Seasonal and Spatial Variation in the Location and Reactivity of a Nitrate‐Contaminated Groundwater Discharge Zone in a Lakebed

Groundwater discharge delivering anthropogenic N from surrounding watersheds can impact lake nutrient budgets. However, upgradient groundwater processes and changing dynamics in N biogeochemistry at the groundwater‐lake interface are complex. In this study, seasonal water‐level variations in a groundwater flow‐through lake altered discharge patterns of a wastewater‐derived groundwater contaminant plume, thereby affecting biogeochemical processes controlling N transport. Pore water collected 15 cm under the lakebed along transects perpendicular to shore varied from oxic to anoxic with increasing nitrate concentrations (10–75 μM) and corresponding gradients in nitrite and nitrous oxide. Pore water depth profiles of nitrate concentrations and stable isotopic compositions largely reflected upgradient groundwater N sources and N cycle processes, with minor additional nitrate reduction in the near‐surface lakebed sediments. Potential denitrification rates determined in laboratory microcosms were 10–100 times higher in near‐surface sediments (0–5 cm) than in deeper sediments (5–30 cm) and were correlated with sediment carbon content and abundance of denitrification genes (nirS, nosZI, and nosZII). Potential anammox‐driven N2 production was detectable in deeper anoxic sediments. Injection of bromide and nitrite in the lake sediments showed that the highest net nitrite consumption rates were within the top 10 cm. However, short transit times owing to rapid upward pore water velocities (4–5 cm hr−1) limited removal of the contaminant nitrate transiting through the sediments. Results demonstrate that local hydrologic and biogeochemical processes at the point of discharge affect the distribution and discharge rate of N through lakebed sediments, but processes in the upgradient groundwater can be more important for affecting N speciation and concentration

How large should whales be?

The evolution and distribution of species body sizes for terrestrial mammals is well-explained by a macroevolutionary tradeoff between short-term selective advantages and long-term extinction risks from increased species body size, unfolding above the 2g minimum size induced by thermoregulation in air. Here, we consider whether this same tradeoff, formalized as a constrained convection-reaction-diffusion system, can also explain the sizes of fully aquatic mammals, which have not previously been considered. By replacing the terrestrial minimum with a pelagic one, at roughly 7000g, the terrestrial mammal tradeoff model accurately predicts, with no tunable parameters, the observed body masses of all extant cetacean species, including the 175,000,000g Blue Whale. This strong agreement between theory and data suggests that a universal macroevolutionary tradeoff governs body size evolution for all mammals, regardless of their habitat. The dramatic sizes of cetaceans can thus be attributed mainly to the increased convective heat loss is water, which shifts the species size distribution upward and pushes its right tail into ranges inaccessible to terrestrial mammals. Under this macroevolutionary tradeoff, the largest expected species occurs where the rate at which smaller-bodied species move up into large-bodied niches approximately equals the rate at which extinction removes them.Comment: 7 pages, 3 figures, 2 data table

Extension of Yeast Chronological Lifespan by Methylamine

Background: Chronological aging of yeast cells is commonly used as a model for aging of human post-mitotic cells. The yeast Saccharomyces cerevisiae grown on glucose in the presence of ammonium sulphate is mainly used in yeast aging research. We have analyzed chronological aging of the yeast Hansenula polymorpha grown at conditions that require primary peroxisome metabolism for growth. Methodology/Principal Findings: The chronological lifespan of H. polymorpha is strongly enhanced when cells are grown on methanol or ethanol, metabolized by peroxisome enzymes, relative to growth on glucose that does not require peroxisomes. The short lifespan of H. polymorpha on glucose is mainly due to medium acidification, whereas most likely ROS do not play an important role. Growth of cells on methanol/methylamine instead of methanol/ammonium sulphate resulted in further lifespan enhancement. This was unrelated to medium acidification. We show that oxidation of methylamine by peroxisomal amine oxidase at carbon starvation conditions is responsible for lifespan extension. The methylamine oxidation product formaldehyde is further oxidized resulting in NADH generation, which contributes to increased ATP generation and reduction of ROS levels in the stationary phase. Conclusion/Significance: We conclude that primary peroxisome metabolism enhanced chronological lifespan of H. polymorpha. Moreover, the possibility to generate NADH at carbon starvation conditions by an organic nitrogen source supports further extension of the lifespan of the cell. Consequently, the interpretation of CLS analyses in yeast should include possible effects on the energy status of the cell.

Imaging and Dynamics of Light Atoms and Molecules on Graphene

Observing the individual building blocks of matter is one of the primary goals of microscopy. The invention of the scanning tunneling microscope [1] revolutionized experimental surface science in that atomic-scale features on a solid-state surface could finally be readily imaged. However, scanning tunneling microscopy has limited applicability due to restrictions, for example, in sample conductivity, cleanliness, and data aquisition rate. An older microscopy technique, that of transmission electron microscopy (TEM) [2, 3] has benefited tremendously in recent years from subtle instrumentation advances, and individual heavy (high atomic number) atoms can now be detected by TEM [4 - 7] even when embedded within a semiconductor material [8, 9]. However, detecting an individual low atomic number atom, for example carbon or even hydrogen, is still extremely challenging, if not impossible, via conventional TEM due to the very low contrast of light elements [2, 3, 10 - 12]. Here we demonstrate a means to observe, by conventional transmision electron microscopy, even the smallest atoms and molecules: On a clean single-layer graphene membrane, adsorbates such as atomic hydrogen and carbon can be seen as if they were suspended in free space. We directly image such individual adatoms, along with carbon chains and vacancies, and investigate their dynamics in real time. These techniques open a way to reveal dynamics of more complex chemical reactions or identify the atomic-scale structure of unknown adsorbates. In addition, the study of atomic scale defects in graphene may provide insights for nanoelectronic applications of this interesting material.Comment: 9 pages manuscript and figures, 9 pages supplementary informatio

The phylogenetic origin of jaws in vertebrates: developmental plasticity and heterochrony

Copyright 2010 the Cleveland Museum of Natural History. Published version of the paper reproduced here with permission from the publisher

Use of Temporally Validated Machine Learning Models To Predict Outcomes of Percutaneous Nephrolithotomy Using Data from the British Association of Urological Surgeons Percutaneous Nephrolithotomy Audit

\ua9 2024 European Association of Urology. Background and objective: Machine learning (ML) is a subset of artificial intelligence that uses data to build algorithms to predict specific outcomes. Few ML studies have examined percutaneous nephrolithotomy (PCNL) outcomes. Our objective was to build, streamline, temporally validate, and use ML models for prediction of PCNL outcomes (intensive care admission, postoperative infection, transfusion, adjuvant treatment, postoperative complications, visceral injury, and stone-free status at follow-up) using a comprehensive national database (British Association of Urological Surgeons PCNL). Methods: This was an ML study using data from a prospective national database. Extreme gradient boosting (XGB), deep neural network (DNN), and logistic regression (LR) models were built for each outcome of interest using complete cases only, imputed, and oversampled and imputed/oversampled data sets. All validation was performed with complete cases only. Temporal validation was performed with 2019 data only. A second round used a composite of the most important 11 variables in each model to build the final model for inclusion in the shiny application. We report statistics for prognostic accuracy. Key findings and limitations: The database contains 12 810 patients. The final variables included were age, Charlson comorbidity index, preoperative haemoglobin, Guy\u27s stone score, stone location, size of outer sheath, preoperative midstream urine result, primary puncture site, preoperative dimercapto-succinic acid scan, stone size, and image guidance (https://endourology.shinyapps.io/PCNL_Demographics/). The areas under the receiver operating characteristic curve was >0.6 in all cases. Conclusions and clinical implications: This is the largest ML study on PCNL outcomes to date. The models are temporally valid and therefore can be implemented in clinical practice for patient-specific risk profiling. Further work will be conducted to externally validate the models. Patient summary: We applied artificial intelligence to data for patients who underwent a keyhole surgery to remove kidney stones and developed a model to predict outcomes for this procedure. Doctors could use this tool to advise patients about their risk of complications and the outcomes they can expect after this surgery

Post-treatment levels of plasma 25- and 1,25-dihydroxy vitamin D and mortality in men with aggressive prostate cancer.

Vitamin D may reduce mortality from prostate cancer (PC). We examined the associations of post-treatment plasma 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D concentrations with PC mortality. Participants were PC cases from the New South Wales Prostate Cancer Care. All contactable and consenting participants, at 4.9 to 8.6 years after diagnosis, were interviewed and had plasma 25-hydroxyvitamin D (25(OH)D) and 1,25-dihydroxyvitamin D (1,25(OH)2D) measured in blood specimens. Cox regression allowing for left-truncation was used to calculate adjusted mortality hazards ratios (HR) and 95% confidence intervals (95% CI) for all-cause and PC-specific mortality in relation to vitamin D levels and other potentially-predictive variables. Of the participants (n = 111; 75·9% response rate), there were 198 deaths from any cause and 41 from PC in the study period. Plasma 25(OH)D was not associated with all-cause or PC-specific mortality (p-values > 0·10). Plasma 1,25(OH)2D was inversely associated with all-cause mortality (HR for highest relative to lowest quartile = 0·45; 95% CI: 0·29-0·69), and PC-specific mortality (HR = 0·40; 95% CI: 0·14-1·19). These associations were apparent only in men with aggressive PC: all-cause mortality HR = 0·28 (95% CI·0·15-0·52; p-interaction = 0·07) and PC-specific mortality HR = 0·26 (95% CI: 0·07-1.00). Time spent outdoors was also associated with lower all-cause (HR for 4th relative to 1st exposure quartile = 0·42; 95% CI: 0·24-0·75) and PC-specific (HR = 0·48; 95% CI: 0·14-1·64) mortality, although the 95% CI for the latter was wide. The inverse association between post-treatment plasma 1,25(OH)2D levels and all-cause and PC-specific mortality in men with aggressive PC, suggest a possible beneficial effect of vitamin D supplementation in these men

Survival gains needed to offset persistent adverse treatment effects in localised prostate cancer

BACKGROUND: Men diagnosed with localised prostate cancer (LPC) face difficult choices between treatment options that can cause persistent problems with sexual, urinary and bowel function. Controlled trial evidence about the survival benefits of the full range of treatment alternatives is limited, and patients' views on the survival gains that might justify these problems have not been quantified. METHODS: A discrete choice experiment (DCE) was administered in a random subsample (n=357, stratified by treatment) of a population-based sample (n=1381) of men, recurrence-free 3 years after diagnosis of LPC, and 65 age-matched controls (without prostate cancer). Survival gains needed to justify persistent problems were estimated by substituting side effect and survival parameters from the DCE into an equation for compensating variation (adapted from welfare economics). RESULTS: Median (2.5, 97.5 centiles) survival benefits needed to justify severe erectile dysfunction and severe loss of libido were 4.0 (3.4, 4.6) and 5.0 (4.9, 5.2) months. These problems were common, particularly after androgen deprivation therapy (ADT): 40 and 41% overall (n=1381) and 88 and 78% in the ADT group (n=33). Urinary leakage (most prevalent after radical prostatectomy (n=839, mild 41%, severe 18%)) needed 4.2 (4.1, 4.3) and 27.7 (26.9, 28.5) months survival benefit, respectively. Mild bowel problems (most prevalent (30%) after external beam radiotherapy (n=106)) needed 6.2 (6.1, 6.4) months survival benefit. CONCLUSION: Emerging evidence about survival benefits can be assessed against these patient-based benchmarks. Considerable variation in trade-offs among individuals underlines the need to inform patients of long-term consequences and incorporate patient preferences into treatment decisions. © 2012 Cancer Research UK. All rights reserved

Prospective association between objective measures of childhood motor coordination and sedentary behaviour in adolescence and adulthood

BACKGROUND: Higher levels of gross motor coordination are positively associated with physical activity in childhood, but little is known about how they relate to sedentary behaviour. The aim of this study was to investigate the longitudinal association between gross motor coordination at childhood and sedentary behaviour in adolescence and adulthood. METHODS: Data were from the 1970 British Cohort Study (the age 10, 16, and 42-year surveys). At age 10 the participant's mother provided information on how often participants watched TV and played sports and a health visitor administered several tests to assess gross motor coordination. At aged 16 and 42-years participants reported their daily screen and TV time, respectively, and physical activity status. We examined associations between gross motor coordination at age 10 with sedentary behaviour and physical activity at age 16 and 42, using logistic regression. RESULTS: In multivariable models, higher levels of gross motor coordination were associated with lower odds of high screen time (n = 3073; OR 0.79, 95% CI 0.64, 0.98) at 16-years although no associations with physical activity were observed (OR 1.16, 95% CI 0.93, 1.44). Similar associations were observed with TV time in adulthood when participants were aged 42, and in addition high gross motor coordination was also associated with physical activity participation (n = 4879; OR 1.18, 95 % CI 1.02, 1.36). CONCLUSIONS: Intervention efforts to increase physical activity participation and reduce sedentary behaviour over the life course may be best targeted towards children with low gross motor coordination