Dynamics of Hyporheic Flow and Heat Transport Across a Bed-to-Bank Continuum in a Large Regulated River

The lower Colorado River (LCR) near Austin, Texas is heavily regulated for hydropower generation. Daily water releases from a dam located 23 km upstream of our study site in the LCR caused the stage to fluctuate by more than 1.5 m about a mean depth of 1.3 m. As a result, the river switches from gaining to losing over a dam storage-release cycle, driving exchange between river water and groundwater. We assessed the hydrologic impacts of this by simultaneous temperature and head monitoring across a bed-to-bank transect. River-groundwater exchange flux is largest close to the bank and decreases away from the bank. Correspondingly, both the depth of the hyporheic zone and the exchange time are largest close to the bank. Adjacent to the bank, the streambed head response is hysteretic, with the hysteresis disappearing with distance from the bank, indicating that transient bank storage affects the magnitude and direction of vertical exchange close to the bank. Pronounced changes in streambed temperature are observed down to a meter. When the river stage is high, which coincides with when the river is coldest, downward advection of heat from a previous cycles\u27 warm-water pulse warms the streambed. When the river is at its lowest stage but warmest temperature, upwelling groundwater cools the streambed. Future research should consider and focus on a more thorough understanding of the impacts of dam regulation on the hydrologic, thermal, biogeochemical, and ecologic dynamics of rivers and their hyporheic and riparian zones

Risk factors associated with fatal pulmonary hemorrhage in locally advanced non-small cell lung cancer treated with chemoradiotherapy

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to identify the risk factors associated with fatal pulmonary hemorrhage (PH) in patients with locally advanced non-small cell lung cancer (NSCLC), treated with chemoradiotherapy.</p> <p>Methods</p> <p>The medical records of 583 patients with locally advanced NSCLC, who were treated with chemoradiotherapy between July 1992 and December 2009 were reviewed. Fatal PH was defined as PH leading to death within 24 h of its onset. Tumor cavitation size was defined by the cavitation diameter/tumor diameter ratio and was classified as minimum (< 0.25), minor (≥ 0.25, but < 0.5), and major (≥ 0.5).</p> <p>Results</p> <p>Of the 583 patients, 2.1% suffered a fatal PH. The numbers of patients with minimum, minor, and major cavitations were 13, 11, and 14, respectively. Among the 38 patients with tumor cavitation, all 3 patients who developed fatal PH had major cavitations. On multivariate analysis, the presence of baseline major cavitation (odds ratio, 17.878), and a squamous cell histology (odds ratio, 5.491) proved to be independent significant risk factors for fatal PH. Interestingly, all patients with fatal PH and baseline major cavitation were found to have tumors with squamous cell histology, and the occurrence of fatal PH in patients having both risk factors was 33.3%.</p> <p>Conclusions</p> <p>Patients at high risk of fatal PH could be identified using a combination of independent risk factors.</p

Integrated genomic characterization of pancreatic ductal adenocarcinoma

We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations. Protein profiling identified a favorable prognosis subset with low epithelial-mesenchymal transition and high MTOR pathway scores. Associations of non-coding RNAs with tumor-specific mRNA subtypes were also identified. Our integrated multi-platform analysis reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine

The effects of storms and a transient sandy veneer on the interannual planform evolution of a low-relief coastal cliff and shore platform at Sargent Beach, Texas, USA

Coastal cliff erosion is alongshore-variable and episodic, with retreat rates that depend upon sediment as either tools of abrasion or protective cover. However, the feedbacks between coastal cliff planform morphology, retreat rate, and sediment cover are poorly quantified. This study investigates Sargent Beach, Texas, USA, at the annual to interannual scale to explore (1) the relationship between temporal and spatial variability in cliff retreat rate, roughness, and sinuosity and (2) the response of retreat rate and roughness to changes in sand and shell hash cover of the underlying mud substrate as well as the impact of major storms using field measurements of sediment cover, erosion, and aerial images to measure shore platform morphology and retreat. A storm event in 2009 increased the planform roughness and sinuosity of the coastal cliff at Sargent Beach. Following the storm, aerial-image-derived shorelines with annual resolution show a decrease in average alongshore erosion rates from 12 to 4 m yr−1, coincident with a decrease in shoreline roughness and sinuosity (smoothing). Like the previous storm, a storm event in 2017 increased the planform roughness and sinuosity of the cliff. Over shorter timescales, monthly retreat of the sea cliff occurred only when the platform was sparsely covered with sediment cover on the shore platform, indicating that the tools and cover effects can significantly affect short-term erosion rates. The timescale to return to a smooth shoreline following a storm or roughening event, given a steady-state erosion rate, is approximately 24 years, with the long-term rate suggesting a maximum of ∼107 years until Sargent Beach breaches, compromising the Gulf Intracoastal Waterway (GIWW) under current conditions and assuming no future storms or intervention. The observed retreat rate varies, both spatially and temporally, with cliff face morphology, demonstrating the importance of multi-scale measurements and analysis for interpretation of coastal processes and patterns of cliff retreat.National Science Foundation (Grant 1745302

Phase and antigenic variation govern competition dynamics through positioning in bacterial colonies

Abstract Cellular positioning towards the surface of bacterial colonies and biofilms can enhance dispersal, provide a selective advantage due to increased nutrient and space availability, or shield interior cells from external stresses. Little is known about the molecular mechanisms that govern bacterial positioning. Using the type IV pilus (T4P) of Neisseria gonorrhoeae, we tested the hypothesis that the processes of phase and antigenic variation govern positioning and thus enhance bacterial fitness in expanding gonococcal colonies. By independently tuning growth rate and T4P-mediated interaction forces, we show that the loss of T4P and the subsequent segregation to the front confers a strong selective advantage. Sequencing of the major pilin gene of the spatially segregated sub-populations and an investigation of the spatio-temporal population dynamics was carried out. Our findings indicate that pilin phase and antigenic variation generate a standing variation of pilin sequences within the inoculation zone, while variants associated with a non-piliated phenotype segregate to the front of the growing colony. We conclude that tuning of attractive forces by phase and antigenic variation is a powerful mechanism for governing the dynamics of bacterial colonies