Upstream Shift Research Articles

A spatial age-structured model for describing sea lamprey (Petromyzon marinus) population dynamics

The control of invasive sea lampreys (Petromyzon marinus) presents large-scale management challenges in the Laurentian Great Lakes. No modeling approach has been developed that describes spatial dynamics of lamprey populations. We developed and validated a spatial and age-structured model and applied it to a sea lamprey population in a large river in the Great Lakes basin. We considered 75 discrete spatial areas, included a stock–recruitment function, spatial recruitment patterns, natural mortality, chemical treatment mortality, and larval metamorphosis. Recruitment was variable, and an upstream shift in recruitment location was observed over time. From 1993 to 2011, recruitment, larval abundance, and the abundance of metamorphosing individuals decreased by 80%, 84%, and 86%, respectively. The model successfully identified areas of high larval abundance and showed that areas of low larval density contribute significantly to the population. Estimated treatment mortality was less than expected but had a large population-level impact. The results and general approach of this work have applications for sea lamprey control throughout the Great Lakes and for the restoration and conservation of native lamprey species globally.

Monte Carlo calculations for reference dosimetry of electron beams with the PTW Roos and NE2571 ion chambers

To investigate recommendations for reference dosimetry of electron beams and gradient effects for the NE2571 chamber and to provide beam quality conversion factors using Monte Carlo simulations of the PTW Roos and NE2571 ion chambers. The EGSnrc code system is used to calculate the absorbed dose-to-water and the dose to the gas in fully modeled ion chambers as a function of depth in water. Electron beams are modeled using realistic accelerator simulations as well as beams modeled as collimated point sources from realistic electron beam spectra or monoenergetic electrons. Beam quality conversion factors are calculated with ratios of the doses to water and to the air in the ion chamber in electron beams and a cobalt-60 reference field. The overall ion chamber correction factor is studied using calculations of water-to-air stopping power ratios. The use of an effective point of measurement shift of 1.55 mm from the front face of the PTW Roos chamber, which places the point of measurement inside the chamber cavity, minimizes the difference between R50, the beam quality specifier, calculated from chamber simulations compared to that obtained using depth-dose calculations in water. A similar shift minimizes the variation of the overall ion chamber correction factor with depth to the practical range and reduces the root-mean-square deviation of a fit to calculated beam quality conversion factors at the reference depth as a function of R50. Similarly, an upstream shift of 0.34 rcav allows a more accurate determination of R50 from NE2571 chamber calculations and reduces the variation of the overall ion chamber correction factor with depth. The determination of the gradient correction using a shift of 0.22 rcav optimizes the root-mean-square deviation of a fit to calculated beam quality conversion factors if all beams investigated are considered. However, if only clinical beams are considered, a good fit to results for beam quality conversion factors is obtained without explicitly correcting for gradient effects. The inadequacy of R50 to uniquely specify beam quality for the accurate selection of kQ factors is discussed. Systematic uncertainties in beam quality conversion factors are analyzed for the NE2571 chamber and amount to between 0.4% and 1.2% depending on assumptions used. The calculated beam quality conversion factors for the PTW Roos chamber obtained here are in good agreement with literature data. These results characterize the use of an NE2571 ion chamber for reference dosimetry of electron beams even in low-energy beams.

Large Eddy Simulations in Turbines: Influence of Roughness and Free-Stream Turbulence

The individual and coupled effects of the incoming free-stream turbulence (FST) and surface roughness on the transition of a separated shear layer over a flat plate is numerically investigated using Large eddy simulation (LES). The upper wall of the test section is inviscid and specifically contoured to impose a streamwise pressure distribution over the flat plate to simulate the suction surface of a low pressure turbine (LPT) blade. The interaction of the streamwise streaks due to FST and roughness with the separated shear layer is captured. The streaks induced by FST are intermittent in nature and the streaks due to roughness are steady for a given topology of the rough surface. Both FST and roughness promoted near-wall mixing. The ‘net effect’ of mixing in the pre-separated region is manifested by a shift the inflection point of the velocity profile towards the wall. This resulted in the upstream shift of the transition point and a significant reduction in the size of the separation bubble. The combined effect of FST and roughness further reduced the size of separation bubble. The streamwise evolution of the boundary layer parameters has been compared for different cases. The potential ‘roughness benefit’ obtained in the case of highly loaded turbine blades in terms of its considerable reduction of profile loss is also shown.

SU-E-T-79: Study On the Effective Depth of Measurement for Gafchromic EBT2 and EBT3 Films

Purpose: To determine the effective depth of measurement for Gafchromic EBT2 and EBT3 filmsMethods: Absolute dose point measurements were made with EBT2 and EBT3 film on the surface of flat phantom and at various depths. The films were cut to an approx. 1–2 mm square size and placed on the beam central axis. Measurements with an Exradin A1SL ion chamber were performed for each irradiation. A dose of 1 Gy was delivered to Dmax=1.5 cm. A previously validated Monte Carlo (MC) model was used for simulation and comparison to measurements. The MC simulation data was collected at 0.1 mm steps along the beam central axis. Film measurements were converted to dose using a post-irradiation signal consisting of the red and blue color channels from an Epson Expression 10000XL scanner. Film analysis was performed using ImageJ software and MATLAB. Measurements were converted to PDD and then compared to MC data to determine an effective depth of film measurement. Results: EBT2 measurements showed a systematic upstream shift of 0.10 mm with respect to the MC data while EBT3 showed the shift to be slightly less at 0.07 mm. The error in film measurement was estimated to be 0.04 mm (2σ). All measurements were within one STD of the MC error of 0.33 mm. Conclusion: The PDD measurements of EBT2 and EBT3 were consistent amongst themselves and agreement with MC was excellent. The observed shift in the results and the measurement error are smaller than the error in MC data, a possible indication that the nominal depth of measurement can be considered as the effective depth of measurement. A study with more accurate geometry for comparison is needed to determine a conclusive depth of measurement.

SU‐C‐105‐05: Reference Dosimetry of High‐Energy Electron Beams with a Farmer‐Type Ionization Chamber

Purpose: To investigate gradient effects and provide Monte Carlo calculated beam quality conversion factors to characterize the Farmer‐type NE2571 ion chamber for high‐energy reference dosimetry of clinical electron beams. Methods: The EGSnrc code system is used to calculate the absorbed dose to water and to the gas in a fully modeled NE2571 chamber as a function of depth in a water phantom. Electron beams incident on the surface of the phantom are modeled using realistic BEAMnrc accelerator simulations and electron beam spectra. Beam quality conversion factors are determined using calculated doses to water and to air in the chamber in high‐energy electron beams and in a cobalt‐60 reference field. Calculated water‐to‐air stopping power ratios are employed for investigation of the overall ion chamber perturbation factor. Results: An upstream shift of 0.3–0.4 multiplied by the chamber radius, r_cav, both minimizes the variation of the overall ion chamber perturbation factor with depth and reduces the difference between the beam quality specifier (R5 0) calculated using ion chamber simulations and that obtained with simulations of dose‐to‐water in the phantom. Beam quality conversion factors are obtained at the reference depth and gradient effects are optimized using a shift of 0.2r_cav. The photon‐electron conversion factor, k_ecal, amounts to 0.906 when gradient effects are minimized using the shift established here and 0.903 if no shift of the data is used. Systematic uncertainties in beam quality conversion factors are investigated and amount to between 0.4 to 1.1% depending on assumptions used. Conclusion: The calculations obtained in this work characterize the use of an NE2571 ion chamber for reference dosimetry of high‐energy electron beams. These results will be useful as the AAPM continues to review their reference dosimetry protocols.

Visualization by discharge illumination technique and modification by plasma actuator of rarefied Mach 2 airflow around a cylinder

The use of plasma actuators for flow control has received considerable attention in recent years. This kind of device seems to be an appropriate means of raising abilities in flow control thanks to total electric control, no moving parts and a fast response time. The experimental work presented here shows, firstly, the non-intrusive character of the visualization of the density field of an airflow around a cylinder obtained using a plasma luminescence technique. Experiments are made in a continuous supersonic wind tunnel. The static pressure in the flow is 8 Pa, the mean free path is about 0.3 mm and the airflow velocity is 510 m s−1. Pressure measurements obtained by means of glass Pitot tube without the visualization discharge are proposed. Measured and simulated pressure profiles are in good agreement in the region near the cylinder. There is good correlation between numerical simulations of the supersonic flow field, analytical model predictions and experimental flow visualizations obtained by a plasma luminescence technique. Consequently, we show that the plasma luminescence technique is non-intrusive. Secondly, the effect of a dc discharge on a supersonic rarefied air flow around a cylinder is studied. An electrode is flush mounted on the cylinder. Stagnation pressure profiles are examined for different electrode positions on the cylinder. A shock wave modification depending on the electrode location is observed. The discharge placed at the upstream stagnation point induces an upstream shift of the bow shock, whereas a modification of the shock wave shape is observed when it is placed at 45° or 90°.

Experimental studies on rectangular jets with trapezoidal tabs

AbstractAn experimental investigation was carried out to study the flow development of a jet issuing from a 2:1 rectangular nozzle with mixing tabs using two-component hotwire anemometry. A pair of tabs of trapezoidal configuration (with 2% total blockage area) is placed on the minor-axis side of the rectangular nozzle and tested for two tab inclination angles of 135° and 45°, with respect to the flow direction. Tests were conducted for a nominal jet exit velocity of 20m/sec corresponding to a Reynolds number based on nozzle equivalent diameter of 5·013 × 104. Relative to the plain jet, the jet with tabs show significant reduction in jet-core length (by 67%) followed by a faster decay in jet centreline velocity (U/Ue). This is also accompanied by a significant upstream shift in peak centreline turbulence intensity (u’/Ue). The presence of tabs is observed to inhibit the jet growth along the minor-axis plane thereby introducing large distortion in the jet cross-sectional development that ultimately leads to jet-core bifurcation along its major-axis. While a mushroom-like flow structure develops behind the tab with 135° inclination, the flow structure behind a 45° inclined tab rather takes the shape of the tab itself. The former flow development is seen to enhance the jet growth more along the minor-axis while the latter improves the jet growth more along the major-axis plane. From application point of view, since both tab inclinations result in more or less similar jet characteristics, a 135° inclined tab would be preferable over a 45° inclined tab from the view of improved jet mixing.

Decadal Response of the Kuroshio Extension Jet to Rossby Waves: Observation and Thin-Jet Theory*

AbstractThis study examines interannual to decadal variability of the Kuroshio Extension (KE) jet using satellite altimeter observations from 1993 to 2010. The leading empirical orthogonal function (EOF) mode of sea level variability in the KE region represents the meridional shift of the KE jet, followed by its strength changes with a few month lag. This shift of the KE jet lags atmospheric fluctuations over the eastern North Pacific by about three years. Broad sea level anomalies (SLAs) emerge in the eastern North Pacific 3–4 years before the upstream KE jet shift, and propagate westward along the KE jet axis. In the course of the propagation, the meridional scale of the SLAs gradually narrows, and their amplitude increases. This westward propagation of SLAs with a speed of about 5 cm s−1 is attributed to the westward propagation of the meridional shift of the jet, consistent with the thin-jet theory, whose importance has been suggested by previous numerical studies. In addition, the westward-propagating signals tend to conserve their quasigeostrophic potential vorticity anomaly, which may explain the characteristic changes of SLAs during the propagation. After the westward-propagating signals of positive (negative) SLAs reach at the east coast of Japan, the upstream KE jet strengthens (weakens) associated with the strength changes of the northern and southern recirculation gyres. Interestingly, this strength change of the KE jet propagates eastward with a speed of about 6 cm s−1, suggesting an importance of advection by the current.

Mechanisms of along-channel sediment transport in the North Passage of the Yangtze Estuary and their response to large-scale interventions

The effects of large-scale interventions in the North Passage of the Yangtze Estuary (the Deep Waterway Project, DWP) on the along-channel flow structure, suspended sediment distribution and its transport along the main channel of this passage are investigated. The focus is explaining the changes in net sediment transport in terms of physical mechanisms. For this, data of flow and suspended sediment concentration (SSC), which were collected simultaneously at several locations and at different depths along the main channel of the North Passage prior to and after the engineering works, were harmonically analyzed to assess the relative importance of the transport components related to residual (time-mean) flow and various tidal pumping mechanisms. Expressions for main residual flow components were derived using theoretical principles. The SSC revealed that the estuarine turbidity maximum (ETM) was intensified due to the interventions, especially in wet seasons, and an upstream shift and extension of the ETM zone occurred. The amplitude of the M2 tidal current considerably increased, and the residual flow structure was significantly altered by engineering works. Prior to the DWP, the residual flow structure was that of a gravitational circulation in both seasons, while after the DWP, there was seaward flow throughout the channel during the wet season. The analysis of net sediment transport reveals that during wet seasons and prior to the DWP, the sediment trapping was due to asymmetric tidal mixing, gravitational circulation, tidal rectification, and M2 tidal pumping, while after the DWP, the trapping was primarily due to seaward transport caused by Stokes return flow and fresh water discharge and landward transport due to M2 tidal pumping and asymmetric tidal mixing. During dry seasons, prior to the DWP, trapping of sediment at the bottom relied on landward transports due to Stokes transport, M4 tidal pumping, asymmetric tidal mixing, and gravitational circulation, while after the DWP the sediment trapping was caused by M2 tidal pumping, Stokes transport, asymmetric tidal mixing, tidal rectification, and gravitational circulation.

Evaluation of the recent morphological evolution of the Gironde estuary through the use of some preliminary synthetic indicators

Sottolichio, A., Hanquiez, V., Perinotto, H., Sabouraud, L. and Weber, O., 2013. Evaluation of the recent morphological evolution of the Gironde estuary through the use of some preliminary synthetic indicators. In: Conley, D.C., Masselink, G., Russell, P.E. and O’Hare, T.J. (eds.), Proceedings 12 th International Coastal Symposium (Plymouth, England), Journal of Coastal Research, Special Issue No. 65, pp. 1224-1229, ISSN 0749-0208. Drastic evolution of the physical coastal environment are expected in the future under the effect of climate change. They make necessary to better understand the past morphology evolution, especially considering areas that are the habitat for some specific ecosystems. Moreover, because the context of the water framework directive (WFD), EU members need to generate indicators to evaluate the status of estuarine water masses. To satisfy these two obectives, the recent evolution of the Gironde estuary has been studied by the analysis of bathymetry with GIS. The Gironde is the largest estuary of western Europe, and one of the most turbid. In this study, the analysis extents from 1962 to 1994. Results show that the zone of maximum volume of deposited sediment has migrated continuously towards the upstream portion of the estuary, which is coherent with the decrease of summer river flow and the upstream shift of the turbidity maximum toward the riverine sections. In addition, zones with relative stable and unstable morphology were identified, showing rythmic distribution similarly to those previously recognized through the evolution over 160 years (18251984). This seems to be independent from the fluvial regime, but rather related to the interaction between tidal cooscillations and estuarine morphology, which is not elucidated yet. Finally, some hydro-morpho-sediemntary (HMS) indicators useful to the WFD have been described : distribution of depths, changes on cross section areas, changes of intertidal areas. They are discussed to discriminate the “natural” and “anthropogenic” contribution to morphological changes observed.

Stability Analysis of Cliff Face around Kegon Falls in Nikko, Eastern Japan: An Implication to Its Erosional Mechanisms

A waterfall highlights the locus of active fluvial erosion of bedrock, and its mechanism has been the subject of several studies; however, erosional processes remain to be clarified for specific rock structures composing a waterfall. Herein, the detailed morphology of cliffs around a waterfall is examined by a terrestrial laser scanning (TLS) approach to analyze erosional processes occurring in the cliffs. The study site is Kegon Falls in Japan, which has a vertical drop of surface water from the top of its cliff and groundwater outflows from its lower portion. The entire cliff is mostly overhanging and minor rockfalls are often observed. The latest major rockfall occurred in 1986, causing an approximate 8-m upstream shift of the waterfall lip. From the point cloud obtained by TLS measurement, a digital elevation model on a vertical plane was generated, and cross-sectional profiles were extracted. A distinct 5- to 10-m depression was found at the bottom of the upper andesite layer of the waterfall cliff, which appears to have been formed by freeze-thaw and wet-dry weathering following the upstream shift of the surface water drop. Stability analysis of the waterfall cliff with an undercutting notch indicates that the igneous rock composing the cliff is sufficiently strong to maintain its current overhanging shape and that catastrophic collapse of the entire waterfall face rarely occurs. Following the formation of the depression, the upper cliff face appears to have been gradually eroded by gravitational collapses of relatively small blocks bounded by columnar and platy joints.

Assessing changes in seawater intrusion and water quality of the Shatt Al-Arab River, Iraq

Many adverse environmental factors influencing the Shatt-al Arab River, southern Iraq, during the past century and especially in recent years, combined with the ever-increasing demand for freshwater in the region, indicate the need to obtain information about its salinity regime. The aim of our study was both to find out what historical data there are and then to compare these with the results of a survey of the salinity and water quality of a stretch of the present river over the year October 2009–September 2010. The evidence suggests that there has been a marked upstream shift in the influence of sea water. Salinity values of 2 and 8‰ were found at two sites where elevated salinity had never been reported previously. Water quality variables indicated increased concentrations over the previous four decades and were beyond the national and international standards. As such changes in a major water resource have serious implications for the inhabitants of Basrah, the biological diversity in the river and the whole Gulf ecosystem, it is suggested that there should be a much more detailed study to provide the evidence needed to convince upstream water users of the need to conserve water and manage the whole catchment properly.

Long-Term Changes in Population Dynamics of the Shrimp Palaemon longirostris in the Gironde Estuary

Spanning 20 years (1979–2007), this study is the longest time series pertaining to the resident shrimp species Palaemon longirostris in a European estuary. Data from monthly faunal surveys undertaken across the middle part of the Gironde estuary from April 1979 along with data from a statistical analysis of the commercial catches throughout the entire estuary and river were considered in order to explore their inter and intra-annual variability and long-term trends. Long-term densities series as well as environmental series (salinity, discharge, temperature and NAO) were decomposed and the effects of environmental variables were also examined using statistical models (GAMs). This revealed important spatio-temporal variability and a significant overall decrease in abundance of this species in the Gironde estuary since the beginning of the 1980s. This long-term decrease in abundance corresponded significantly to long-term decreases in both discharge and the NAO index, as well a long-term increase in temperature and salinity in the middle part of the estuary. However, models showed that environmental factors explained only a small part of the variability. The upstream shift of the population highlighted in this study, probably due to the intrusion of marine waters into the middle section of the estuary, may also have contributed to its decrease in abundance. Inter-annual variability of densities was also significantly linked with inter-annual fecundity fluctuations, and a significant decrease in both mean female size and fecundity was shown for preserved samples from 1992. Moreover, the breeding period has been temporally stretched out and began earlier in more recent years, potentially due to the increase in spring temperature.

Effect of Tab Geometry on the Development of a Jet Issuing from a Rectangular Nozzle

An experimental investigation was carried out to study the effect of tab geometry on the flow characteristics of a jet issuing from a 2:1 rectangular nozzle using two-component hotwire anemometry. A pair of tabs of trapezoidal and square configurations (2% total blockage area) is placed on the minor-axis side of the rectangular nozzle and tested for two tab inclination angles of 135° and 45°, respectively. Tests were conducted for a nominal jet exit velocity of 20 ms-1 corresponding to a Reynolds number based on nozzle equivalent diameter of 5.02×104. Relative to the plain jet, the potential-core length of the jet with trapezoidal tabs shows a reduction of 62% while the jet with square tabs shows a reduction of 75%, respectively. This is also accompanied by a significant upstream shift in peak centerline turbulence intensity (u'/Ue). The tab inclination of 135° results in further enhanced jet characteristics in each case. The presence of each tab configuration is observed to inhibit the jet growth along the minor-axis plane thereby introducing large distortion in the jet cross-sectional development that ultimately leads to jet-core bifurcation along its major-axis. However, it is observed that while the jet with trapezoidal tabs switches its axis at some downstream location, the jet with square tabs does not switch axis at all. This indicates a strong influence of tab geometry on the overall jet flow development.

Steering Vaccinomics Innovations with Anticipatory Governance and Participatory Foresight

Vaccinomics is the convergence of vaccinology and population-based omics sciences. The success of knowledge-based innovations such as vaccinomics is not only contingent on access to new biotechnologies. It also requires new ways of governance of science, knowledge production, and management. This article presents a conceptual analysis of the anticipatory and adaptive approaches that are crucial for the responsible design and sustainable transition of vaccinomics to public health practice. Anticipatory governance is a new approach to manage the uncertainties embedded on an innovation trajectory with participatory foresight, in order to devise governance instruments for collective "steering" of science and technology. As a contrast to hitherto narrowly framed "downstream impact assessments" for emerging technologies, anticipatory governance adopts a broader and interventionist approach that recognizes the social construction of technology design and innovation. It includes in its process explicit mechanisms to understand the factors upstream to the innovation trajectory such as deliberation and cocultivation of the aims, motives, funding, design, and direction of science and technology, both by experts and publics. This upstream shift from a consumer "product uptake" focus to "participatory technology design" on the innovation trajectory is an appropriately radical and necessary departure in the field of technology assessment, especially given that considerable public funds are dedicated to innovations. Recent examples of demands by research funding agencies to anticipate the broad impacts of proposed research--at a very upstream stage at the time of research funding application--suggest that anticipatory governance with foresight may be one way how postgenomics scientific practice might transform in the future toward responsible innovation. Moreover, the present context of knowledge production in vaccinomics is such that policy making for vaccines of the 21st century is occurring in the face of uncertainties where the "facts are uncertain, values in dispute, stakes high and decisions urgent and where no single one of these dimensions can be managed in isolation from the rest." This article concludes, however, that uncertainty is not an accident of the scientific method, but its very substance. Anticipatory governance with participatory foresight offers a mechanism to respond to such inherent sociotechnical uncertainties in the emerging field of vaccinomics by making the coproduction of scientific knowledge by technology and the social systems explicit. Ultimately, this serves to integrate scientific and social knowledge thereby steering innovations to coproduce results and outputs that are socially robust and context sensitive.

Effect of Density Ratio on Flat Plate Film Cooling With Shaped Holes Using PSP

Detailed film-cooling effectiveness distributions are obtained on a flat plate using the pressure sensitive paint (PSP) technique. The applicability of the PSP technique is expanded to include a coolant-to-mainstream density ratio of 1.4. The effect of density ratio on the film-cooling effectiveness is coupled with varying blowing ratio (M=0.25–2.0), freestream turbulence intensity (Tu=1–12.5%), and film hole geometry. The effectiveness distributions are obtained on three separate flat plates containing either simple angle, cylindrical holes, simple angle, fanshaped holes (α=10 deg), or simple angle, laidback, fanshaped holes (α=10 deg and γ=10 deg). In all three cases, the film-cooling holes are angled at θ=35 deg from the mainstream flow. Using the PSP technique, the combined effects of blowing ratio, turbulence intensity, and density ratio are captured for each film-cooling geometry. The detailed film-cooling effectiveness distributions, for cylindrical holes, clearly show that the effectiveness at the lowest blowing ratio is enhanced at the lower density ratio (DR=1). However, as the blowing ratio increases, a transition occurs, leading to increased effectiveness with the elevated density ratio (DR=1.4). In addition, the PSP technique captures an upstream shift of the coolant jet reattachment point as the density ratio increases or the turbulence intensity increases (at moderate blowing ratios for cylindrical holes). With the decreased momentum of the shaped film-cooling holes, the greatest film-cooling effectiveness is obtained at the lower density ratio (DR=1.0) over the entire range of blowing ratios considered. In all cases, as the freestream turbulence intensity increases, the film effectiveness decreases; this effect is reduced as the blowing ratio increases for all three film hole configurations.

Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region

Saccharomyces cerevisiae Hmo1 binds to the promoters of ∼70% of ribosomal protein genes (RPGs) at high occupancy, but is observed at lower occupancy on the remaining RPG promoters. In Δhmo1 cells, the transcription start site (TSS) of the Hmo1-enriched RPS5 promoter shifted upstream, while the TSS of the Hmo1-limited RPL10 promoter did not shift. Analyses of chimeric RPS5/RPL10 promoters revealed a region between the RPS5 upstream activating sequence (UAS) and core promoter, termed the intervening region (IVR), responsible for strong Hmo1 binding and an upstream TSS shift in Δhmo1 cells. Chromatin immunoprecipitation analyses showed that the RPS5-IVR resides within a nucleosome-free region and that pre-initiation complex (PIC) assembly occurs at a site between the IVR and a nucleosome overlapping the TSS (+1 nucleosome). The PIC assembly site was shifted upstream in Δhmo1 cells on this promoter, indicating that Hmo1 normally masks the RPS5-IVR to prevent PIC assembly at inappropriate site(s). This novel mechanism ensures accurate transcriptional initiation by delineating the 5′- and 3′-boundaries of the PIC assembly zone.

Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation

Recent estimates indicate that approximately 60% of human genes include alternative polyadenylation sites. Hence, control of alternative polyadenylation can have a great impact on gene expression and cellular function. Cleavage factor (CF) Im is a 3'-end processing factor that is essential for in vitro processing. CFIm purified from HeLa cells is associated with three polypeptides of 25, 59 and 68 kD, and it is generally thought to be a heterodimer composed of the 25-kD subunit and one of the larger subunits. Previously, we serendipitously discovered that knockdown of CFIm25 causes an upstream shift in the utilization of alternative polyadenylation sites. Here, we investigated whether this is because of an inherent property of the CFIm complex and, if so, what structural elements are important for its function. The major conclusions of this study are that (i) contrary to previous assumptions, CFIm forms stable heterotetramers through dimerization of CFIm25 and (ii) the CFIm complex per se is responsible for the control of alternative polyadenylation. (iii) However, the structurally related CFIm68 and CFIm59 are functionally redundant and (iv) CFIm68 appears to have a higher specific activity. Thus, this study establishes that CFIm not only plays a general role in 3'-end processing but also plays a regulatory role in poly(A) site selection.

Ecological consequences of hybridization between native westslope cutthroat (Oncorhynchus clarkii lewisi) and introduced rainbow (Oncorhynchus mykiss) trout: effects on life history and habitat use

In the Upper Oldman River, Alberta, Canada, hybridization between introduced rainbow trout (RT; Oncorhynchus mykiss ) and native westslope cutthroat trout (WCT; Oncorhynchus clarkii lewisi ) has produced a genotypic gradient with rainbow trout alleles undetectable (<1%) at high elevations and increasing in abundance downstream. Few F1 hybrids were found, and genotype frequencies suggest strong backcrossing of hybrids to pure parental populations at both ends of the gradient. The increasing prevalence of RT alleles downstream is accompanied by a life history gradient such that RT alleles were positively associated with growth rate and negatively associated with survivorship. Although physical barriers extended the distribution of pure WCT downstream, several streams held genetically pure WCT in their uppermost reaches, even when no barriers were present. For example, RT alleles were undetectable in headwaters of Dutch Creek, which had no barriers but was very cold (average summer temperature <7.3 °C). We propose that RT alleles affect the choice of habitat, as well the metabolic characteristics that determine their life history and competitive abilities. Factors such as climate change, clear-cut logging, and anthropogenic enrichment that can lead to increased temperature and (or) productivity might be expected to result in an upstream shift of RT alleles.

Effective point of measurement of thimble ion chambers in megavoltage photon beams

Determine the effective point of measurement (EPOM) of 12 thimble ion chambers, including miniature chambers and three models widely used for clinical reference dosimetry. The EPOM is the point at which the measured dose would arise in the measurement medium in the absence of the probe: For cylindrical chambers, it is shifted upstream relative to the central axis of the chamber. Although current dosimetry protocols prescribe a blanket upstream EPOM shift of 0.6r, with r as the chamber cavity radius, it has been shown in recent years that the EPOM does, in fact, depend on every detail of the chamber design and on the beam characteristics. In the wake of this finding, the authors undertake a comprehensive study of the EPOM for a series of chambers in water. This work relies on EGSnrc Monte Carlo calculations for the central axis depth dose in a water phantom and in ion chambers. They use a full Elekta Precise linac treatment head simulation to generate realistic photon beams with nominal energies of 6 and 25 MV and fields sizes of 10 x 10 and 40 x 40 cm2. The correct EPOM shift for the 12 ion chambers, modeled in realistic detail, is taken as the one minimizing the deviation of the ratio between the dose to water and the dose to the gas of the chamber cavity, according to a method proposed and validated in previous work. The analysis reveals that the actual EPOM shift is significantly smaller than the recommended value in current dosimetry protocols, by up to 25% for reference-class chambers and 80% for miniature chambers. The location of the EPOM also depends on the characteristics of the incident beam and varies in a well-defined way with the cavity length, the central electrode radius, and the thimble wall thickness. The authors confirm that an upstream EPOM shift of 0.6r is too large for thimble ion chambers in high energy photon beams. Proper values for the EPOM shift could be tabulated per beam and per chamber, but they envisage that a single shift for all practical beams may prove sufficient. Moreover, the systematic dependence on chamber characteristics provides evidence that a universal parametrization in terms of a few design parameters is conceivable and has implication for the calculation of chamber correction factors.