Abstract
Food production, sustainable development, population growth, and agricultural environmental impacts are linked global problems that require complex solutions. Many efforts evaluating these ...challenges primarily evaluate dietary strategies designed for health and environmental objectives without considering the subsequent adaptations required by the global food supply. Here we use a complementary approach to summarize trends and variability in the current agricultural system in the context of the growing population and impending environmental challenges. Globally, agricultural systems produce sufficient nutrients to feed 10 billion people with the exception of Ca, DHA + EPA, vitamins B4, D, and E. In a network analysis, greenhouse gas emissions were conditionally dependent on ruminant meat and milk, while water use was conditionally dependent on vegetable and fruit production; however, supplies of most nutrients were also dependent on these same production categories, suggesting trade-offs between nutritional and environmental objectives. Future work should evaluate strategies to address these compromises (i.e., improving water use efficiency and reducing greenhouse gas emissions), to explore to what extent such compromises are biophysically essential or merely a product of the current agricultural system structures. Given the time-sensitive nature of population growth and environmental concerns, strategies to make more effective use of currently produced agricultural products will also be critical complementary strategies to sustainably feed the growing population which can work in concert with other agricultural-, diet- and policy-focused efforts.
Globally, ruminant production systems used to synthesize meat and milk differ tremendously in terms of their efficiency, productivity, and environmental impacts. Regardless of this variability, milk ...has been repeatedly identified as an essential source of nutrients for humans. The objective of this work was to characterize global contributions of fluid milk to human food and nutrient supplies, greenhouse gas emissions, and water withdrawal. Data were leveraged from the United Nations Food and Agriculture Organization to estimate global supplies of agricultural products. Trade of agricultural products and waste of those products, along with use of human food for livestock feed were accounted for before estimating human nutrient supplies. The contributions of milk to human-edible nutrient supplies were then enumerated in terms of their proportion of total nutrients supplied by the agricultural system and in terms of the human population's requirement for that nutrient. We identified that fluid milk provides over 10% of consumable supplies of vitamin B12, vitamin A, riboflavin, and calcium available for humans globally. In terms of human nutrient requirements, milk provides sufficient vitamin B12 to meet the needs of over 60% of the global population, riboflavin to satisfy 50% of the population, and calcium and phosphorus for over 35% of the population. Compared with other foods, milk ranked among the highest in terms of nutrient-to-calorie ratio for numerous amino acids, phosphorus, calcium, and riboflavin. Conditional dependencies were identified between greenhouse gas emissions and ruminant milk and meat, but not between water withdrawal and milk production. When evaluating the trade-offs in nutrient use versus nutrient provision for producing milk or producing all ruminant products, the production of ruminants worldwide was associated with both net increases and net decreases of several key nutrients. Continued work focusing on strategies to reduce the environmental impact of milk production will improve the utility of milk for feeding the growing global population.
A number of neurologic diseases associated with expanded nucleotide repeats, including an inherited form of amyotrophic lateral sclerosis, have an unconventional form of translation called ...repeat-associated non-AUG (RAN) translation. It has been speculated that the repeat regions in the RNA fold into secondary structures in a length-dependent manner, promoting RAN translation. Repeat protein products are translated, accumulate, and may contribute to disease pathogenesis. Nucleotides that flank the repeat region, especially ones closest to the initiation site, are believed to enhance translation initiation. A machine learning model has been published to help identify ATG and near-cognate translation initiation sites; however, this model has diminished predictive power due to its extensive feature selection and limited training data. Here, we overcome this limitation and increase prediction accuracy by the following: a) capture the effect of nucleotides most critical for translation initiation via feature reduction, b) implement an alternative machine learning algorithm better suited for limited data, c) build comprehensive and balanced training data (via sampling without replacement) that includes previously unavailable sequences, and d) split ATG and near-cognate translation initiation codon data to train two separate models. We also design a supplementary scoring system to provide an additional prognostic assessment of model predictions. The resultant models have high performance, with ~85-88% accuracy, exceeding that of the previously published model by >18%. The models presented here are used to identify translation initiation sites in genes associated with a number of neurologic repeat expansion disorders. The results confirm a number of sites of translation initiation upstream of the expanded repeats that have been found experimentally, and predict sites that are not yet established.
The forthcoming Surface Water and Ocean Topography (SWOT) NASA satellite mission will measure water surface width, height, and slope of major rivers worldwide. The resulting data could provide an ...unprecedented account of river discharge at continental scales, but reliable methods need to be identified prior to launch. Here we present a novel algorithm for discharge estimation from only remotely sensed stream width, slope, and height at multiple locations along a mass‐conserved river segment. The algorithm, termed the Bayesian AMHG‐Manning (BAM) algorithm, implements a Bayesian formulation of streamflow uncertainty using a combination of Manning's equation and at‐many‐stations hydraulic geometry (AMHG). Bayesian methods provide a statistically defensible approach to generating discharge estimates in a physically underconstrained system but rely on prior distributions that quantify the a priori uncertainty of unknown quantities including discharge and hydraulic equation parameters. These were obtained from literature‐reported values and from a USGS data set of acoustic Doppler current profiler (ADCP) measurements at USGS stream gauges. A data set of simulated widths, slopes, and heights from 19 rivers was used to evaluate the algorithms using a set of performance metrics. Results across the 19 rivers indicate an improvement in performance of BAM over previously tested methods and highlight a path forward in solving discharge estimation using solely satellite remote sensing.
Key Points
A new method is presented for estimating discharge using satellite observations
The method uses Bayesian inference via hydraulics‐derived likelihood and empirical priors from existing data sources
Performance improvements over previous estimation algorithms are demonstrated on benchmark data sets
Inflammatory pseudotumour is a generic term applied to a variety of neoplastic and non-neoplastic entities that share a common histological appearance, namely a cytologically bland spindle cell ...proliferation with a prominent, usually chronic inflammatory infiltrate. Over the last two decades, inflammatory myofibroblastic tumour (IMT) has emerged from within the broad category of inflammatory pseudotumour, with distinctive clinical, pathological and molecular features. IMT shows a predilection for the visceral soft tissues of children and adolescents and has a tendency for local recurrence, but only a small risk of distant metastasis. Characteristic histological patterns include the fasciitis-like, compact spindle cell and hypocellular fibrous patterns, which are often seen in combination within the same tumour. Chromosomal translocations leading to activation of the ALK tyrosine kinase can be detected in approximately 50% of IMTs, particularly those arising in young patients. This review will examine the clinical, pathological, and molecular genetic features of IMT and discuss an approach to diagnosis and differential diagnosis.
The Surface Water and Ocean Topography (SWOT) satellite mission planned for launch in 2020 will map river elevations and inundated area globally for rivers >100 m wide. In advance of this launch, we ...here evaluated the possibility of estimating discharge in ungauged rivers using synthetic, daily “remote sensing” measurements derived from hydraulic models corrupted with minimal observational errors. Five discharge algorithms were evaluated, as well as the median of the five, for 19 rivers spanning a range of hydraulic and geomorphic conditions. Reliance upon a priori information, and thus applicability to truly ungauged reaches, varied among algorithms: one algorithm employed only global limits on velocity and depth, while the other algorithms relied on globally available prior estimates of discharge. We found at least one algorithm able to estimate instantaneous discharge to within 35% relative root‐mean‐squared error (RRMSE) on 14/16 nonbraided rivers despite out‐of‐bank flows, multichannel planforms, and backwater effects. Moreover, we found RRMSE was often dominated by bias; the median standard deviation of relative residuals across the 16 nonbraided rivers was only 12.5%. SWOT discharge algorithm progress is therefore encouraging, yet future efforts should consider incorporating ancillary data or multialgorithm synergy to improve results.
Key Points:
SWOT discharge algorithms were tested on synthetic observations for 19 rivers
Algorithms accurately characterized temporal dynamics of river discharge
At least one algorithm estimated discharge to <35% relative RMSE on 14/16 of nonbraided rivers
Drosophila community composition is complex in temperate regions with different abundance of flies and species across the growing season. Monitoring Drosophila populations provides insights into the ...phenology of both native and invasive species. Over a single growing season, we collected Drosophila at regular intervals and determined the number of individuals of the nine species we found in Kansas, USA. Species varied in their presence and abundance through the growing season with peak diversity occurring after the highest seasonal temperatures. We developed models for the abundance of the most common species, Drosophila melanogaster, D. simulans, D. algonquin, and the recent invasive species, D. suzukii. These models revealed that temperature played the largest role in abundance of each species across the season. For the two most commonly studied species, D. melanogaster and D. simulans, the best models indicate shifted thermal optima compared to laboratory studies, implying that fluctuating temperature may play a greater role in the physiology and ecology of these insects than indicated by laboratory studies, and should be considered in global climate change studies.
Although numerous studies exist relating ruminal volatile fatty acid (VFA) concentrations to diet composition and animal performance, minimal information is available describing how VFA dynamics ...respond to diets within the context of the whole rumen environment. The objective of this study was to characterize how protein and fiber sources affect dry matter intake, rumen pH, fluid dynamics, fermentation parameters, and epithelial gene expression. Four diet treatments (soybean meal or heat-treated soybean meal and beet pulp or timothy hay) were delivered to 10 wethers. The soybean meals served as crude protein (CP) sources while the beet pulp and timothy hay represented neutral detergent fiber (NDF) sources. Feed intake, rumen pH, fluid pool size, and fluid passage rate were unaffected by treatment. Butyrate synthesis and absorption were greater on the beet pulp treatment whereas synthesis and absorption of other VFA remained unchanged. Both CP and NDF treatment effects were associated with numerous VFA interconversions. Expression levels of rumen epithelial genes were not altered by diet treatment. These results indicate that rumen VFA dynamics are altered by changes in dietary sources of nutrients but that intake, rumen environmental parameters, and the rumen epithelium may be less responsive to such changes.
Annual coral bleaching events, which are predicted to occur as early as the next decade in the Florida Keys, are expected to cause catastrophic coral mortality. Despite this, there is little field ...data on how Caribbean coral communities respond to annual thermal stress events. At Cheeca Rocks, an inshore patch reef near Islamorada, FL, the condition of 4234 coral colonies was followed over 2 yr of subsequent bleaching in 2014 and 2015, the two hottest summers on record for the Florida Keys. In 2014, this site experienced 7.7 degree heating weeks (DHW) and as a result 38.0% of corals bleached and an additional 36.6% were pale or partially bleached. In situ temperatures in summer of 2015 were even warmer, with the site experiencing 9.5 DHW. Despite the increased thermal stress in 2015, only 12.1% of corals were bleached in 2015, which was 3.1 times less than 2014. Partial mortality dropped from 17.6% of surveyed corals to 4.3% between 2014 and 2015, and total colony mortality declined from 3.4 to 1.9% between years. Total colony mortality was low over both years of coral bleaching with 94.7% of colonies surviving from 2014 to 2016. The reduction in bleaching severity and coral mortality associated with a second stronger thermal anomaly provides evidence that the response of Caribbean coral communities to annual bleaching is not strictly temperature dose dependent and that acclimatization responses may be possible even with short recovery periods. Whether the results from Cheeca Rocks represent an aberration or a true resilience potential is the subject of ongoing research.
Recent advances in remote sensing and the upcoming launch of the joint NASA/CNES/CSA/UKSA Surface Water and Ocean Topography (SWOT) satellite point toward improved river discharge estimates in ...ungauged basins. Existing discharge methods rely on “prior river knowledge” to infer parameters not directly measured from space. Here, we show that discharge estimation is improved by classifying and parameterizing rivers based on their unique geomorphology and hydraulics. Using over 370,000 in situ hydraulic observations as training data, we test unsupervised learning and an “expert” method to assign these hydraulics and geomorphology to rivers via remote sensing. This intervention, along with updates to model physics, constitutes a new method we term “geoBAM,” an update of the Bayesian At‐many‐stations hydraulic geometry‐Manning's (BAM) algorithm. We tested geoBAM on Landsat imagery over more than 7,500 rivers (108 are gauged) in Canada's Mackenzie River basin and on simulated hydraulic data for 19 rivers that mimic SWOT observations without measurement error. geoBAM yielded considerable improvement over BAM, improving the median Nash‐Sutcliffe efficiency (NSE) for the Mackenzie River from −0.05 to 0.26 and from 0.16 to 0.46 for the SWOT rivers. Further, NSE improved by at least 0.10 in 78/108 gauged Mackenzie rivers and 8/19 SWOT rivers. We attribute geoBAM improvement to parameterizing rivers by type rather than globally, but prediction accuracy worsens if parameters are misassigned. This method is easily mapped to rivers at the global scale and paves the way for improving future discharge estimates, especially when coupled with hydrologic models.
Key Points
We introduce geoBAM, an improved version of a remote sensing of river discharge algorithm (BAM)
geoBAM is tested successfully on over 7,500 river reaches in the Canadian Arctic and on a suite of simulated SWOT observations
Discharge estimation accuracy is improved by using river‐specific prior information informed by classification of a large field data set
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