A Partial African Ancestry for the Creole Cattle Populations of the Caribbean

Seventy-eight cattle samples from three Creole Caribbean islands and one Brazilian breed were analyzed for sequence variation in the hypervariable segment of the mitochondrial DNA control region. Seventy-three samples displayed Bos taurus haplotypes, and five samples exhibited haplotypes that were of Bos indicus ancestry. Phylogenetic analysis revealed that all sampled B. taurus sequences fell into two distinct clusters with separate African and European origins. European sequences were encountered in each population; however, the distribution of African haplotypes was uneven, with the highest proportion of African influence found in the Guadeloupe Creole. The reduced levels of African haplotypic variation within the Caribbean and Brazilian are consistent with prior founder effects. Additionally, genetic variation at three microsatellite loci illustrated African influence uniquely in the Guadeloupe Creole. Collectively, the data suggest that this African influence is, at least in part, attributable to the historical importation of African cattle to the Americas. Furthermore, alleles of B. indicus ancestry were detected at appreciable frequencies in all Caribbean Creole populations and may reflect zebu introgressions from either West Africa or the Indian subcontinen

PhotoSpec: A new instrument to measure spatially distributed red and far-red Solar-Induced Chlorophyll Fluorescence

Solar-Induced Chlorophyll Fluorescence (SIF) is an emission of light in the 650–850 nm spectral range from the excited state of the chlorophyll-a pigment after absorption of photosynthetically active radiation (PAR). As this is directly linked to the electron transport chain in oxygenic photosynthesis, SIF is a powerful proxy for photosynthetic activity. SIF observations are relatively new and, while global scale measurements from satellites using high-resolution spectroscopy of Fraunhofer bands are becoming more available, observations at the intermediate canopy scale using these techniques are sparse. We present a novel ground-based spectrometer system - PhotoSpec - for measuring SIF in the red (670–732 nm) and far-red (729–784 nm) wavelength range as well as canopy reflectance (400–900 nm) to calculate vegetation indices, such as the normalized difference vegetation index (NDVI), the enhanced vegetation index (EVI), and the photochemical reflectance index (PRI). PhotoSpec includes a 2D scanning telescope unit which can be pointed to any location in a canopy with a narrow field of view (FOV = 0.7°). PhotoSpec has a high signal-to-noise ratio and spectral resolution, which allows high precision solar Fraunhofer line retrievals over the entire fluorescence wavelength range under all atmospheric conditions using a new two-step linearized least-squares retrieval procedure. Initial PhotoSpec observations include the diurnal SIF cycle of single broad leaves, grass, and dark-light transitions. Results from the first tower-based measurements in Costa Rica show that the instrument can continuously monitor SIF of several tropical species throughout the day. The PhotoSpec instrument can be used to explore the relationship between SIF, photosynthetic efficiencies, Gross Primary Productivity (GPP), and the impact of canopy radiative transfer, viewing geometry, and stress conditions at the canopy scale

Artificial Olfaction in the 21st Century

The human olfactory system remains one of the most challenging biological systems to replicate. Humans use it without thinking, where it can measure offer protection from harm and bring enjoyment in equal measure. It is the system's real-time ability to detect and analyze complex odors that makes it difficult to replicate. The field of artificial olfaction has recruited and stimulated interdisciplinary research and commercial development for several applications that include malodor measurement, medical diagnostics, food and beverage quality, environment and security. Over the last century, innovative engineers and scientists have been focused on solving a range of problems associated with measurement and control of odor. The IEEE Sensors Journal has published Special Issues on olfaction in 2002 and 2012. Here we continue that coverage. In this article, we summarize early work in the 20th Century that served as the foundation upon which we have been building our odor-monitoring instrumental and measurement systems. We then examine the current state of the art that has been achieved over the last two decades as we have transitioned into the 21st Century. Much has been accomplished, but great progress is needed in sensor technology, system design, product manufacture and performance standards. In the final section, we predict levels of performance and ubiquitous applications that will be realized during in the mid to late 21st Century

Extreme events driving year-to-year differences in gross primary productivity across the US

Solar-Induced chlorophyll Fluorescence (SIF) has previously been shown to strongly correlate with gross primary productivity (GPP), however this relationship has not yet been quantified for the recently launched TROPOspheric Monitoring Instrument (TROPOMI). Here we use a Gaussian mixture model to develop a parsimonious relationship between SIF from TROPOMI and GPP from flux towers across the conterminous United States (CONUS). The mixture model indicates the SIF-GPP relationship can be characterized by a linear model with two terms. We then estimate GPP across CONUS at 500-m spatial resolution over a 16-day moving window. We find that CONUS GPP varies by less than 4% between 2018 and 2019. However, we observe four extreme precipitation events that induce regional GPP anomalies: drought in west Texas, flooding in the midwestern US, drought in South Dakota, and drought in California. Taken together, these events account for 28% of the year-to-year GPP differences across CONUS

A novel approach to task abstraction to make better sense of provenance data

Working Group Report in 'Provenance and Logging for Sense Making' report from Dagstuhl Seminar 18462: Provenance and Logging for Sense Making, Dagstuhl Reports, Volume 8, Issue 1

A double peak in the seasonality of California's photosynthesis as observed from space

Solar-induced chlorophyll fluorescence (SIF) has been shown to be a powerful proxy for photosynthesis and gross primary productivity (GPP). The recently launched TROPOspheric Monitoring Instrument (TROPOMI) features the required spectral resolution and signal-to-noise ratio to retrieve SIF from space. Here, we present a downscaling method to obtain 500 m spatial resolution SIF over California. We report daily values based on a 14 d window. TROPOMI SIF data show a strong correspondence with daily GPP estimates at AmeriFlux sites across multiple ecosystems in California. We find a linear relationship between SIF and GPP that is largely invariant across ecosystems with an intercept that is not significantly different from zero. Measurements of SIF from TROPOMI agree with MODerate Resolution Imaging Spectroradiometer (MODIS) vegetation indices – the normalized difference vegetation index (NDVI), enhanced vegetation index (EVI), and near-infrared reflectance of vegetation index (NIR_v) – at annual timescales but indicate different temporal dynamics at monthly and daily timescales. TROPOMI SIF data show a double peak in the seasonality of photosynthesis, a feature that is not present in the MODIS vegetation indices. The different seasonality in the vegetation indices may be due to a clear-sky bias in the vegetation indices, whereas previous work has shown SIF to have a low sensitivity to clouds and to detect the downregulation of photosynthesis even when plants appear green. We further decompose the spatiotemporal patterns in the SIF data based on land cover. The double peak in the seasonality of California's photosynthesis is due to two processes that are out of phase: grasses, chaparral, and oak savanna ecosystems show an April maximum, while evergreen forests peak in June. An empirical orthogonal function (EOF) analysis corroborates the phase offset and spatial patterns driving the double peak. The EOF analysis further indicates that two spatiotemporal patterns explain 84 % of the variability in the SIF data. Results shown here are promising for obtaining global GPP at sub-kilometer spatial scales and identifying the processes driving carbon uptake

Extreme events driving year-to-year differences in gross primary productivity across the US

Solar-Induced chlorophyll Fluorescence (SIF) has previously been shown to strongly correlate with gross primary productivity (GPP), however this relationship has not yet been quantified for the recently launched TROPOspheric Monitoring Instrument (TROPOMI). Here we use a Gaussian mixture model to develop a parsimonious relationship between SIF from TROPOMI and GPP from flux towers across the conterminous United States (CONUS). The mixture model indicates the SIF-GPP relationship can be characterized by a linear model with two terms. We then estimate GPP across CONUS at 500-m spatial resolution over a 16-day moving window. We find that CONUS GPP varies by less than 4% between 2018 and 2019. However, we observe four extreme precipitation events that induce regional GPP anomalies: drought in west Texas, flooding in the midwestern US, drought in South Dakota, and drought in California. Taken together, these events account for 28% of the year-to-year GPP differences across CONUS

Branching of the Falkner-Skan solutions for λ < 0

The Falkner-Skan equation f'" + ff" + λ(1 - f'^2) = 0, f(0) = f'(0) = 0, is discussed for λ < 0. Two types of problems, one with f'(∞) = 1 and another with f'(∞) = -1, are considered. For λ = 0- a close relation between these two types is found. For λ < -1 both types of problem allow multiple solutions which may be distinguished by an integer N denoting the number of zeros of f' - 1. The numerical results indicate that the solution branches with f'(∞) = 1 and those with f'(∞) = -1 tend towards a common limit curve as N increases indefinitely. Finally a periodic solution, existing for λ < -1, is presented.

Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification.

Improved access to effective tests for diagnosing tuberculosis (TB) has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA) is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC) DNA in <20 minutes at 39 °C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110) and 20 fg (IS1081)were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9) and 86.1% (95%CI: 78.1, 94.1) respectively (n = 71). Specificities were 100% and 88.6% (95% CI: 80.8, 96.1) respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2) and 70.8% (95%CI: 62.9, 78.7) were obtained (n = 90). Specificities were 95.4 (95% CI: 92.3,98.1) and 88% (95% CI: 83.6, 92.4) respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB assays could be of use for integration into a point-of-care test for use in resource constrained settings