River Response to Sediment Supply: The Sand Bed Case

Effective management of in-channel and floodplain habitat requires an ability to forecast river response to changes in water and sediment supply. These changes may result from dam construction/decommissioning, changes in reservoir operations, or changes in grazing or forestry practices. If a change in water and sediment supply causes sediment to be delivered faster than the channel’s capacity to transport it, sediment will accumulate in the reach, leading to changes in channel form and increasing the potential for flooding. A decrease in sediment supply relative to transport capacity can lead to channel incision. The extent and timing of sediment accumulation or evacuation can be moderated, even reversed, by poorly understood changes in the river bed grain size. This dissertation explores the joint response of river bed texture and sediment storage in order to better predict the magnitude of channel change in response to upstream changes in infrastructure or land use in sand bed rivers. We use a combination of field measurements of sediment transport, analysis of channel change from repeat aerial images, and numerical modeling to explore the interaction among sediment supply rate and grain size with bed grain size and morphologic adjustment. We find that sand sizes are sorted throughout the alluvial channel and floodplain such that the in-channel response may be different than floodplain adjustments. At our field site, certain sand sizes evacuate as the bed coarsened while other sand sizes accumulated in the floodplains. These findings indicate that conditions of sediment accumulation or evacuation cannot reveal important changes in the river and size fractional sediment budgets are needed to evaluate channel change. Our numerical modeling indicates that the supply grain size has a strong effect on the grain size of sand on the bed, making the river more or less effective at transporting sediment. Under conditions when the sediment supply increases, such as after wildfires, dam removals, or changes in land use or forestry practices, small changes in the grain size of sand on the channel bed can cause sediment to accumulate, evacuate, or there may be no morphologic adjustment depending on the length of the disturbance and how the supply grain size changes. This has important implications for forecasting downstream impacts. Management concerns may be delayed or even eliminated depending on the bed grain size response. These findings demonstrate the importance of considering the supply grain size and behavior and destination of the fractional sizes in transport when predicting a sand-bed river response to a watershed disturbance

Measuring Channel Planform Change From Image Time Series: A Generalizable, Spatially Distributed, Probabilistic Method for Quantifying Uncertainty

Abstract Channels change in response to natural or anthropogenic fluctuations in streamflow and/or sediment supply and measurements of channel change are critical to many river management applications. Whereas repeated field surveys are costly and time‐consuming, remote sensing can be used to detect channel change at multiple temporal and spatial scales. Repeat images have been widely used to measure long‐term channel change, but these measurements are only significant if the magnitude of change exceeds the uncertainty. Existing methods for characterizing uncertainty have two important limitations. First, while the use of a spatially variable image co‐registration error avoids the assumption that errors are spatially uniform, this type of error, as originally formulated, can only be applied to linear channel adjustments, which provide less information on channel change than polygons of erosion and deposition. Second, previous methods use a level‐of‐detection (LoD) threshold to remove non‐significant measurements, which is problematic because real changes that occurred but were smaller than the LoD threshold would be removed. In this study, we present a new method of quantifying uncertainty associated with channel change based on probabilistic, spatially varying estimates of co‐registration error and digitization uncertainty that obviates a LoD threshold. The spatially distributed probabilistic (SDP) method can be applied to both linear channel adjustments and polygons of erosion and deposition, making this the first uncertainty method generalizable to all metrics of channel change. Using a case study from the Yampa River, Colorado, we show that the SDP method reduced the magnitude of uncertainty and enabled us to detect smaller channel changes as significant. Additionally, the distributional information provided by the SDP method allowed us to report the magnitude of channel change with an appropriate level of confidence in cases where a simple LoD approach yielded an indeterminate result

Genetic variation in hippocampal microRNA expression differences in C57BL/6 J X DBA/2 J (BXD) recombinant inbred mouse strains

Background miRNAs are short single-stranded non-coding RNAs involved in post-transcriptional gene regulation that play a major role in normal biological functions and diseases. Little is currently known about how expression of miRNAs is regulated. We surveyed variation in miRNA abundance in the hippocampus of mouse inbred strains, allowing us to take a genetic approach to the study of miRNA regulation, which is novel for miRNAs. The BXD recombinant inbred panel is a very well characterized genetic reference panel which allows quantitative trait locus (QTL) analysis of miRNA abundance and detection of correlates in a large store of brain and behavioural phenotypes. Results We found five suggestive trans QTLs for the regulation of miRNAs investigated. Further analysis of these QTLs revealed two genes, Tnik and Phf17, under the miR-212 regulatory QTLs, whose expression levels were significantly correlated with miR-212 expression. We found that miR-212 expression is correlated with cocaine-related behaviour, consistent with a reported role for this miRNA in the control of cocaine consumption. miR-31 is correlated with anxiety and alcohol related behaviours. KEGG pathway analysis of each miRNA’s expression correlates revealed enrichment of pathways including MAP kinase, cancer, long-term potentiation, axonal guidance and WNT signalling. Conclusions The BXD reference panel allowed us to establish genetic regulation and characterize biological function of specific miRNAs. QTL analysis enabled detection of genetic loci that regulate the expression of these miRNAs. eQTLs that regulate miRNA abundance are a new mechanism by which genetic variation influences brain and behaviour. Analysis of one of these QTLs revealed a gene, Tnik, which may regulate the expression of a miRNA, a molecular pathway and a behavioural phenotype. Evidence of genetic covariation of miR-212 abundance and cocaine related behaviours is strongly supported by previous functional studies, demonstrating the value of this approach for discovery of new functional roles and downstream processes regulated by miRNA

Effectiveness of an Inpatient Movement Disorders Program for Patients with Atypical Parkinsonism

This paper investigated the effectiveness of an inpatient movement disorders program for patients with atypical parkinsonism, who typically respond poorly to pharmacologic intervention and are challenging to rehabilitate as outpatients. Ninety-one patients with atypical parkinsonism participated in an inpatient movement disorders program. Patients received physical, occupational, and speech therapy for 3 hours/day, 5 to 7 days/week, and pharmacologic adjustments based on daily observation and data. Differences between admission and discharge scores were analyzed for the functional independence measure (FIM), timed up and go test (TUG), two-minute walk test (TMW), Berg balance scale (BBS) and finger tapping test (FT), and all showed significant improvement on discharge (P > .001). Clinically significant improvements in total FIM score were evident in 74% of the patients. Results were similar for ten patients whose medications were not adjusted. Patients with atypical parkinsonism benefit from an inpatient interdisciplinary movement disorders program to improve functional status

X-ray, Optical, and Radio Observations of the Type II Supernovae 1999em and 1998S

Observations of the Type II-P (plateau) Supernova (SN) 1999em and Type IIn (narrow emission line) SN 1998S have enabled estimation of the profile of the SN ejecta, the structure of the circumstellar medium (CSM) established by the pre-SN stellar wind, and the nature of the shock interaction. SN 1999em is the first Type II-P detected at both X-ray and radio wavelengths. The Chandra X-ray data indicate non-radiative interaction of SN ejecta with a power-law density profile (rho \propto r^{-n} with n ~ 7) with a pre-SN wind with a low mass-loss rate of ~2 \times 10^{-6} M_sun/yr for a wind velocity of 10 km/sec, in agreement with radio mass-loss rate estimates. The Chandra data show an unexpected, temporary rise in the 0.4--2.0 keV X-ray flux at ~100 days after explosion. SN 1998S, at an age of >3 years, is still bright in X-rays and is increasing in flux density at cm radio wavelengths. Spectral fits to the Chandra data show that many heavy elements (Ne, Al, Si, S, Ar, and Fe) are overabundant with respect to solar values. We compare the observed elemental abundances and abundance ratios to theoretical calculations and find that our data are consistent with a progenitor mass of approximately 15-20 M_sun if the heavy element ejecta are radially mixed out to a high velocity. If the X-ray emission is from the reverse shock wave region, the supernova density profile must be moderately flat at a velocity ~10^4 km/sec, the shock front is non-radiative at the time of the observations, and the mass-loss rate is 1-2 \times 10^{-4} M_sun/yr for a pre-supernova wind velocity of 10 km/sec. This result is also supported by modeling of the radio emission which implies that SN 1998S is surrounded by a clumpy or filamentary CSM established by a high mass-loss rate, ~2 \times 10^{-4} M_sun/yr, from the pre-supernova star.Comment: 14 pages, 10 figures, accepted by ApJ, includes new data (one new obs. each of SN 1999em and SN 1998S), expanded discussion of spectral fit

A stratified random survey of the proportion of poor quality oral artesunate sold at medicine outlets in the Lao PDR – implications for therapeutic failure and drug resistance

<p>Abstract</p> <p>Background</p> <p>Counterfeit oral artesunate has been a major public health problem in mainland SE Asia, impeding malaria control. A countrywide stratified random survey was performed to determine the availability and quality of oral artesunate in pharmacies and outlets (shops selling medicines) in the Lao PDR (Laos).</p> <p>Methods</p> <p>In 2003, 'mystery' shoppers were asked to buy artesunate tablets from 180 outlets in 12 of the 18 Lao provinces. Outlets were selected using stratified random sampling by investigators not involved in sampling. Samples were analysed for packaging characteristics, by the Fast Red Dye test, high-performance liquid chromatography (HPLC), mass spectrometry (MS), X-ray diffractometry and pollen analysis.</p> <p>Results</p> <p>Of 180 outlets sampled, 25 (13.9%) sold oral artesunate. Outlets selling artesunate were more commonly found in the more malarious southern Laos. Of the 25 outlets, 22 (88%; 95%CI 68–97%) sold counterfeit artesunate, as defined by packaging and chemistry. No artesunate was detected in the counterfeits by any of the chemical analysis techniques and analysis of the packaging demonstrated seven different counterfeit types. There was complete agreement between the Fast Red dye test, HPLC and MS analysis. A wide variety of wrong active ingredients were found by MS. Of great concern, 4/27 (14.8%) fakes contained detectable amounts of artemisinin (0.26–115.7 mg/tablet).</p> <p>Conclusion</p> <p>This random survey confirms results from previous convenience surveys that counterfeit artesunate is a severe public health problem. The presence of artemisinin in counterfeits may encourage malaria resistance to artemisinin derivatives. With increasing accessibility of artemisinin-derivative combination therapy (ACT) in Laos, the removal of artesunate monotherapy from pharmacies may be an effective intervention.</p

Architecture and secondary structure of an entire HIV-1 RNA genome

Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS, and other serious health threats. Viral replication is regulated at many levels, including using conserved genomic RNA structures. Most potential regulatory elements within viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions. Highly used splice acceptors lie in unstructured motifs and hypervariable regions are sequestered from flanking genome regions by stable insulator helices. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by numerous previously unrecognized regulatory motifs and that extensive RNA structure may constitute an additional level of the genetic code

HRAS1 and LASS1 with APOE are associated with human longevity and healthy aging

The search for longevity-determining genes in human has largely neglected the operation of genetic interactions. We have identified a novel combination of common variants of three genes that has a marked association with human lifespan and healthy aging. Subjects were recruited and stratified according to their genetically inferred ethnic affiliation to account for population structure. Haplotype analysis was performed in three candidate genes, and the haplotype combinations were tested for association with exceptional longevity. An HRAS1 haplotype enhanced the effect of an APOE haplotype on exceptional survival, and a LASS1 haplotype further augmented its magnitude. These results were replicated in a second population. A profile of healthy aging was developed using a deficit accumulation index, which showed that this combination of gene variants is associated with healthy aging. The variation in LASS1 is functional, causing enhanced expression of the gene, and it contributes to healthy aging and greater survival in the tenth decade of life. Thus, rare gene variants need not be invoked to explain complex traits such as aging; instead rare congruence of common gene variants readily fulfills this role. The interaction between the three genes described here suggests new models for cellular and molecular mechanisms underlying exceptional survival and healthy aging that involve lipotoxicity. © 2010 The Authors Aging Cell © 2010 Blackwell Publishing Ltd/Anatomical Society of Great Britain and Ireland

Viewpoints on Factors for Successful Employment for Adults with Autism Spectrum Disorder

This article explores the key factors for successful employment from the viewpoints of adults with autism spectrum disorder (ASD) and employers. Two groups of individuals participated in this study, 40 adults with ASD and 35 employers. Q method was used to understand and contrast the viewpoints of the two groups. Data were analysed using by-person varimax rotation factor analysis. Results showed that although both groups appear committed to the employment process, the difference in their understanding regarding the type of workplace support required, job expectations and productivity requirements continues to hinder successful employment. These results highlight the need to facilitate communication between employees and employers to ensure a clear understanding of the needs of both groups are met. The use of an ASD-specific workplace tool may assist in facilitating the necessary communication between these two groups

A Collaborative Epidemiological Investigation into the Criminal Fake Artesunate Trade in South East Asia

Paul Newton and colleagues' international, collaborative study found evidence that counterfeit artesunate was being manufactured in China, which prompted a criminal investigation