On the flow of non-axisymmetric perturbations of cylinders via surface diffusion

We study the surface diffusion flow acting on a class of general (non--axisymmetric) perturbations of cylinders $\mathcal{C}_r$ in ${\rm I \! R}^3$. Using tools from parabolic theory on uniformly regular manifolds, and maximal regularity, we establish existence and uniqueness of solutions to surface diffusion flow starting from (spatially--unbounded) surfaces defined over $\mathcal{C}_r$ via scalar height functions which are uniformly bounded away from the central cylindrical axis. Additionally, we show that $\mathcal{C}_r$ is normally stable with respect to $2 \pi$--axially--periodic perturbations if the radius $r > 1$,and unstable if $0 < r < 1$. Stability is also shown to hold in settings with axial Neumann boundary conditions.Comment: 20 pages, 1 figure, submitted for publicatio

The Importance of Craniofacial Sutures in Biomechanical Finite Element Models of the Domestic Pig

Craniofacial sutures are a ubiquitous feature of the vertebrate skull. Previous experimental work has shown that bone strain magnitudes and orientations often vary when moving from one bone to another, across a craniofacial suture. This has led to the hypothesis that craniofacial sutures act to modify the strain environment of the skull, possibly as a mode of dissipating high stresses generated during feeding or impact. This study tests the hypothesis that the introduction of craniofacial sutures into finite element (FE) models of a modern domestic pig skull would improve model accuracy compared to a model without sutures. This allowed the mechanical effects of sutures to be assessed in isolation from other confounding variables. These models were also validated against strain gauge data collected from the same specimen ex vivo. The experimental strain data showed notable strain differences between adjacent bones, but this effect was generally not observed in either model. It was found that the inclusion of sutures in finite element models affected strain magnitudes, ratios, orientations and contour patterns, yet contrary to expectations, this did not improve the fit of the model to the experimental data, but resulted in a model that was less accurate. It is demonstrated that the presence or absence of sutures alone is not responsible for the inaccuracies in model strain, and is suggested that variations in local bone material properties, which were not accounted for by the FE models, could instead be responsible for the pattern of results

HIV-1 integrase polymorphisms are associated with prior antiretroviral drug exposure

In a recent summary of integrase sequences, primary integrase inhibitor mutations were rare. In a review of integrase inhibitor-naïve Australian HIV-1 sequences, primary mutations were not identified, although the accessory mutation G140S was detected. A link with previous antiretroviral therapy, intra-subtype B divergence across the integrase gene and transmission of integrase polymorphisms were also noted. Based on these findings, we would recommend ongoing surveillance of integrase mutations, and integrase region sequencing for patients prior to commencement of integrase inhibitors

"Do I really want to do this?" Longitudinal cohort study participants' perspectives on postal survey design: a qualitative study

<p>Abstract</p> <p>Background</p> <p>Randomised controlled trials have investigated aspects of postal survey design yet cannot elaborate on reasons behind participants' decision making and survey behaviour. This paper reports participants' perspectives of the design of, and participation in, a longitudinal postal cohort survey. It describes strengths and weaknesses in study design from the perspectives of study participants and aims to contribute to the: 1) design of future cohort surveys and questionnaires generally and, 2) design of cohort surveys for people with musculoskeletal disorders (MSDs) specifically.</p> <p>Methods</p> <p>In-depth interviews explored the design of postal surveys previously completed by participants. Interviews used open ended questioning with a topic guide for prompts if areas of interest were not covered spontaneously. Thematic data analysis was undertaken based on the framework method. A second researcher verified all coding.</p> <p>Results</p> <p>Data from fourteen interviews were analysed within three main themes; participation, survey design and survey content. One of the main findings was the importance of clear communication aimed at the correct audience both when inviting potential participants to take part and within the survey itself. Providing enough information about the study, having a topic of interest and an explanation of likely benefits of the study were important when inviting people to participate. The neutrality of the survey and origination from a reputable source were both important; as was an explanation about why information was being collected within the survey itself. Study findings included participants' impressions when invited to take part, why they participated, the acceptability of follow-up of non-responders and why participants completed the follow-up postal survey. Also discussed were participants' first impression of the survey, its length, presentation and participants' views about specific questions within the survey.</p> <p>Conclusions</p> <p>Ideas generated in this study provide an insight into participants' decision making and survey behaviour and may enhance the acceptability of future surveys to potential participants. As well as clear communication, participants valued incentives and survey questions that were relevant to them. However, opinions varied as to the preferred format for responses with some advising more opportunity for open-ended feedback. We also found that some standard format questions can raise quandaries for individual participants.</p

The Healthy Men Study: An Evaluation of Exposure to Disinfection By-Products in Tap Water and Sperm Quality

BackgroundChlorination of drinking water generates disinfection by-products (DBPs), which have been shown to disrupt spermatogenesis in rodents at high doses, suggesting that DBPs could pose a reproductive risk to men. In this study we assessed DBP exposure and testicular toxicity, as evidenced by altered semen quality.MethodsWe conducted a cohort study to evaluate semen quality in men with well-characterized exposures to DBPs. Participants were 228 presumed fertile men with different DBP profiles. They completed a telephone interview about demographics, health history, water consumption, and other exposures and provided a semen sample. Semen outcomes included sperm concentration and morphology, as well as DNA integrity and chromatin maturity. Exposures to DBPs were evaluated by incorporating data on water consumption and bathing and showering with concentrations measured in tap water. We used multivariable linear regression to assess the relationship between exposure to DBPs and adverse sperm outcomes.ResultsThe mean (median) sperm concentration and sperm count were 114.2 (90.5) million/mL and 362 (265) million, respectively. The mean (median) of the four trihalomethane species (THM4) exposure was 45.7 (65.3) μg/L, and the mean (median) of the nine haloacetic acid species (HAA9) exposure was 30.7 (44.2) μg/L. These sperm parameters were not associated with exposure to these classes of DBPs. For other sperm outcomes, we found no consistent pattern of increased abnormal semen quality with elevated exposure to trihalomethanes (THMs) or haloacetic acids (HAAs). The use of alternate methods for assessing exposure to DBPs and site-specific analyses did not change these results.ConclusionsThe results of this study do not support an association between exposure to levels of DBPs near or below regulatory limits and adverse sperm outcomes in humans

Farmer seed networks make a limited contribution to agriculture? Four common misconceptions

The importance of seed provisioning in food security and nutrition, agricultural development and rural livelihoods, and agrobiodiversity and germplasm conservation is well accepted by policy makers, practitioners and researchers. The role of farmer seed networks is less well understood and yet is central to debates on current issues ranging from seed sovereignty and rights for farmers to GMOs and the conservation of crop germplasm. In this paper we identify four common misconceptions regarding the nature and importance of farmer seed networks today. (1) Farmer seed networks are inefficient for seed dissemination. (2) Farmer seed networks are closed, conservative systems. (3) Farmer seed networks provide ready, egalitarian access to seed. (4) Farmer seed networks are destined to weaken and disappear. We challenge these misconceptions by drawing upon recent research findings and the authors’ collective field experience in studying farmer seed systems in Africa, Europe, Latin America and Oceania. Priorities for future research are suggested that would advance our understanding of seed networks and better inform agricultural and food policy

A systems approach to model natural variation in reactive properties of bacterial ribosomes

<p>Abstract</p> <p>Background</p> <p>Natural variation in protein output from translation in bacteria and archaea may be an organism-specific property of the ribosome. This paper adopts a systems approach to model the protein output as a measure of specific ribosome reactive properties in a ribosome-mediated translation apparatus. We use the steady-state assumption to define a transition state complex for the ribosome, coupled with mRNA, tRNA, amino acids and reaction factors, as a subsystem that allows a focus on the completed translational output as a measure of specific properties of the ribosome.</p> <p>Results</p> <p>In analogy to the steady-state reaction of an enzyme complex, we propose a steady-state translation complex for mRNA from any gene, and derive a maximum specific translation activity, <it>T</it>_{<it>a</it>(max)}, as a property of the ribosomal reaction complex. <it>T</it>_{<it>a</it>(max)}has units of <it>a</it>-protein output per time per <it>a</it>-specific mRNA. A related property of the ribosome, <inline-formula><m:math name="1752-0509-2-62-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:msub><m:mover accent="true"><m:mi>T</m:mi><m:mo>˜</m:mo></m:mover><m:mrow><m:mi>a</m:mi><m:mo stretchy="false">(</m:mo><m:mi>max</m:mi><m:mo>⁡</m:mo><m:mo stretchy="false">)</m:mo></m:mrow></m:msub></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmivaqLbaGaadaWgaaWcbaGaemyyaeMaeiikaGIagiyBa0MaeiyyaeMaeiiEaGNaeiykaKcabeaaaaa@3464@</m:annotation></m:semantics></m:math></inline-formula>, has units of <it>a</it>-protein per time per total RNA with the relationship <inline-formula><m:math name="1752-0509-2-62-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:msub><m:mover accent="true"><m:mi>T</m:mi><m:mo>˜</m:mo></m:mover><m:mrow><m:mi>a</m:mi><m:mo stretchy="false">(</m:mo><m:mi>max</m:mi><m:mo>⁡</m:mo><m:mo stretchy="false">)</m:mo></m:mrow></m:msub></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmivaqLbaGaadaWgaaWcbaGaemyyaeMaeiikaGIagiyBa0MaeiyyaeMaeiiEaGNaeiykaKcabeaaaaa@3464@</m:annotation></m:semantics></m:math></inline-formula> = <it>ρ</it>_{<it>a </it>}<it>T</it>_{<it>a</it>(max)}, where <it>ρ</it>_{<it>a </it>}represents the fraction of total RNA committed to translation output of <it>P</it>_{<it>a </it>}from gene <it>a </it>message. <it>T</it>_{<it>a</it>(max)}as a ribosome property is analogous to <it>k</it>_catfor a purified enzyme, and <inline-formula><m:math name="1752-0509-2-62-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:msub><m:mover accent="true"><m:mi>T</m:mi><m:mo>˜</m:mo></m:mover><m:mrow><m:mi>a</m:mi><m:mo stretchy="false">(</m:mo><m:mi>max</m:mi><m:mo>⁡</m:mo><m:mo stretchy="false">)</m:mo></m:mrow></m:msub></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmivaqLbaGaadaWgaaWcbaGaemyyaeMaeiikaGIagiyBa0MaeiyyaeMaeiiEaGNaeiykaKcabeaaaaa@3464@</m:annotation></m:semantics></m:math></inline-formula> is analogous to enzyme specific activity in a crude extract.</p> <p>Conclusion</p> <p>Analogy to an enzyme reaction complex led us to a ribosome reaction model for measuring specific translation activity of a bacterial ribosome. We propose to use this model to design experimental tests of our hypothesis that specific translation activity is a ribosomal property that is subject to natural variation and natural selection much like <it>V</it>_maxand <it>K</it>_mfor any specific enzyme.</p

Locked and loading megathrust linked to active subduction beneath the Indo-Burman Ranges

The Indo-Burman mountain rangesmarkthe boundary between the Indian and Eurasian plates, north of the Sumatra–Andaman subduction zone. Whether subduction still occurs along this subaerial section of the plate boundary, with 46mm/yr of highly oblique motion, is contentious. About 21mm/yr of shear motion is taken up along the Sagaing Fault, on the eastern margin of the deformation zone. It has been suggested that the remainder of the relative motion is taken up largely or entirely by horizontal strike-slip faulting and that subduction has stopped. Here we present GPS measurements of plate motions in Bangladesh, combined with measurements from Myanmar and northeast India, taking advantage of a more than 300 km subaerial accretionary prism spanning the Indo-Burman Ranges to the Ganges–Brahmaputra Delta. They reveal 13–17mm/yr of plate convergence on an active, shallowly dipping and locked megathrust fault. Most of the strike-slip motion occurs on a few steep faults, consistent with patterns of strain partitioning in subduction zones. Our results strongly suggest that subduction in this region is active, despite the highly oblique plate motion and thick sediments. We suggest that the presence of a locked megathrust plate boundary represents an underappreciated hazard in one of the most densely populated regions of the world

Very Bright Green Fluorescent Proteins from the Pontellid Copepod Pontella mimocerami

Marguerite E. Hunt is with UT Austin; Michael P. Scherrer is with UT Austin; Frank D. Ferrari is with the National Museum of Natural History at the Smithsonian Institution; Mikhail V. Matz is with UT Austin.Background -- Fluorescent proteins (FP) homologous to the green fluorescent protein (GFP) from the jellyfish Aequorea victoria have revolutionized biomedical research due to their usefulness as genetically encoded fluorescent labels. Fluorescent proteins from copepods are particularly promising due to their high brightness and rapid fluorescence development. Results -- Here we report two novel FPs from Pontella mimocerami (Copepoda, Calanoida, Pontellidae), which were identified via fluorescence screening of a bacterial cDNA expression library prepared from the whole-body total RNA of the animal. The proteins are very similar in sequence and spectroscopic properties. They possess high molar extinction coefficients (79,000 M−1 cm−) and quantum yields (0.92), which make them more than two-fold brighter than the most common FP marker, EGFP. Both proteins form oligomers, which we were able to counteract to some extent by mutagenesis of the N-terminal region; however, this particular modification resulted in substantial drop in brightness. Conclusions -- The spectroscopic characteristics of the two P. mimocerami proteins place them among the brightest green FPs ever described. These proteins may therefore become valuable additions to the in vivo imaging toolkit.This work was supported by the Ocean Exploration program of the National Oceanic and Atmospheric Administration (“Operation Deep Scope 2007”), and the National Institutes of Health grant R01 GM078247 to M. V. M. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o