Corrigendum: The effects of sampling and instrument orientation on LiDAR data from crop plots.

[This corrects the article DOI: 10.3389/fpls.2023.1087239.].

Characterization of leaf surface phenotypes based on light interaction.

BACKGROUND: Leaf surface phenotypes can indicate plant health and relate to a plant's adaptations to environmental stresses. Identifying these phenotypes using non-invasive techniques can assist in high-throughput phenotyping and can improve decision making in plant breeding. Identification of these surface phenotypes can also assist in stress identification. Incorporating surface phenotypes into leaf optical modelling can lead to improved biochemical parameter retrieval and species identification. RESULTS: In this paper, leaf surface phenotypes are characterized for 349 leaf samples based on polarized light reflectance measured at Brewster's Angle, and microscopic observation. Four main leaf surface phenotypes (glossy wax, glaucous wax, high trichome density, and glabrous) were identified for the leaf samples. The microscopic and visual observations of the phenotypes were used as ground truth for comparison with the spectral classification. In addition to surface classification, the microscope images were used to assess cell size, shape, and cell cap aspect ratios; these surface attributes were not found to correlate significantly with spectral measurements obtained in this study. Using a quadratic discriminant analysis function, a series of 10,000 classifications were run with the data randomly split between training and testing datasets, with 150 and 199 samples, respectively. The average correct classification rate was 72.9% with a worst-case classification of 60.3%. CONCLUSIONS: Leaf surface phenotypes were successfully correlated with spectral measurements that can be obtained remotely. Remote identification of these surface phenotypes will improve leaf optical modelling and biochemical parameter estimations. Phenotyping of leaf surfaces can inform plant breeding decisions and assist with plant health monitoring.

The effects of sampling and instrument orientation on LiDAR data from crop plots.

Wheat is one of the most widely consumed grains in the world and improving its yield, especially under severe climate conditions, is of great importance to world food security. Phenotyping methods can evaluate plants according to their different traits, such as yield and growth characteristics. Assessing the vertical stand structure of plants can provide valuable information about plant productivity and processes, mainly if this trait can be tracked throughout the plant's growth. Light Detection And Ranging (LiDAR) is a method capable of gathering three-dimensional data from wheat field trials and is potentially suitable for providing non-destructive, high-throughput estimations of the vertical stand structure of plants. The current study considers LiDAR and focuses on investigating the effects of sub-sampling plot data and data collection parameters on the canopy vertical profile (CVP). The CVP is a normalized, ground-referenced histogram of LiDAR point cloud data representing a plot or other spatial domain. The effects of sub-sampling of plot data, the angular field of view (FOV) of the LiDAR and LiDAR scan line orientation on the CVP were investigated. Analysis of spatial sub-sampling effects on CVP showed that at least 144000 random points (600 scan lines) or an area equivalent to three plants along the row were adequate to characterize the overall CVP of the aggregate plot. A comparison of CVPs obtained from LiDAR data for different FOV showed that CVPs varied with the angular range of the LiDAR data, with narrow ranges having a larger proportion of returns in the upper canopy and a lower proportion of returns in the lower part of the canopy. These findings will be necessary to establish minimum plot and sample sizes and compare data from studies where scan direction or field of view differ. These advancements will aid in making comparisons and inform best practices for using close-range LiDAR in phenotypic studies in crop breeding and physiology research.

The effect of plant weight on estimations of stalk lodging resistance.

BACKGROUND: Stalk lodging (breaking of agricultural plant stalks prior to harvest) is a multi-billion dollar a year problem. Stalk lodging occurs when bending moments induced by a combination of external loading (e.g. wind) and self-loading (e.g. the plant's own weight) exceed the stalk bending strength of plant stems. Previous studies have investigated external loading and self-loading of plants as separate and independent phenomena. However, these two types of loading are highly interconnected and mutually dependent. The purpose of this paper is twofold: (1) to investigate the combined effect of external loads and plant weight on the flexural response of plant stems, and (2) to provide a generalized framework for accounting for self-weight during mechanical phenotyping experiments used to predict stalk lodging resistance. RESULTS: A mathematical methodology for properly accounting for the interconnected relationship between self-loading and external loading of plants stems is presented. The method was compared to numerous finite element models of plants stems and found to be highly accurate. The resulting interconnected set of equations from the derivation were used to produce user-friendly applications by presenting (1) simplified self-loading correction factors for common loading configurations of plants, and (2) a generalized Microsoft Excel framework that calculates the influence of self-loading on crop stems. Results indicate that ignoring the effects of self-loading when calculating stalk flexural stiffness is appropriate for large and stiff plants such as maize, bamboo, and sorghum. However, significant errors result when ignoring the effects of self-loading in smaller plants with larger relative grain sizes, such as rice (8% error) and wheat (16% error). CONCLUSIONS: Properly accounting for self-weight can be critical to determining the structural response of plant stems. Equations and tools provided herein enable researchers to properly account for the plant's weight during mechanical phenotyping experiments used to determine stalk lodging resistance.

The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples.

BACKGROUND: Quantitative and qualitative assessment of visual and morphological traits of seed is slow and imprecise with potential for bias to be introduced when gathered with handheld tools. Colour, size and shape traits can be acquired from properly calibrated seed images. New automated tools were requested to improve data acquisition efficacy with an emphasis on developing research workflows. RESULTS: A portable imaging system (BELT) supported by image acquisition and analysis software (phenoSEED) was created for small-seed optical analysis. Lentil (Lens culinaris L.) phenotyping was used as the primary test case. Seeds were loaded into the system and all seeds in a sample were automatically individually imaged to acquire top and side views as they passed through an imaging chamber. A Python analysis script applied a colour calibration and extracted quantifiable traits of seed colour, size and shape. Extraction of lentil seed coat patterning was implemented to further describe the seed coat. The use of this device was forecasted to eliminate operator biases, increase the rate of acquisition of traits, and capture qualitative information about traits that have been historically analyzed by eye. CONCLUSIONS: Increased precision and higher rates of data acquisition compared to traditional techniques will help to extract larger datasets and explore more research questions. The system presented is available as an open-source project for academic and non-commercial use.

Developing Prepare2Thrive, a community-based intervention targeting treatment engagement among African American individuals living with HIV and serious mental illness.

African American individuals living with HIV and serious mental illness (SMI) may report relatively low treatment engagement, despite treatment engagement being critical to managing both health conditions. Here, we have two aims: to describe the methodology we used to collect focus group data on treatment engagement with a sample of African American individuals living with HIV and SMI, and to describe the results of those focus groups in the context of intervention development. We conducted two focus groups (N = 15), integrating a social-ecological model for our theoretical framework, Community-Based Participatory Research for study design and execution, and group concept mapping for data analysis. Three thematic clusters relating to treatment engagement emerged from each group, with overlap across groups: Medication knowledge, Patient-provider relationships, and Barriers to treatment engagement. Items related to the Patient-provider relationship loaded onto all emergent clusters, demonstrating the pervasive impact of this variable. Findings informed the design of Prepare2Thrive, a community-based, culture-specific intervention aiming to increase treatment engagement among African American individuals living with HIV and SMI. Both our design and findings can be used in future collaborations aiming to maximize treatment engagement, and more broadly health, among individuals in this community.

Engaging African Americans Living with HIV and Serious Mental Illness: Piloting Prepare2Thrive-A Peer-Led Intervention.

BACKGROUND: African American individuals living with HIV (AALWH) and serious mental illness (SMI) represent a vulnerable intersectional group with relatively poor health. These individuals may require consistent treatment engagement to manage both of their chronic conditions; however, due to multilevel factors they are relatively less likely to engage in treatment consistently. OBJECTIVES: To test the acceptability, feasibility, fidelity, and participant outcomes of a brief psychoeducational and behavioral peer-led intervention. METHODS: Participants engaged in four weekly 90-minute pilot intervention sessions developed by the current community-based participatory research (CBPR) team. Sessions focused on problem-solving, communication skills, and coping with stigma, and were delivered by CBPR peerinterventionists. Participants completed pre- and postintervention surveys assessing treatment engagement and self-efficacy. RESULTS: Participants (N = 16) rated the intervention as acceptable, and attendance rates were high (87% average). Intervention leaders demonstrated exceptionally high fidelity to the intervention protocol. Participants reported a trend toward increasing antiretroviral therapy (ART) adherence from pre- to post-intervention (on average, an 8% increase, p = 0.063), notable in the context of a pilot study. Those who attended all four intervention sessions reported a 17.5% increase in ART adherence. From pre- to post-intervention medical appointment attendance decreased, mental health appointment attendance increased, and HIV treatment selfefficacy significantly increased. CONCLUSIONS: This study provides initial evidence for the feasibility of a CBPR-designed and tested, peer-led psychoeducation and behavioral intervention aiming to improve treatment engagement among AALWH and SMI, a marginalized group who could benefit from additional communitybased health research efforts.

Investigation of white line separation under load in bovine claws with and without toe-tip necrosis.

OBJECTIVE: To compare the degree of white line separation created by increasing physiologic loads between bovine claws with and without toe-tip necrosis (TTN). SAMPLE: Cadaveric bovine hind limbs with (n = 10) and without (10) TTN. PROCEDURES: Hind limbs in which 1 or both claws had evidence of apical white line separation were considered to have TTN. Hind limbs in which neither claw had evidence of white line separation were considered controls. Each hind limb was mounted in a materials testing system with the bottom surface of the hoof angled at approximately 5° to the horizontal plane such that the apex of the claws made initial contact with the clear testing surface to simulate physiologic loading conditions. A digital camera mounted underneath the testing surface was used to obtain images of the bottom of the hoof during the application of each of 3 increasing static loads (1, 2, and 3 kN). The images were analyzed with commercial image-processing software to quantify white line separation area. RESULTS: White line separation area was significantly greater for claws with TTN than for control claws and increased as the applied load increased. White line separation was almost nonexistent in control claws and was not affected by increasing load. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that mechanical loading exacerbated TTN, but compressive loading alone, even at excessive levels, did not initiate the condition. Interventions (eg, hoof blocks) that decrease loading of affected claws may be beneficial for the treatment of TTN at its earliest stages.

Comparison of acrylic polymer adhesive tapes and silicone optical grease in light sharing detectors for positron emission tomography.

Optical coupling is an important factor in detector design as it improves optical photon transmission by mitigating internal reflections at light-sharing boundaries. In this work we compare optical coupling materials, namely double-sided acrylic polymer tapes and silicone optical grease (SiG), in the context of positron emission tomography. Four double-sided tapes from 3 M of varying thicknesses (0.229 mm-1.016 mm) and adhesive materials ('100MP', 'A100', and 'GPA') were characterized with spectrophotometer measurements as well as photopeak amplitude and energy resolution measurements using lutetium-yttrium oxy-orthosilicate (LYSO) coupled to photomultiplier tubes (PMT) or silicon photomultipliers (SiPMs). Transmission spectra from the spectrophotometer showed over 80% transmission for all tapes at 420 nm and above, with 89.6% and 88.8% transmission for the 0.508 mm and 1.016 mm thick GPA tapes, respectively, at 420 nm. Measurements with single-pixel LYSO-PMT and 4 × 4 array (one-to-one coupled) LYSO-SiPM setups determined that SiG had the greatest photopeak amplitude, with tapes showing 2.1%-14.8% reduction in photopeak amplitude with respect to SiG. Energy resolution changed by less than 4% on a relative basis between tapes and SiG with PMT measurements, however for the SiPM array measurements the energy resolution improved from 15.6% ± 2.7% full-width at half-maximum to 11.4% ± 1.2% for SiG and 1 mm GPA respectively. Data acquired with dual-layer offset LYSO arrays (light sharing detector designs) demonstrated that a detector coupled with 1 mm thick GPA tape produced equivalent detector flood histograms to those from a design coupled with SiG and a 1 mm thick glass lightguide. No significant degradation in photopeak amplitude and energy resolution was observed over five months of measurements, indicating the tapes maintain their coupling integrity over several months. Though minimal photopeak amplitude degradation compared to SiG occurs, double-sided tapes are convenient alternatives for optical coupling materials since they diffuse light intrinsically, acting as a light guide, offer mechanical support and durability, are easily applied and removed from scintillators/photodetectors, and are relatively inexpensive and readily available.

Modifiers of solid RNP granules control normal RNP dynamics and mRNA activity in early development.

Ribonucleoproteins (RNPs) often coassemble into supramolecular bodies with regulated dynamics. The factors controlling RNP bodies and connections to RNA regulation are unclear. During Caenorhabditis elegans oogenesis, cytoplasmic RNPs can transition among diffuse, liquid, and solid states linked to mRNA regulation. Loss of CGH-1/Ddx6 RNA helicase generates solid granules that are sensitive to mRNA regulators. Here, we identified 66 modifiers of RNP solids induced by cgh-1 mutation. A majority of genes promote or suppress normal RNP body assembly, dynamics, or metabolism. Surprisingly, polyadenylation factors promote RNP coassembly in vivo, suggesting new functions of poly(A) tail regulation in RNP dynamics. Many genes carry polyglutatmine (polyQ) motifs or modulate polyQ aggregation, indicating possible connections with neurodegenerative disorders induced by CAG/polyQ expansion. Several RNP body regulators repress translation of mRNA subsets, suggesting that mRNAs are repressed by multiple mechanisms. Collectively, these findings suggest new pathways of RNP modification that control large-scale coassembly and mRNA activity during development.

Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus.

We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth.

Translation repressors, an RNA helicase, and developmental cues control RNP phase transitions during early development.

Like membranous organelles, large-scale coassembly of macromolecules can organize functions in cells. Ribonucleoproteins (RNPs) can form liquid or solid aggregates, but control and consequences of these RNP states in living, developing tissue are poorly understood. Here, we show that regulated RNP factor interactions drive transitions among diffuse, semiliquid, or solid states to modulate RNP sorting and exchange in the Caenorhabditis elegans oocyte cytoplasm. Translation repressors induce an intrinsic capacity of RNP components to coassemble into either large semiliquids or solid lattices, whereas a conserved RNA helicase prevents polymerization into nondynamic solids. Developmental cues dramatically alter both fluidity and sorting within large RNP assemblies, inducing a transition from RNP segregation in quiescent oocytes to dynamic exchange in the early embryo. Therefore, large-scale organization of gene expression extends to the cytoplasm, where regulation of supramolecular states imparts specific patterns of RNP dynamics.

The effects of an oral distraction on cattle during a painful procedure.

An oral distraction was investigated as a way to reduce struggle and heart rate of beef cattle undergoing freeze branding. Oral distraction reduced the struggle of steers, regardless of branding treatment. No effect on heart rate was found. Distractions may provide a way to reduce struggle by animals during restraint.

Les effets de la distraction orale sur le bétail durant une intervention douloureuse. La distraction orale a été étudiée comme méthode pour réduire la résistance physique et la fréquence cardiaque des bovins de boucherie subissant le cryomarquage. La distraction orale a réduit la lutte des bouvillons, sans égard au traitement de marquage. Aucun effet sur la fréquence cardiaque n'a été constaté. Les distractions peuvent fournir une façon de réduire la résistance physique des animaux durant la retenue.(Traduit par Isabelle Vallières).

Maternal mRNAs are regulated by diverse P body-related mRNP granules during early Caenorhabditis elegans development.

Processing bodies (P bodies) are conserved mRNA-protein (mRNP) granules that are thought to be cytoplasmic centers for mRNA repression and degradation. However, their specific functions in vivo remain poorly understood. We find that repressed maternal mRNAs and their regulators localize to P body-like mRNP granules in the Caenorhabditis elegans germ line. Surprisingly, several distinct types of regulated granules form during oocyte and embryo development. 3' untranslated region elements direct mRNA targeting to one of these granule classes. The P body factor CAR-1/Rap55 promotes association of repressed mRNA with granules and contributes to repression of Notch/glp-1 mRNA. However, CAR-1 controls Notch/glp-1 only during late oogenesis, where it functions with the RNA-binding regulators PUF-5, PUF-6, and PUF-7. The P body protein CGH-1/Rck/Dhh1 differs from CAR-1 in control of granule morphology and promotes mRNP stability in arrested oocytes. Therefore, a system of diverse and regulated RNP granules elicits stage-specific functions that ensure proper mRNA control during early development.

Sample holder and methodology for measuring the reflectance and transmittance of narrow-leaf samples.

Measuring the reflectance and transmittance of narrow samples can be difficult, as the width of the illuminating beam may be greater than the width of the sample. The small sample area can also compound the already time-consuming process of reconfiguring the instrument between reflectance and transmittance measurements by introducing additional alignment problems. A method of measuring the reflectance and transmittance properties of narrow-leaf samples using reflectance configurations only is developed and tested. The method uses a mask and mask correction and relationships between reflectance measurements against contrasting backgrounds to determine sample reflectance and transmittance. The design of the accompanying sample-holding apparatus is also described. In testing, the mean error was less than 1% reflectance/transmittance, and standard deviation of the error was approximately 1% reflectance and 2% transmittance as compared to samples measured using conventional measurement configurations.