Chemotaxis in uncertain environments: hedging bets with multiple receptor types

Eukaryotic cells are able to sense chemical gradients in a wide range of environments. We show that, if a cell is exposed to a highly variable environment, it may gain chemotactic accuracy by expressing multiple receptor types with varying affinities for the same signal, as found commonly in chemotaxing cells like Dictyostelium. As environment uncertainty is increased, there is a transition between cells preferring a single receptor type and a mixture of types - hedging their bets against the possibility of an unfavorable environment. We predict the optimal receptor affinities given a particular environment. In chemotaxing, cells may also integrate their measurement over time. Surprisingly, time-integration with multiple receptor types is qualitatively different from gradient sensing by a single type -- cells may extract orders of magnitude more chemotactic information than expected by naive time integration. Our results show when cells should express multiple receptor types to chemotax, and how cells can efficiently interpret the data from these receptors

Modeling Fire-Related Debris Flow Volumes in MATLAB Using Surveyed Data Collected from the Middle-Fork Salmon River, Idaho to Determine Contribution of Episodic Fire-Related Debris Flows on Long Term (10\u3csup\u3e3\u3c/sup\u3e – 10\u3csup\u3e4\u3c/sup\u3e) Sediment Yield

Fire-related debris flows play a significant role on the long term sediment yield of the Salmon River Basin. Previous studies (Kirchner et al., 2001) quantified the total long term sediment yield of the Salmon Basin at 261 36 tkm/yr. This study aims to quantify the Middle Fork’s contribution of sediment from fire-related debris flows to the long term sediment yield. Multiple debris flow deposits were surveyed on the Middle Fork and the Kotch Creek deposit was analyzed using the program MATLAB to find the volume of deposition. Using charcoal found in stratigraphic profiles of the deposits and C14 dating, the timing and occurrence of periods of deposition were found. Volume calculations coupled with timing data from carbon dating allows for the reconstruction of the long term sediment yield contribution of fire-related debris flows on the Middle Fork Salmon River. Calculated volumes will be compared with estimated volumes from empirical formulas based on remotely sensed spatial data (burn severity and slope), measured geometric data (longitudinal profile, cross sectional area, flow banking angle), and precipitation records (Cannon et al.,2010

A Comparison of DEM-based methods for fluvial terrace mapping and sediment volume calculation: Application to the Sheepscot River Watershed, Maine

Thesis advisor: Noah P. SnyderThesis advisor: Gail KinekeFluvial terraces form in both erosional and depositional landscapes and are important recorders of land-use, climate, and tectonic history. Terrace morphology consists of a flat surface bounded by valley walls and a steep-sloping scarp adjacent to the river channel. Combining these defining characteristics with high-resolution digital elevation models (DEMs) derived from airborne light detection and ranging (lidar) surveys, several methods have been developed to identify and map terraces. This research introduces a newly developed objective terrace mapping method and compares it with three existing DEM-based techniques to determine which is most applicable over entire watersheds. This work also tests multiple methods that use lidar DEMs to quantify the thickness and volume of fill terrace deposits identified upstream of dam sites. The preliminary application is to the Sheepscot River watershed, Maine, where strath and fill terraces are present and record Pleistocene deglaciation, Holocene eustatic forcing, and Anthropocene land-use change. Terraces were mapped at four former dam sites along the river using four separate methodologies and compared to manually delineated area. The methods tested were: (1) edge detection using MATLAB, (2) feature classification algorithms developed by Wood (1996), (3) spatial relationships between interpreted terraces and surrounding natural topography (Walter et al., 2007), and (4) the TerEx terrace mapping toolbox developed by Stout and Belmont (2013). Thickness and volume estimates of fill sediment were calculated at two of the study sites using three DEM-based models and compared to in situ data collected from soil pits, cut bank exposures, and ground penetrating radar surveys. The results from these comparisons served as the basis for selecting methods to map terraces throughout the watershed and quantify fill sediment upstream of current and historic dam sites. Along the main stem and West Branch of the Sheepscot River, terraces were identified along the longitudinal profile of the river using an algorithm developed by Finnegan and Balco (2013), which computes the elevation frequency distribution at regularly spaced cross-sections normal to the channel, and then mapped using the feature classification (Wood, 1996) method. For terraces upstream of current or historic dam sites, thickness and volume estimates were calculated using the two best performing datum surfaces. If all analyzed terraces are composed of impounded sediment, these DEM-based results suggest that terraces along the main stem and West Branch of the Sheepscot River potentially contain up to 1.5 x 106 m3 of fill. These findings suggest powerful new ways to quickly analyze landscape history over large regions using high-resolution, LiDAR DEMs while relying less heavily on the need for detailed and costly field data collection.Thesis (MS) — Boston College, 2014.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Geology and Geophysics

Intercellular Friction and Motility Drive Orientational Order in Cell Monolayers

Spatiotemporal patterns in multicellular systems are important to understanding tissue dynamics, for instance, during embryonic development and disease. Here, we use a multiphase field model to study numerically the behavior of a near-confluent monolayer of deformable cells with intercellular friction. Varying friction and cell motility drives a solid-liquid transition, and near the transition boundary, we find the emergence of nematic order of cell deformation driven by shear-aligning cellular flows. Intercellular friction endows the monolayer with a finite viscosity, which significantly increases the spatial correlation in the flow and, concomitantly, the extent of nematic order. We also show that hexatic and nematic order are tightly coupled and propose a mechanical-geometric model for the colocalization of +1/2 nematic defects and 5-7 disclination pairs, which are the structural defects in the hexatic phase. Such topological defects coincide with regions of high cell-cell overlap, suggesting that they may mediate cellular extrusion from the monolayer, as found experimentally. Our results delineate a mechanical basis for the recent observation of nematic and hexatic order in multicellular collectives in experiments and simulations and pinpoint a generic pathway to couple topological and physical effects in these systems

Zika Virus: Infectious Process and Public Health Response

The Zika virus has become a growing concern as a global pandemic. Since being identified in Uganda in 1947, the virus has spread around the world, recently emerging in South America with a great impact on Brazil. As of 2016, Zika has made its appearance in the United States and is now actively being transmitted in Florida. The virus is a mosquito-vectored flavivirus primarily transmitted by the Aedes mosquito which infects a human through biting. Transmission through sexual intercourse is also possible as well as transmission from a pregnant woman to her fetus. This latter form of transmission presents the primary problem with the Zika virus; transmission to the fetus can cause microcephaly as well as other brain and developmental problems. Proper precautions should be taken based on these identified modes of transmission. Symptoms of Zika are similar to flu-like symptoms, such as low-grade fever, muscle pain and headache. About 20 percent of patients that come in contact with the Zika virus will originally present as asymptomatic and will not display symptoms until almost two weeks after initial contact with the virus. Zika virus can remain in the blood for about a week, but can remain in the semen for months. There are a number of methods used to detect the Zika virus—urine, blood or semen samples may be used to assess if a patient is infected

Health Risks and Emerging Trends with the Use of Electronic Cigarettes

Cigarette smoking is associated with many health risks and complications. Despite smokers\u27 strong desire to quit, most battle with nicotine withdrawal and relapse. Because electronic cigarettes (e-cigarettes) do not contain tobacco, some believe them to be safer than traditional cigarettes and have used them as a replacement or adjunct nicotine source to prevent withdrawal symptoms. Electronic cigarettes are designed to mimic traditional cigarettes and expel a vapor composed of nicotine, water, glycerol, propylene glycol and other flavorings. Many e-cigarette companies use appealing platforms, which promise smoking cessation and harm reduction, to attract consumers; however, several studies have found e-cigarettes actually contain ingredients that are harmful to one\u27s health. Studies have demonstrated that the use of e-cigarettes can be toxic to patients\u27 health if patients do not research the products they intend to purchase. The flavoring of e-cigarettes may be a major contributor to e-cigarette cytotoxicity. If flavoring and other cytotoxic contents of e-cigarettes can be eliminated, e-cigarettes may be useful in smoking reduction and cessation. Many clinicians today support traditional forms of nicotine replacement therapy for smoking cessation rather than e-cigarettes. Due to the lack of regulation and studies by the U.S. Food and Drug Administration, e-cigarettes may not be as safe as users may perceive and should not be a preferred product for smoking cessation therapy until they are further studied and regulated

Assessing Within-Field Variation in Alfalfa Leaf Area Index Using UAV Visible Vegetation Indices

This study examines the use of leaf area index (LAI) to inform variable-rate irrigation (VRI) for irrigated alfalfa (Medicago sativa). LAI is useful for predicting zone-specific evapotranspiration (ETc). One approach toward estimating LAI is to utilize the relationship between LAI and visible vegetation indices (VVIs) using unmanned aerial vehicle (UAV) imagery. This research has three objectives: (1) to measure and describe the within-field variation in LAI and canopy height for an irrigated alfalfa field, (2) to evaluate the relationships between the alfalfa LAI and various VVIs with and without field average canopy height, and (3) to use UAV images and field average canopy height to describe the within-field variation in LAI and the potential application to VRI. The study was conducted in 2021–2022 in Rexburg, Idaho. Over the course of the study, the measured LAI varied from 0.23 m2 m−2 to 11.28 m2 m−2 and canopy height varied from 6 cm to 65 cm. There was strong spatial clustering in the measured LAI but the spatial patterns were dynamic between dates. Among eleven VVIs evaluated, the four that combined green and red wavelengths but excluded blue wavelengths showed the most promise. For all VVIs, adding average canopy height to multiple linear regression improved LAI prediction. The regression model using the modified green–red vegetation index (MGRVI) and canopy height (R2 = 0.93) was applied to describe the spatial variation in the LAI among VRI zones. There were significant (p \u3c 0.05) but not practical differences

The concurrent validity of a rugby-specific Yo-Yo Intermittent Recovery Test (Level 1) for assessing match-related running performance

This is a non-final version of an article published in final form in Dobbin, N., Moss, S. L., Hunwicks, R., Highton, J., & Twist, C. (2018). The concurrent validity of a rugby-specific Yo-Yo Intermittent Recovery Test (Level 1) for assessing match-related running performance. Journal of Strength and Conditioning Research, 35(1), 176-182. http://doi.org/10.1519/JSC.0000000000002621This study investigated the concurrent validity of a rugby-specific high-intensity intermittent running test (HIIR) against the internal, external and perceptual responses to simulated match-play. Thirty-six rugby league players (age 18.5 ± 1.8 years; stature 181.4 ± 7.6 cm; body mass 83.5 ± 9.8 kg) completed the prone Yo-Yo IR1, of which sixteen also completed the Yo-Yo IR1, and 2 x ~20 min bouts of a simulated match-play (RLMSP-i). Most likely reductions in relative total, low-speed and high-speed distance, mean speed and time above 20 W·kg-1 (HMP) were observed between bouts of the RLMSP-i. Likewise, rating of perceived exertion (RPE) and percentage of peak heart rate (%HRpeak) were very likely and likely higher during the second bout. Pearson’s correlations revealed a large relationship for the change in relative distance (r = 0.57-0.61) between bouts with both Yo-Yo IR1 tests. The prone Yo-Yo IR1 was more strongly related to the RLMSP-i for change in repeated sprint speed (r = 0.78 cf. 0.56), mean speed (r = 0.64 cf. 0.36), HMP (r = 0.48 cf. 0.25), fatigue index (r = 0.71 cf. 0.63), %HRpeak (r = -0.56 cf. -0.35), RPEbout1 (r = -0.44 cf. -0.14), and RPEbout2 (r = -0.68 cf. -0.41) than the Yo-Yo IR1, but not for blood lactate concentration (r = -0.20 to -0.28 cf. -0.35 to -0.49). The relationships between prone Yo-Yo IR1 distance and measure of load during the RLMSP-i suggests it possesses concurrent validity and is more strongly associated with measures of training or match load than the Yo-Yo IR1 using rugby league players

Paleobiology Database User Guide Version 1.0

The Paleobiology Database is an online, non-governmental, non-profit public resource for paleontological data. It is organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. This volume is designed to be a comprehensive guide for Paleobiology Database users, both General and Contributory. It covers most database uses from data retrieval and mapping to data contribution of all types. It contains numerous examples to illustrate database use as well as definitions of terms and additional links to numerous other sources. We hope that this user guide will help all users access the great volume of data in the Paleobiology Database and lead others to start and continue to add data to the system

Performance of the Xpert HPV assay in women attending for cervical screening

© 2015 The Authors. Objectives: This study evaluated the Xpert HPV Assay in women attending screening in general practice by comparing Xpert with two established HPV tests, cytology and histology. Methods: A prospective study in women aged 20-60 years attending screening in Bristol, Edinburgh and London using residual Preservcyt cytology samples. Sample order was randomised between Roche cobas4800 and Cepheid Xpert assays with Qiagen hc2 third. Results: 3408 cases were included in the primary analysis. Positivity for Xpert was 19.6%, cobas 19.2% and hc2 19.9% with high concordance (kappa=86.8% vs cobas, 81.55 vs hc2). Xpert, cobas and hc2 showed similar sensitivity (98.7%, 97.5%, 98.7%) for CIN2+. All pairwise comparisons had high concordance (Kappa ≥0.78 with any abnormal cytology. Xpert and hc2 were positive for all cases of ≥moderate dyskaryosis ( N=63)), cobas was negative in two. Histology was available for 172 participants. 79 reported CIN2+, 47 CIN3+. All CIN3+ was positive on Xpert and hc2 and one case negative for cobas. One case of CIN2 was negative for all assays. Conclusions: The performance of Xpert HPV Assay in a general screening population is comparable to established HPV tests. It offers simplicity of testing, flexibility with non-batching of individual samples and rapid turnaround time