Prevalence and Risk Assessment of Aflatoxin in Iowa Corn during a Drought Year.

Warm temperatures and drought conditions in the United States (US) Corn Belt in 2012 raised concern for widespread aflatoxin (AFL) contamination in Iowa corn. To identify the prevalence of AFL in the 2012 corn crop, the Iowa Department of Agriculture and Land Stewardship (IDALS) conducted a sample of Iowa corn to assess the incidence and severity of AFL contamination. Samples were obtained from grain elevators in all of Iowa's 99 counties, representing nine crop reporting districts (CRD), and 396 samples were analyzed by IDALS using rapid test methods. The statewide mean for AFL in parts per billion (ppb) was 5.57 ppb. Regions of Iowa differed in their incidence levels, with AFL levels significantly higher in the Southwest (SW; mean 15.13 ppb) and South Central (SC; mean 10.86 ppb) CRD (p < 0.05) regions of Iowa. This sampling demonstrated high variability among samples collected within CRD and across the entire state of Iowa in an extreme weather event year. In years when Iowa has AFL contamination in corn, there is a need for a proactive and preventive strategy to minimize hazards in domestic and export markets.

Monitoring the temporal changes in herbicide-resistant Amaranthus tuberculatus: a landscape-scale probability-based estimation in Iowa.

BACKGROUND: A landscape-scale probability-based sampling of Iowa soybean [Glycine max (L.) Merr.] fields was conducted in 2013 and 2019; Amaranthus tuberculatus [Moq.] J.D. Sauer seed was collected from 97 random geospatial selected fields. The objectives were to evaluate the prevalence and distribution of herbicide-resistant A. tuberculatus (waterhemp) in soybean fields and evaluate temporal changes over 6 years. Amaranthus tuberculatus seedlings were evaluated for resistance to imazethapyr, atrazine, glyphosate, lactofen and mesotrione at 1× and 4× label rates. RESULTS: Resistance to imazethapyr, glyphosate, lactofen and mesotrione at the 1× rate increased significantly from 2013 to 2019 and was found in 99%, 97%, 16% and 15% of Iowa A. tuberculatus populations in 2019, respectively. Resistance to atrazine at the 4× rate increased over time; atrazine resistance was found in 68% of populations in 2019. Three-way multiple herbicide-resistant A. tuberculatus was the most frequent and increased significantly to 4× rates from 16% in 2013 to 43% of populations in 2019. All A. tuberculatus populations resistant to HPPD-inhibitor herbicides also were resistant to atrazine. CONCLUSION: To the best of our knowledge, this is the first probability-based study that presented evolution of A. tuberculatus herbicide resistance over time. The results demonstrated that imazethapyr, atrazine and glyphosate resistance in Iowa A. tuberculatus populations was frequent whereas resistance to lactofen and mesotrione was less frequent. Most Iowa A. tuberculatus populations evolved resistance to multiple sites of action over time. The results of our study are widely applicable given the similarities in weed management practices throughout the Midwest United States. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

WhoseEgg: classification software for invasive carp eggs.

The collection of fish eggs is a commonly used technique for monitoring invasive carp. Genetic identification is the most trusted method for identifying fish eggs but is expensive and slow. Recent work suggests random forest models could provide an inexpensive method for identifying invasive carp eggs based on morphometric egg characteristics. While random forests provide accurate predictions, they do not produce a simple formula for obtaining new predictions. Instead, individuals must have knowledge of the R coding language, limiting the individuals who can use the random forests for resource management. We present WhoseEgg: a web-based point-and-click application that allows non-R users to access random forests via a point and click interface to rapidly identify fish eggs with an objective of detecting invasive carp (Bighead, Grass, and Silver Carp) in the Upper Mississippi River basin. This article provides an overview of WhoseEgg, an example application, and future research directions.

A cluster-randomized trial comparing two SWITCH implementation support strategies for school wellness intervention effectiveness.

BACKGROUND: The School Wellness Integration Targeting Child Health (SWITCH) intervention has demonstrated feasibility as an implementation approach to help schools facilitate changes in students' physical activity (PA), sedentary screen time (SST), and dietary intake (DI). This study evaluated the comparative effectiveness of enhanced (individualized) implementation and standard (group-based) implementation. METHODS: Twenty-two Iowa elementary schools participated, with each receiving standardized training (wellness conference and webinars). Schools were matched within region and randomized to receive either individualized or group implementation support. The PA, SST, and DI outcomes of 1097 students were assessed at pre- and post-intervention periods using the Youth Activity Profile. Linear mixed models evaluated differential change in outcomes by condition, for comparative effectiveness, and by gender. RESULTS: Both implementation conditions led to significant improvements in PA and SST over time (p < 0.01), but DI did not improve commensurately (p value range: 0.02‒0.05). There were no differential changes between the group and individualized conditions for PA (p = 0.51), SST (p = 0.19), or DI (p = 0.73). There were no differential effects by gender (i.e., non-significant condition-by-gender interactions) for PA (pfor interaction = 0.86), SST (pfor interaction = 0.46), or DI (pfor interaction = 0.15). Effect sizes for both conditions equated to approximately 6 min more PA per day and approximately 3 min less sedentary time. CONCLUSION: The observed lack of difference in outcomes suggests that group implementation of SWITCH is equally effective as individualized implementation for building capacity in school wellness programming. Similarly, the lack of interaction by gender suggests that SWITCH can be beneficial for both boys and girls. Additional research is needed to understand the school-level factors that influence implementation (and outcomes) of SWITCH.

Lengthening of maize maturity time is not a widespread climate change adaptation strategy in the US Midwest.

Increasing temperatures in the US Midwest are projected to reduce maize yields because warmer temperatures hasten reproductive development and, as a result, shorten the grain fill period. However, there is widespread expectation that farmers will mitigate projected yield losses by planting longer season hybrids that lengthen the grain fill period. Here, we ask: (a) how current hybrid maturity length relates to thermal availability of the local climate, and (b) if farmers are shifting to longer season hybrids in response to a warming climate. To address these questions, we used county-level Pioneer brand hybrid sales (Corteva Agriscience) across 17 years and 650 counties in 10 Midwest states (IA, IL, IN, MI, MN, MO, ND, OH, SD, and WI). Northern counties were shown to select hybrid maturities with growing degree day (GDD°C) requirements more closely related to the environmentally available GDD compared to central and southern counties. This measure, termed "thermal overlap," ranged from complete 106% in northern counties to a mere 63% in southern counties. The relationship between thermal overlap and latitude was fit using split-line regression and a breakpoint of 42.8°N was identified. Over the 17-years, hybrid maturities shortened across the majority of the Midwest with only a minority of counties lengthening in select northern and southern areas. The annual change in maturity ranged from -5.4 to 4.1 GDD year-1 with a median of -0.9 GDD year-1 . The shortening of hybrid maturity contrasts with widespread expectations of hybrid maturity aligning with magnitude of warming. Factors other than thermal availability appear to more strongly impact farmer decision-making such as the benefit of shorter maturity hybrids on grain drying costs, direct delivery to ethanol biorefineries, field operability, labor constraints, and crop genetics availability. Prediction of hybrid choice under future climate scenarios must include climatic factors, physiological-genetic attributes, socio-economic, and operational constraints.

Calibration of the Online Youth Activity Profile Assessment for School-Based Applications.

A balance between the feasibility and validity of measures is an important consideration for physical activity research - particularly in school-based research with youth. The present study extends previously tested calibration methods to develop and test new equations for an online version of the Youth Activity Profile (YAP) tool, a self-report tool designed for school applications. Data were collected across different regions and seasons to develop more robust, generalizable equations. The study involved a total of 717 youth from 33 schools (374 elementary (ages 9-11), 224 middle (ages 11-14), and 119 high school (ages 14-18)) in two different states in the U.S. Participants wore a Sensewear monitor for a full week and then completed the online YAP at school to report physical activity (PA) and sedentary behaviors (SB) in school and at home. Accelerometer data were processed using an R-based segmentation program to compute PA and SB levels. Quantile regression models were used with half of the sample to develop item-specific YAP calibration equations and these were cross validated with the remaining half of the sample. Computed values of Mean Absolute Percent Error (MAPE) ranged from 15-25% with slightly lower error observed for the middle school sample. The new equations had improved precision compared to the previous versions when tested on the same sample. The online version of the YAP provides an efficient and effective way to capture school level estimates of PA and SB in youth.

Precipitation Impacts Dissemination of Three Sooty Blotch and Flyspeck Taxa on Apple Fruit.

The spatial dissemination of three prevalent taxa of sooty blotch and flyspeck (SBFS) fungi under several levels of precipitation was compared during 2015 and 2016 in an Iowa apple orchard. Overhead irrigation was used to supplement ambient precipitation in order to insure SBFS spore dissemination and colony development. There were five irrigation levels, involving 1-min-long periods of irrigation that were imposed either once or twice per hour at intervals of 3, 6, or 12 h, as well as a nonirrigated control. Preselected apple fruit were inoculated with one of the three SBFS taxa to serve as sources of inoculum. Dissemination from these inoculated apple fruit was assessed at harvest by counting SBFS colonies on water-sprayed and nontreated fruit. As a further control, additional fruit were enclosed in fruit bags throughout the fruit development period. In both 2015 and 2016, the number of colonies of the SBFS fungus Peltaster gemmifer per apple increased sharply as the duration of irrigation increased, whereas the number of colonies of Microcyclosporella mali increased to a lesser extent and Stomiopeltis sp. RS1 showed no increase. In 2015, the linear relationship between the duration of irrigation-imposed precipitation levels and the number of colonies on the water-sprayed apple fruit was similar for P. gemmifer (slope = 0.09), Stomiopeltis sp. RS1 (slope = 0.07), and Microcyclosporella mali (slope = 0.13); whereas, in 2016, the slope was higher for P. gemmifer (0.28) than for Stomiopeltis sp. RS1 (-0.09) or M. mali (0.06). The results indicated that dissemination of P. gemmifer increased sharply in response to increased irrigation-imposed precipitation, and that dissemination patterns differed considerably among the three SBFS taxa. The apparent advantage of P. gemmifer in precipitation-triggered dissemination may stem from its ability to produce spores rapidly by budding. To our knowledge, this is the first article to assess splash dispersal by SBFS fungi in the field and the first to document taxon-specific patterns of dissemination in this pathogen complex.

Calibration and Validation of the Youth Activity Profile as a Physical Activity and Sedentary Behaviour Surveillance Tool for English Youth.

Self-reported youth physical activity (PA) is typically overestimated. We aimed to calibrate and validate a self-report tool among English youth. Four-hundred-and-two participants (aged 9-16 years; 212 boys) wore SenseWear Armband Mini devices (SWA) for eight days and completed the self-report Youth Activity Profile (YAP) on the eighth day. Calibration algorithms for temporally matched segments were generated from the YAP data using quantile regression. The algorithms were applied in an independent cross-validation sample, and student- and school-level agreement were assessed. The utility of the YAP algorithms to assess compliance to PA guidelines was also examined. The school-level bias for the YAP estimates of in-school, out-of-school, and weekend moderate-to-vigorous PA (MVPA) were 17.2 (34.4), 31.6 (14.0), and -4.9 (3.6) min·week-1, respectively. Out-of-school sedentary behaviour (SB) was over-predicted by 109.2 (11.8) min·week-1. Predicted YAP values were within 15%-20% equivalence of the SWA estimates. The classification accuracy of the YAP MVPA estimates for compliance to 60 min·day-1 and 30 min·school-day-1 MVPA recommendations were 91%/37% and 89%/57% sensitivity/specificity, respectively. The YAP generated robust school-level estimates of MVPA and SB and has potential for surveillance to monitor compliance with PA guidelines. The accuracy of the YAP may be further improved through research with more representative UK samples to enhance the calibration process and to refine the resultant algorithms.

Changes in sedentary time are associated with changes in mental wellbeing over 1 year in young adults.

Excessive sedentary time is related to poor mental health. However, much of the current literature uses cross-sectional data and/or self-reported sedentary time, and does not assess factors such as sedentary bout length. To address these limitations, the influence of objectively measured sedentary time including sedentary bout length (i.e. <30 min, ≥30 min) on mood, stress, and sleep, was assessed in 271 healthy adults (49% women; age 27.8 ±â€¯3.7) across a 1-year period between 2011 and 2013 in Columbia, SC. Participants completed the Profile of Mood States and the Perceived Stress Scale, and wore a Sensewear Armband to assess sedentary time, physical activity, and sleep for ten days at baseline and one year. A series of fixed-effects regressions was used to determine the influence of both baseline levels and changes in daily sedentary time (total and in bouts) and physical activity on changes in mood, stress, and sleep over one year. Results showed that across the year, decreases in total sedentary time, and time in both short and long bouts, were associated with improvements in mood, stress and sleep (p < 0.05). Increases in physical activity were only significantly predictive of increases in sleep duration (p < 0.05). Thus, reductions in sedentary time, regardless of bout length, positively influenced mental wellbeing. Specifically, these results suggest that decreasing daily sedentary time by 60 min may significantly attenuate the negative effects of high levels of pre-existing sedentary time on mental wellbeing. Interventions manipulating sedentary behavior are needed to determine a causal link with wellbeing and further inform recommendations.

Adapted Sojourn Models to Estimate Activity Intensity in Youth: A Suite of Tools.

The challenges of using physical activity data from accelerometers have been compounded with the recent focus on wrist-worn monitors and raw acceleration (as opposed to activity counts). PURPOSE: This study developed and systematically evaluated a suite of new accelerometer processing models for youth. METHODS: Four adaptations of the Sojourn method were developed using data from a laboratory-based experiment in which youth (N = 54) performed structured activity routines. The adaptations corresponded to all possible pairings of hip or wrist attachment with activity counts (AC) or raw acceleration (RA), and they estimated time in sedentary behavior, light activity, and moderate-to-vigorous physical activity. Criterion validity was assessed using direct observation in an independent free-living sample (N = 27). Monitors were worn on both wrists to evaluate the effect of handedness on accuracy, and status quo methods for each configuration were also evaluated as benchmarks for comparison. Tests of classification accuracy (percent accuracy, κ statistics, and sensitivity and specificity) were used to summarize utility. RESULTS: In the development sample, percent accuracy ranged from 68.5% (wrist-worn AC, κ = 0.42) to 71.6% (hip-worn RA, κ = 0.50). Accuracy was lower in the free-living evaluation, with values ranging from 49.3% (hip-worn RA, κ = 0.25) to 56.7% (hip-worn AC, κ = 0.36). Collectively, the suite predicted moderate-to-vigorous physical activity well, with the models averaging 96.5% sensitivity and 67.5% specificity. However, in terms of overall accuracy, the new models performed similarly to the status quo methods. There were no meaningful differences in performance at either wrist. CONCLUSIONS: The new models offered minimal improvements over existing methods, but a major advantage is that further tuning of the models is possible with continued research.

A Primer on the Use of Equivalence Testing for Evaluating Measurement Agreement.

PURPOSE: Statistical equivalence testing is more appropriate than conventional tests of difference to assess the validity of physical activity (PA) measures. This article presents the underlying principles of equivalence testing and gives three examples from PA and fitness assessment research. METHODS: The three examples illustrate different uses of equivalence tests. Example 1 uses PA data to evaluate an activity monitor's equivalence to a known criterion. Example 2 illustrates the equivalence of two field-based measures of physical fitness with no known reference method. Example 3 uses regression to evaluate an activity monitor's equivalence across a suite of 23 activities. RESULTS: The examples illustrate the appropriate reporting and interpretation of results from equivalence tests. In the first example, the mean criterion measure is significantly within ±15% of the mean PA monitor. The mean difference is 0.18 METs and the 90% confidence interval of -0.15 to 0.52 is inside the equivalence region of -0.65 to 0.65. In the second example, we chose to define equivalence for these two measures as a ratio of mean values between 0.98 and 1.02. The estimated ratio of mean V˙O2 values is 0.99, which is significantly (P = 0.007) inside the equivalence region. In the third example, the PA monitor is not equivalent to the criterion across the suite of activities. The estimated regression intercept and slope are -1.23 and 1.06. Neither confidence interval is within the suggested regression equivalence regions. CONCLUSIONS: When the study goal is to show similarity between methods, equivalence testing is more appropriate than traditional statistical tests of differences (e.g., ANOVA and t-tests).

Escherichia coli attachment to model particulates: The effects of bacterial cell characteristics and particulate properties.

E. coli bacteria move in streams freely in a planktonic state or attached to suspended particulates. Attachment is a dynamic process, and the fraction of attached microorganisms is thought to be affected by both bacterial characteristics and particulate properties. In this study, we investigated how the properties of cell surfaces and stream particulates influence attachment. Attachment assays were conducted for 77 E. coli strains and three model particulates (ferrihydrite, Ca-montmorillonite, or corn stover) under environmentally relevant conditions. Surface area, particle size distribution, and total carbon content were determined for each type of particulate. Among the three particulates, attachment fractions to corn stover were significantly larger than the attachments to 2-line ferrihydrite (p-value = 0.0036) and Ca-montmorillonite (p-value = 0.022). Furthermore, attachment to Ca-montmorillonite and corn stover was successfully modeled by a Generalized Additive Model (GAM) using cell characteristics as predictor variables. The natural logarithm of the net charge on the bacterial surface had a significant, positive, and linear impact on the attachment of E. coli bacteria to Ca-montmorillonite (p-value = 0.013), but it did not significantly impact the attachment to corn stover (p-value = 0.36). The large diversities in cell characteristics among 77 E. coli strains, particulate properties, and attachment fractions clearly demonstrated the inadequacy of using a static parameter or linear coefficient to predict the attachment behavior of E. coli in stream water quality models.

Evaluating the Performance of a Relative Humidity-Based Warning System for Sooty Blotch and Flyspeck in Iowa.

A warning system for the sooty blotch and flyspeck (SBFS) fungal disease complex of apple, developed originally for use in the southeastern United States, was modified to provide more reliable assessment of SBFS risk in Iowa. Modeling results based on previous research in Iowa and Wisconsin had suggested replacing leaf wetness duration with cumulative hours of relative humidity (RH) ≥97% as the weather input to the SBFS warning system. The purpose of the present study was to evaluate the performance of a RH-based SBFS warning system, and to assess the potential economic benefits for its use in Iowa. The warning system was evaluated in two separate sets of trials-trial 1 during 2010 and 2011, and trial 2 during 2013-2015-using action thresholds based on cumulative hours of RH ≥97% and ≥90%, respectively, in conjunction with two different fungicide regimes. The warning system was compared with a traditional calendar-based system that specified spraying at predetermined intervals of 10 to 14 days. In trial 1, use of the RH ≥97% threshold caused substantial differences between two RH sensors in recording number of hours exceeding the threshold. When both RH thresholds were compared for 2013-2015, on average, RH ≥90% resulted in a 53% reduction in variation of cumulative hours between two identical RH sensors placed adjacent to each other in an apple tree canopy. Although both the SBFS warning system and the calendar-based system resulted in equivalent control of SBFS, the warning system required fewer fungicide sprays than the calendar-based system, with an average of 3.8 sprays per season (min = 2; max = 5) vs. 6.4 sprays per season (min = 5; max = 8), respectively. The two fungicide regimes provided equivalent SBFS control when used in conjunction with the warning system. A partial budget analysis showed that using the SBFS warning system with a threshold of RH ≥90% was cost effective for orchard sizes of >1 ha. The revised warning system has potential to become a valuable decision support tool for Midwest apple growers because it reduces fungicide costs while protecting apples as effectively as a calendar-based spray schedule. The next step toward implementation of the SBFS warning system in the North Central U.S. should be multiyear field testing in commercial orchards throughout the region.

E. coli Surface Properties Differ between Stream Water and Sediment Environments.

The importance of E. coli as an indicator organism in fresh water has led to numerous studies focusing on cell properties and transport behavior. However, previous studies have been unable to assess if differences in E. coli cell surface properties and genomic variation are associated with different environmental habitats. In this study, we investigated the variation in characteristics of E. coli obtained from stream water and stream bottom sediments. Cell properties were measured for 77 genomically different E. coli strains (44 strains isolated from sediments and 33 strains isolated from water) under common stream conditions in the Upper Midwestern United States: pH 8.0, ionic strength 10 mM and 22°C. Measured cell properties include hydrophobicity, zeta potential, net charge, total acidity, and extracellular polymeric substance (EPS) composition. Our results indicate that stream sediment E. coli had significantly greater hydrophobicity, greater EPS protein content and EPS sugar content, less negative net charge, and higher point of zero charge than stream water E. coli. A significant positive correlation was observed between hydrophobicity and EPS protein for stream sediment E. coli but not for stream water E. coli. Additionally, E. coli surviving in the same habitat tended to have significantly larger (GTG)5 genome similarity. After accounting for the intrinsic impact from the genome, environmental habitat was determined to be a factor influencing some cell surface properties, such as hydrophobicity. The diversity of cell properties and its resulting impact on particle interactions should be considered for environmental fate and transport modeling of aquatic indicator organisms such as E. coli.

Thresholds in marsh resilience to the Deepwater Horizon oil spill.

Ecosystem boundary retreat due to human-induced pressure is a generally observed phenomenon. However, studies that document thresholds beyond which internal resistance mechanisms are overwhelmed are uncommon. Following the Deepwater Horizon (DWH) oil spill, field studies from a few sites suggested that oiling of salt marshes could lead to a biogeomorphic feedback where plant death resulted in increased marsh erosion. We tested for spatial generality of and thresholds in this effect across 103 salt marsh sites spanning ~430 kilometers of shoreline in coastal Louisiana, Alabama, and Mississippi, using data collected as part of the natural resource damage assessment (NRDA). Our analyses revealed a threshold for oil impacts on marsh edge erosion, with higher erosion rates occurring for ~1-2 years after the spill at sites with the highest amounts of plant stem oiling (90-100%). These results provide compelling evidence showing large-scale ecosystem loss following the Deepwater Horizon oil spill. More broadly, these findings provide rare empirical evidence identifying a geomorphologic threshold in the resistance of an ecosystem to increasing intensity of human-induced disturbance.

Comparison of Consumer and Research Monitors under Semistructured Settings.

PURPOSE: This study evaluated the relative validity of different consumer and research activity monitors during semistructured periods of sedentary activity, aerobic exercise, and resistance exercise. METHODS: Fifty-two (28 male and 24 female) participants age 18-65 yr performed 20 min of self-selected sedentary activity, 25 min of aerobic exercise, and 25 min of resistance exercise, with 5 min of rest between each activity. Each participant wore five wrist-worn consumer monitors [Fitbit Flex, Jawbone Up24, Misfit Shine (MS), Nike+ Fuelband SE (NFS), and Polar Loop] and two research monitors [ActiGraph GT3X+ on the waist and BodyMedia Core (BMC) on the arm] while being concurrently monitored with Oxycon Mobile (OM), a portable metabolic measuring system. Energy expenditure (EE) on different activity sessions was measured by OM and estimated by all monitors. RESULTS: Mean absolute percent error (MAPE) values for the full 80-min protocol ranged from 15.3% (BMC) to 30.4% (MS). EE estimates from ActiGraph GT3X+ were found to be equivalent to those from OM (± 10% equivalence zone, 285.1-348.5). Correlations between OM and the various monitors were generally high (ranged between 0.71 and 0.90). Three monitors had MAPE values lower than 20% for sedentary activity: BMC (15.7%), MS (18.2%), and NFS (20.0%). Two monitors had MAPE values lower than 20% for aerobic exercise: BMC (17.2%) and NFS (18.5%). None of the monitors had MAPE values lower than 25% for resistance exercise. CONCLUSION: Overall, the research monitors and Fitbit Flex, Jawbone Up24, and NFS provided reasonably accurate total EE estimates at the individual level. However, larger error was evident for individual activities, especially resistance exercise. Further research is needed to examine these monitors across various activities and intensities as well as under real-world conditions.

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes.

Detection of somatic mutations in human leukocyte antigen (HLA) genes using whole-exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which prevents alignment of sequencing reads to the human reference genome. We describe a computational pipeline that enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using the inferred alleles as a reference. Analysis of WES data from 7,930 pairs of tumor and healthy tissue from the same patient revealed 298 nonsilent HLA mutations in tumors from 266 patients. These 298 mutations are enriched for likely functional mutations, including putative loss-of-function events. Recurrence of mutations suggested that these 'hotspot' sites were positively selected. Cancers with recurrent somatic HLA mutations were associated with upregulation of signatures of cytolytic activity characteristic of tumor infiltration by effector lymphocytes, supporting immune evasion by altered HLA function as a contributory mechanism in cancer.

Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists.

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1-S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.

A case-control study to examine the association between breastfeeding during late pregnancy and risk of a small-for-gestational-age birth in Lima, Peru.

Excessive demands on maternal nutritional status may be a risk factor for poor birth outcomes. This study examined the association between breastfeeding during late pregnancy (≥ 28 weeks) and the risk of having a small-for-gestational-age (SGA) newborn, using a matched case-control design (78 SGA cases: birthweight <10th percentile for gestational age; 150 non-SGA controls: 50th percentile

Benchmark study on glyphosate-resistant crop systems in the United States. Economics of herbicide resistance management practices in a 5 year field-scale study.

BACKGROUND: Since the introduction of glyphosate-resistant (GR) crops, growers have often relied on glyphosate-only weed control programs. As a result, multiple weeds have evolved resistance to glyphosate. A 5 year study including 156 growers from Illinois, Iowa, Indiana, Nebraska, North Carolina and Mississippi in the United States was conducted to compare crop yields and net returns between grower standard weed management programs (SPs) and programs containing best management practices (BMPs) recommended by university weed scientists. The BMPs were designed to prevent or mitigate/manage evolved herbicide resistance. RESULTS: Weed management costs were greater for the BMP approach in most situations, but crop yields often increased sufficiently for net returns similar to those of the less expensive SPs. This response was similar across all years, geographical regions, states, crops and tillage systems. CONCLUSIONS: Herbicide use strategies that include a diversity of herbicide mechanisms of action will increase the long-term sustainability of glyphosate-based weed management strategies. Growers can adopt herbicide resistance BMPs with confidence that net returns will not be negatively affected in the short term and contribute to resistance management in the long term.