Pressure flow effects on scour at bridges

Department Head: Marvin E. Criswell.Includes bibliographical references (pages 122-126).Scour caused by the occurrence of pressure flow requires a comprehensive understanding. Pressure flow can be defined as flow in which the low chord of a bridge becomes inundated and the flow through the bridge opening transitions from free surface flow to a pressurized condition, leading to a submerged or partially submerged bridge deck condition. A pressure flow condition often occurs at a bridge during a flood, potentially leading to bridge failure. Scour of bridge foundations (piers and abutments) represents the largest single cause of bridge failure in the United States (ASCE, 1999). Methodical scour research began in 1949 with the research of E.M. Laursen. Unfortunately, the application of scour research to the design of bridges did not occur until several bridges failed due to local scour. Over the years, bridge scour research has focused on the study of free surface flow. During the past decade, research related to pressure flow scour has become increasingly important. A testing program was developed and performed at the Hydraulics Laboratory of Colorado State University to examine pressure flow effects on scour at and around bridges. Flume experiments were conducted incorporating a physical model of a generic bridge with supporting abutments constructed at an approximate scale of 8:1. In an effort to simulate varying magnitudes of a pressure flow condition, the model was constructed in a manner that permitted the bridge deck to be lowered into the flow. By lowering the bridge deck and holding the level of the approach flow constant, multiple levels of deck submergence could be examined. Six vertical bridge positions, three discharges, two abutment widths and two sediment sizes were incorporated into a matrix comprising 69 tests. Data collected included hydraulic parameters and topographic surveys. Analysis of data collected during the study resulted in the formulation of a set of multivariate linear regression equations enabling the user to estimate abutment, local and deck scour depths during a pressure flow condition. Results of a dimensional analysis indicate that the dominant variables in predicting scour depths for a pressure flow condition include; the critical velocity of a given sediment size, the average velocity under the bridge deck, the height of the bridge deck above the initial and final bed surface, the depth of flow upstream of the bridge and the Froude number of the approach flow. Coefficients of determination for the developed equations ranged from 0.82 to 0.95

Unification of large-scale laboratory rainfall erosion testing

2014 Fall.Includes bibliographical references.Water pollution degrades surface waters making them unsafe for drinking, fishing, swimming, and other activities. The movement of sediment and pollutants carried by sediment over land surfaces and into water bodies is of increasing concern with regards to clean waters, pollution control, and environmental protection. Due to increasing environmental concerns about sediment in water bodies derived from construction sites, along with increasingly stringent United States Environmental Protection Agency (USEPA) regulations, it is imperative to be able to have a uniform means to compute soil loss determined at large-scale laboratory rainfall-induced erosion facilities that can eventually be applied to construction sites. This dissertation utilized bare-soil data from the most commonly-utilized large-scale rainfall testing laboratories in the erosion-control industry to develop a unifying prediction equation that can be utilized to provide a proper foundation for determining design parameters to meet USEPA stabilization requirements. The developed equation was determined to be a function of the following key parameters: rainfall intensity, plot area, duration, slope gradient, median raindrop size, raindrop kinetic energy, percentage of clay in the soil, and compacted soil percentage. The developed equation for the prediction of rainfall-induced soil loss, developed from sixty-eight data points collected for this study, had a coefficient of determination (R2) of 0.88. The prediction equation unifies large-scale laboratory rainfall erosion testing and provides a means to determine the appropriate design parameters for USEPA stabilization requirements

Trapping virtual pores by crystal retro-engineering

Stable guest-free porous molecular crystals are uncommon. By contrast, organic molecular crystals with guest-occupied cavities are frequently observed, but these cavities tend to be unstable and collapse on removal of the guests—this feature has been referred to as ‘virtual porosity’. Here, we show how we have trapped the virtual porosity in an unstable low-density organic molecular crystal by introducing a second molecule that matches the size and shape of the unstable voids. We call this strategy ‘retro-engineering’ because it parallels organic retrosynthetic analysis, and it allows the metastable two-dimensional hexagonal pore structure in an organic solvate to be trapped in a binary cocrystal. Unlike the crystal with virtual porosity, the cocrystal material remains single crystalline and porous after removal of guests by heating

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/ year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (

Wild pigs

High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation

<p>Abstract</p> <p>Background</p> <p>Neurofibrillary tangles (NFT), a cardinal neuropathological feature of Alzheimer's disease (AD) that is highly correlated with synaptic loss and dementia severity, appear to be partly attributable to increased phosphorylation of the microtubule stabilizing protein tau at certain AD-related residues. Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments.</p> <p>Results</p> <p>We report results from a screen of 572 kinases in the human genome for effects on tau hyperphosphorylation using a loss of function, high-throughput RNAi approach. We confirm effects of three kinases from this screen, the eukaryotic translation initiation factor 2 α kinase 2 (EIF2AK2), the dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and the A-kinase anchor protein 13 (AKAP13) on tau phosphorylation at the 12E8 epitope (serine 262/serine 356). We provide evidence that EIF2AK2 effects may result from effects on tau protein expression, whereas DYRK1A and AKAP13 are likely more specifically involved in tau phosphorylation pathways.</p> <p>Conclusions</p> <p>These findings identify novel kinases that phosphorylate tau protein and provide a valuable reference data set describing the kinases involved in phosphorylating tau at an AD-relevant epitope.</p

Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers

<p>Abstract</p> <p>Background</p> <p>The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms.</p> <p>Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers.</p> <p>Results</p> <p>The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism.</p> <p>Conclusion</p> <p>The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of Bdelloidea and Eutardigrada in a variety of soils.</p

Post-intervention Status in Patients With Refractory Myasthenia Gravis Treated With Eculizumab During REGAIN and Its Open-Label Extension

OBJECTIVE: To evaluate whether eculizumab helps patients with anti-acetylcholine receptor-positive (AChR+) refractory generalized myasthenia gravis (gMG) achieve the Myasthenia Gravis Foundation of America (MGFA) post-intervention status of minimal manifestations (MM), we assessed patients' status throughout REGAIN (Safety and Efficacy of Eculizumab in AChR+ Refractory Generalized Myasthenia Gravis) and its open-label extension. METHODS: Patients who completed the REGAIN randomized controlled trial and continued into the open-label extension were included in this tertiary endpoint analysis. Patients were assessed for the MGFA post-intervention status of improved, unchanged, worse, MM, and pharmacologic remission at defined time points during REGAIN and through week 130 of the open-label study. RESULTS: A total of 117 patients completed REGAIN and continued into the open-label study (eculizumab/eculizumab: 56; placebo/eculizumab: 61). At week 26 of REGAIN, more eculizumab-treated patients than placebo-treated patients achieved a status of improved (60.7% vs 41.7%) or MM (25.0% vs 13.3%; common OR: 2.3; 95% CI: 1.1-4.5). After 130 weeks of eculizumab treatment, 88.0% of patients achieved improved status and 57.3% of patients achieved MM status. The safety profile of eculizumab was consistent with its known profile and no new safety signals were detected. CONCLUSION: Eculizumab led to rapid and sustained achievement of MM in patients with AChR+ refractory gMG. These findings support the use of eculizumab in this previously difficult-to-treat patient population. CLINICALTRIALSGOV IDENTIFIER: REGAIN, NCT01997229; REGAIN open-label extension, NCT02301624. CLASSIFICATION OF EVIDENCE: This study provides Class II evidence that, after 26 weeks of eculizumab treatment, 25.0% of adults with AChR+ refractory gMG achieved MM, compared with 13.3% who received placebo

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/ year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations