Combining computer vision and deep learning to enable ultra-scale aerial phenotyping and precision agriculture: A case study of lettuce production:AirSurf-Lettuce

Aerial imagery is regularly used by crop researchers, growers and farmers to monitor crops during the growing season. To extract meaningful information from large-scale aerial images collected from the field, high-throughput phenotypic analysis solutions are required, which not only produce high-quality measures of key crop traits, but also support professionals to make prompt and reliable crop management decisions. Here, we report AirSurf, an automated and open-source analytic platform that combines modern computer vision, up-to-date machine learning, and modular software engineering in order to measure yield-related phenotypes from ultra-large aerial imagery. To quantify millions of in-field lettuces acquired by fixed-wing light aircrafts equipped with normalised difference vegetation index (NDVI) sensors, we customised AirSurf by combining computer vision algorithms and a deep-learning classifier trained with over 100,000 labelled lettuce signals. The tailored platform, AirSurf-Lettuce, is capable of scoring and categorising iceberg lettuces with high accuracy (>98%). Furthermore, novel analysis functions have been developed to map lettuce size distribution across the field, based on which associated global positioning system (GPS) tagged harvest regions have been identified to enable growers and farmers to conduct precision agricultural practises in order to improve the actual yield as well as crop marketability before the harvest

A Pilot Randomized Controlled Trial of Omega-3 Fatty Acids for Autism Spectrum Disorder

We conducted a pilot randomized controlled trial to determine the feasibility and initial safety and efficacy of omega-3 fatty acids (1.3 g/day) for the treatment of hyperactivity in 27 children ages 3–8 with autism spectrum disorder (ASD). After 12 weeks, hyperactivity, as measured by the Aberrant Behavior Checklist, improved 2.7 (±4.8) points in the omega-3 group compared to 0.3 (±7.2) points in the placebo group (p = 0.40; effect size = 0.38). Correlations were found between decreases in five fatty acid levels and decreases in hyperactivity, and the treatment was well tolerated. Although this pilot study did not find a statistically significant benefit from omega-3 fatty acids, the small sample size does not rule out small to moderate beneficial effects

Association of Attitudes and Beliefs towards Antiretroviral Therapy with HIV-Seroprevalence in the General Population of Kisumu, Kenya

Since antiretroviral therapy (ART) became available in the developed world, the prevalence of unprotected sex and the incidence of sexually transmitted infections (STIs) and HIV have increased. We hypothesized that a similar phenomenon may be occurring in sub-Saharan Africa concomitant with the scale-up of HIV treatment.We conducted a general population-based survey in Kisumu, Kenya. Participants completed an interview that included demographics as well as ART-related attitudes and beliefs (AB) and then underwent HIV serological testing. Exploratory and confirmatory factor analyses of AB about ART indicated two factors: 1) ART-related risk compensation (increased sexual risk taking now that ART is available); and 2) a perception that HIV is more controllable now that ART is available. Logistic regression was used to determine associations of these factors with HIV-seroprevalence after controlling for age.1,655 (90%) of 1,844 people aged 15-49 contacted, including 749 men and 906 women, consented to participate in the study. Most participants (n = 1164; 71%) had heard of ART. Of those who had heard of ART, 23% believed ART was a cure for HIV. ART-related risk compensation (Adjusted (A)OR = 1.45, 95% CI 1.16-1.81), and a belief that ART cures HIV (AOR = 2.14, 95% CI 1.22-3.76) were associated with an increased HIV seroprevalence in men but not women after controlling for age. In particular, ART-related risk compensation was associated with an increased HIV-seroprevalence in young (aged 15-24 years) men (OR = 1.56; 95% CI 1.12-2.19).ART-related risk compensation and a belief that ART cures HIV were associated with an increased HIV seroprevalence among men but not women. HIV prevention programs in sub-Saharan Africa that target the general population should include educational messages about ART and address the changing beliefs about HIV in the era of greater ART availability

A New Fluorescence-Based Method Identifies Protein Phosphatases Regulating Lipid Droplet Metabolism

In virtually every cell, neutral lipids are stored in cytoplasmic structures called lipid droplets (LDs) and also referred to as lipid bodies or lipid particles. We developed a rapid high-throughput assay based on the recovery of quenched BODIPY-fluorescence that allows to quantify lipid droplets. The method was validated by monitoring lipid droplet turnover during growth of a yeast culture and by screening a group of strains deleted in genes known to be involved in lipid metabolism. In both tests, the fluorimetric assay showed high sensitivity and good agreement with previously reported data using microscopy. We used this method for high-throughput identification of protein phosphatases involved in lipid droplet metabolism. From 65 yeast knockout strains encoding protein phosphatases and its regulatory subunits, 13 strains revealed to have abnormal levels of lipid droplets, 10 of them having high lipid droplet content. Strains deleted for type I protein phosphatases and related regulators (ppz2, gac1, bni4), type 2A phosphatase and its related regulator (pph21 and sap185), type 2C protein phosphatases (ptc1, ptc4, ptc7) and dual phosphatases (pps1, msg5) were catalogued as high-lipid droplet content strains. Only reg1, a targeting subunit of the type 1 phosphatase Glc7p, and members of the nutrient-sensitive TOR pathway (sit4 and the regulatory subunit sap190) were catalogued as low-lipid droplet content strains, which were studied further. We show that Snf1, the homologue of the mammalian AMP-activated kinase, is constitutively phosphorylated (hyperactive) in sit4 and sap190 strains leading to a reduction of acetyl-CoA carboxylase activity. In conclusion, our fast and highly sensitive method permitted us to catalogue protein phosphatases involved in the regulation of LD metabolism and present evidence indicating that the TOR pathway and the SNF1/AMPK pathway are connected through the Sit4p-Sap190p pair in the control of lipid droplet biogenesis

Bionic bodies, posthuman violence and the disembodied criminal subject

This article examines how the so-called disembodied criminal subject is given structure and form through the law of homicide and assault. By analysing how the body is materialised through the criminal law’s enactment of death and injury, this article suggests that the biological positioning of these harms of violence as uncontroversial, natural, and universal conditions of being ‘human’ cannot fully appreciate what makes violence wrongful for us, as embodied entities. Absent a theory of the body, and a consideration of corporeality, the criminal law risks marginalising, or altogether eliding, experiences of violence that do not align with its paradigmatic vision of what bodies can and must do when suffering its effects. Here I consider how the bionic body disrupts the criminal law’s understanding of human violence by being a body that is both organic and inorganic, and capable of experiencing and performing violence in unexpected ways. I propose that a criminal law that is more receptive to the changing, technologically mediated conditions of human existence would be one that takes the corporeal dimensions of violence more seriously and, as an extension of this, adopts an embodied, embedded, and relational understanding of human vulnerability to violence

A genome-wide association search for type 2 diabetes genes in African Americans.

African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations

Modifications to a Cavity Ringdown Spectrometer to Improve Data Acquisition Rates

Cavity ringdown spectroscopy (CRDS) makes use of light retention in an optical cavity to enhance the sensitivity to absorption or extinction of light from a sample inside the cavity. When light entering the cavity is stopped, the output is an exponential decay with a decay constant that can be used to determine the quantity of the analyte if the extinction or absorption coefficient is known. The precision of the CRDS is dependent on the rate at which the system it acquires and processes ringdowns, assuming randomly distributed errors. We have demonstrated a CRDS system with a ringdown acquisition rate of 1.5 kHz, extendable to a maximum of 3.5 kHz, using new techniques that significantly changed the way in which the ringdowns are both initiated and processed. On the initiation side, we combined a custom high-resolution laser controller with a linear optical feedback configuration and a novel optical technique for initiating a ringdown. Our optical injection unlock method switches the laser off-resonance, while allowing the laser to immediately return to resonance, after terminating the unlock, to allow for another ringdown (on the same cavity resonance mode). This part of the system had a demonstrated ringdown initiation rate of 3.5 kHz. To take advantage of this rate, we developed an optimized cost-effective FGPA-based data acquisition and processing system for CRDS, capable of determining decay constants at a maximum rate of 4.4 kHz, by modifying a commercial ADC-FPGA evaluation board and programming it to apply a discrete Fourier transform-based algorithm for determining decay constants. The entire system shows promise with a demonstrated ability to determine gas concentrations for H2O with a measured concentration accuracy of ±3.3%. The system achieved an absorption coefficient precision of 0.1% (95% confidence interval). It also exhibited a linear response for varying H2O concentrations, a 2.2% variation (1σ) for repeated measurements at the same H2O concentration, and a corresponding precision of 0.6% (standard error of the mean). The absorption coefficient limit of detection was determined to be 1.6 x 10-8 cm-1 (root mean square of the baseline residual). Proposed modifications to our prototype system offer the promise of more substantial gains in both precision and limit of detection. The system components developed here for faster ringdown acquisition and processing have broader applications for CRDS in atmospheric science and other fields that need fast response systems operating at high-precision

Contraception use and effectiveness among women in a trial of the diaphragm for HIV prevention.

BACKGROUND: There is little data on contraceptive effectiveness or use patterns from sub-Saharan Africa. STUDY DESIGN: We analyzed data from women at risk of pregnancy (n=4905) in the Methods for Improving Reproductive Health in Africa trial of the diaphragm for HIV prevention. We described reported contraceptive method use and calculated rates of pregnancy by contraceptive method. We compared time to first pregnancy by study arm (condoms or condoms plus diaphragm), and estimated a Cox proportional hazards model to identify predictors of pregnancy. RESULTS: Condoms (25.8%), injectables (25.4%) and OC (21.6%) were the most commonly used methods; long-acting method use was rare. During the trial, 51.6% of women used the same method, 27.4% switched to a more effective method and 20.9% switched to a less effective method; 21.4% of women became pregnant. Pregnancy rates by contraceptive group mirrored published estimates; frequency of study product use was not associated with pregnancy. CONCLUSION: Long-acting methods of contraception should be made available in HIV prevention trials and to women in Southern Africa