic cascade effects. Such studies have prompted calls to prohibit lethal top-predator control with the expectation that doing so will result in widespread benefits for biodiversity at all trophic levels. However, applied experiments investigating in situ responses of prey populations to contemporary top-predator management practices are few and none have previously been conducted on the eclectic suite of native and exotic mammalian, reptilian, avian and amphibian predator and prey taxa we simultaneously assess. We conducted a series of landscape-scale, multi-year, manipulative experiments at nine sites spanning five ecosystem types across the Australian continental rangelands to investigate the responses of sympatric prey populations to contemporary poison-baiting programs intended to control top-predators (dingoes) for livestock protection. Results: Prey populations were almost always in similar or greater abundances in baited areas. Short-term prey responses to baiting were seldom apparent. Longer-term prey population trends fluctuated independently of baiting for every prey species at all sites, and divergence or convergence of prey population trends occurred rarely. Top-predator population trends fluctuated independently of baiting in all cases, and never did diverge or converge. Mesopredator population trends likewise fluctuated independently of baiting in almost all cases, but did diverge or converge in a few instances. Conclusions: These results demonstrate that Australian populations of prey fauna at lower trophic levels are typically unaffected by top-predator control because top-predator populations are not substantially affected by contemporary control practices, thus averting a trophic cascade. We conclude that alteration of current top-predator management practices is probably unnecessary for enhancing fauna recovery in the Australian rangelands. More generally, our results suggest that theoretical and observational studies advancing the idea that lethal control of top-predators induces trophic cascades may not be as universal as previously supposed

Reply to the criticism by Johnson et al. (2014) on the report by Allen et al (2013)

We recently reported summary results from a series of applied top-predator manipulation experiments conducted across Australia since the early 1990s (Allen et al. 2013, Frontiers in Zoology 10:39). These experiments permitted the highest level of inference achievable in open rangeland areas and collectively comprise the second-largest predator manipulation experiment conducted on any species anywhere in the world. Johnson et al. (2014) have criticised these experiments, claiming to identify several “serious problems” with our subsequent analyses which, they say, mean that “all inferences that Allen et al. draw from their results should be regarded as unreliable”. Here, we demonstrate that their claims are insignificant, being based on misrepresentations of our stated methods, results and conclusions. We clarify 10 issues they raise in order of their appearance

Ab initio molecular dynamics calculations of ion hydration free energies

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD Delta G(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+-> Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of Delta G(hyd) for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.Comment: 18 pages, 8 figures. This version is essentially the one published in J. Chem. Phy

Experimental Approaches to Theoretical Thinking: Artefacts and Proofs

This chapter discusses some strands of experimental mathematics from both an epistemological and a didactical point of view. We introduce some ancient and recent historical examples in Western and Eastern cultures in order to illustrate how the use of mathematical tools has driven the genesis of many abstract mathematical concepts. We show how the interaction between concrete tools and abstract ideas introduces an "experimental" dimension in mathematics and a dynamic tension between the empirical nature of the activities with the tools and the deductive nature of the discipline. We then discuss how the heavy use of the new technology in mathematics teaching gives new dynamism to this dialectic, specifically through students' proving activities in digital electronic environments. Finally, we introduce some theoretical frameworks to examine and interpret students' thoughts and actions whilst the students work in such environments to explore problematic situations, formulate conjectures and logically prove them. The chapter is followed by a response by Jonathan Borwein and Judy-anne Osborn

Ethnic diversity, social capital and the potential for co-managemet - a case study of Hawaii's longline fishery.pdf

Social networks and social capital can facilitate or constrain collaborative arrangements which can enhance resource governance and adaptability in complex social-ecological systems such as fisheries. Yet, the impact of ethnic diversity among resource users on social network capital in the context of resource governance has not been previously examined. To explore this effect, a social network analysis of the entire population of resource users in Hawaii’s longline fishery was performed, which is currently characterized by a division along ethnic lines and competition over resource use. Results show that ethnicity significantly influences social network structure and is responsible for a homophily effect, with higher levels of bonding and bridging ties found within ethnic groups. In contrast to previous research on social capital, the greatest evidence of linking social capital ties was found in a minority ethnic group rather than the dominant ethnic group. However, results suggest that ethnic fragmentation may be responsible for the marginalization of another minority group, which reported a significantly low level of linking ties to industry leaders, government or management officials, and the scientific community. This study provides the first empirical evidence of the effect of ethnic diversity on social network capital in the fisheries literature, and has implications for the success of collaborative management

Evaporation Rate of Water in Hydrophobic Confinement

The drying of hydrophobic cavities is believed to play an important role in biophysical phenomena such as the folding of globular proteins, the opening and closing of ligand-gated ion channels, and ligand binding to hydrophobic pockets. We use forward flux sampling, a molecular simulation technique, to compute the rate of capillary evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of gap, surface size and temperature. Over the range of conditions investigated (gaps between 9 and 14 {\AA} and surface areas between 1 and 9 nm^2) the free energy barrier to evaporation scales linearly with the gap between hydrophobic surfaces, suggesting that line tension makes the predominant contribution to the free energy barrier. The exponential dependence of the evaporation rate on the gap between confining surfaces causes a ten order-of-magnitude decrease in the rate when the gap increases from 9 to 14 {\AA}. The computed free energy barriers are of the order of 50kT, and are predominantly enthalpic. Evaporation rates per unit area are found to be two orders of magnitude faster in confinement by the larger (9 nm^2) than by the smaller (1nm^2) surfaces considered here, at otherwise identical conditions. We show that this is a direct consequence of the dependence of hydrophobic hydration on the size of solvated objects. For sufficiently large surfaces, the critical nucleus for the evaporation process is a gap-spanning cylindrical vapor tube

Adequate Yearly Progress in Small Rural Schools and Rural Low-Income Schools

Adequate yearly progress (AYP) on No Child Left Behind criteria was examined for a randomly selected sample of districts that qualify for the Rural Education Achievement Program (REAP). The sample involved 10% of districts that were eligible for the Small Rural Schools Achievement (SRSA) program and 10% that were eligible for the Rural and Low-income Schools (RLIS) program. Based on district reports, nearly 80% of SRSA schools made AYP, 11% failed, and 11% did not have adequate data. For schools in the RLIS program, districts reported that 65% made AYP, 29% failed, and 6% did not report adequate data. The SRSA and RLIS samples had different patterns for the categories of students that did not make AYP. Also, SRSA and RLIS districts were differentially distributed across the United States. Implications for interventions are discussed