Fast and Efficient Root Phenotyping via Pose Estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity). Here, we present a segmentation-free approach that leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that pose-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

Fast and efficient root phenotyping via pose estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity). Here we present a segmentation-free approach which leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that landmark-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

Views and experiences of hepatitis C testing and diagnosis among people who inject drugs: systematic review of qualitative research

BACKGROUND

Many developed countries are facing a major challenge to improve identification of individuals acutely and chronically infected with hepatitis C virus (HCV) infection. We explored the views and experiences of people who inject drugs (PWID) in relation to HCV testing, and diagnosis through a review and synthesis of qualitative research.

METHODS

Based on the thematic synthesis of qualitative research. Searches were conducted in 14 databases and supplemented by reference checking, hand searching of selected journals, and searches of relevant websites. Studies of any qualitative design that examined the views and experiences of, and attitudes towards, HCV testing and diagnosis among PWID or practitioners involved in their care were included. Key themes and sub-themes were systematically coded according to the meaning and content of the findings of each study which proceeded to the preparation of a narrative account of the synthesis.

RESULTS

28 qualitative studies were identified. We identified a number of overarching descriptive themes in the literature, finding overall that PWID hold complex and differing views and experiences of testing and diagnosis. Three major themes emerged: missed opportunities for the provision of information and knowledge; shifting priorities between HCV testing and other needs; and testing as unexpected and routine. Evidence of missed opportunities for the provision of knowledge and information about HCV were clear, contributing to delays in seeking testing and providing a context to poor experiences of diagnosis. Influenced by the nature of their personal circumstances, perceptions of the risk associated with HCV and the prioritisation of other needs acted both to encourage and discourage the uptake of HCV testing. Undergoing HCV testing as part of routine health assessment, and an unawareness of being testing was common. An unexpected positive diagnosis exacerbated anxiety and confusion.

CONCLUSION

This review has identified that there are modifiable factors that affect the uptake of HCV testing and experiences of HCV diagnosis among PWID. Intervention development should focus on addressing these factors. There is a need for further research that engages PWID from a diverse range of populations to identify interventions, strategies and approaches that they consider valuable.

Foodborne agents associated with the consumption of aquaculture catfish

In the Food, Conservation, and Energy Act (Farm Bill) of 2008, Congress amended the Federal Meat Inspection Act to provide that catfish be inspected by the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS). As part of the development of its inspection program, the FSIS conducted an assessment of the food safety risk associated with consuming farm-raised catfish. To thoroughly identify hazards for consideration in the risk assessment, the scientific literature was surveyed for all potential agents that have been linked to illness associated with farm-raised catfish consumption. A review of microbial hazards suggested that Salmonella is the foodborne pathogen most likely to be associated with catfish, but the impact of other pathogens remains unclear. This review also summarizes the current data available on chemical residues in catfish, including pesticides and heavy metals, and any regulatory levels that have been established for these compounds. The current usage of veterinary drugs in aquaculture also is outlined, including information on unapproved usage of drugs in catfish.

The efficacy of pharyngeal packing during routine nasal surgery--a prospective randomised controlled study

The efficacy of pharyngeal packing in the prevention of postoperative nausea and vomiting (PONV) in patients undergoing nasal surgery was evaluated in a prospective randomised controlled study. The effect of the presence of the pharyngeal pack on the incidence of postoperative sore throat was also assessed. One hundred patients were randomly allocated to one of two groups; the first had packing and the second received no packing. The placement of a pharyngeal pack was found to have no effect on the incidence of PONV but was associated with a significantly increased incidence of sore throat. The absence of a pharyngeal pack was not associated with an increase in postoperative aspiration or vomiting. We conclude that the routine placement of pharyngeal packs during uncomplicated nasal surgery has no effect on the incidence of PONV and will increase the incidence of postoperative sore throat.

Clearing the cervical spine in unconscious polytrauma victims, balancing risks and effective screening

Cervical spine injury occurs in 5-10% of cases of blunt polytrauma. A missed or delayed diagnosis of cervical spine injury may be associated with permanent neurological sequelae. However, there is no consensus about the ideal evaluation and management of the potentially injured cervical spine and, despite the publication of numerous clinical guidelines, this issue remains controversial. In addition, many studies are limited in their application to the obtunded or unconscious trauma victim. This review will provide the clinician managing unconscious trauma victims with an assessment of the actual performance of clinical examination and imaging modalities in detecting cervical spine and isolated ligamentous injury, a review of existing guidelines in light of the available evidence, relative risk estimates and a proposed management scheme.

Potency estimation of mivacurium: comparison of two different modes of nerve stimulation

We have assessed the potency of mivacurium, a new non-depolarizing neuromuscular blocker, using two different modes of nerve stimulation in patients anaesthetized with thiopentone, fentanyl and nitrous oxide in oxygen. The force of contraction of adductor pollicis was measured after single twitch stimulation at 0.1 Hz or train-of-four stimulation (TOF) at 2 Hz every 10 s. Dose-response curves were constructed using a single-dose method for each mode of stimulation. The ED50 and ED95 were 43 micrograms kg-1 and 83 micrograms kg-1, respectively, for the single twitch responses and 34 micrograms kg-1 and 66 micrograms kg-1, respectively, for the first response of the TOF stimulation. The difference between the ED95 doses was not significant (P = 0.051), but the difference between the ED50 doses was significant (P = 0.03), suggesting greater sensitivity of the neuromuscular junction using TOF stimulation. The results show that the information obtained using single twitch stimulation at 0.1 Hz is not the same as that obtained from the first response of the TOF stimulation.

Outreach to injecting drug users and female sexual partners of drug users on the lower east side of New York City

In 1984, outreach to injecting drug users and their female sexual partners was initiated as part of HIV behavioral research projects. HIV, health, drug treatment and family planning information and services were provided in addition to recruiting subjects to the research program. Such outreach also poses certain problems--especially potential disruption of neighborhood day-to-day life and clashes with police. This paper discusses an outreach program to injecting drug users and their female sexual partners that was initiated in New York City to provide HIV-related information and services. We examine the successes of the program and problems that were involved in conducting outreach to persons who are typically not accessible through formal institutional channels.

Routine pre-operative electrocardiography

In a study of 877 patients presenting for anaesthesia with an ECG, 45 per cent of the ECGs were found to be abnormal. The incidence of abnormal ECGs was found to be highest in the over-40 age group, and also in those patients of ASA Grades II, III, IV and V, and this investigation is therefore recommended in these patients.

Biochemical studies on the catalysis of nitrosation by bacteria

Biochemical and microbiological studies were conducted to characterize the mechanism of bacterial formation of N-nitrosomorpholine from morpholine and nitrite at neutral pH. Nitrosating activity was markedly induced when bacteria were cultured anaerobically in minimal culture medium containing nitrate, while the presence of cysteine or tungsten in the medium inhibited induction. Of various metals, coenzymes and inhibitors tested for their effects on in vitro nitrosation of morpholine, potassium cyanide, sodium azide, NAD(P)H and nitrate strongly inhibited nitrosation. Several mutants of Escherichia coli A10 strain were prepared in order to examine whether nitrosation activity is linked to specific loci. Niridazole-resistant mutants, which lack nitroreductase, had as much nitrosating activity as the original E. coli A10, but chlorate-resistant mutants had completely lost this activity. A good correlation was observed between nitrate reductase activity and nitrosating activity in these mutants. These results indicate that bacterial nitrosation is an enzyme-mediated reaction closely associated with molybdenoenzymes such as the nitrate reductase/formate hydrogenlyase system.

Rapid and transient rise in diacylglycerol concentration in Daudi cells exposed to interferon

Human beta-interferon stimulates a 4-fold increase in the concentration of diacyglycerol and a 2-fold increase in the concentration of inositol monophosphate in Daudi (human B-lymphoblastoid) cells within 30 sec of exposure of the cells to interferon. The increase in diacylglycerol and in inositol monophosphate is transient and the concentrations of these compounds decrease to basal levels within 10 min. Preincubation of human beta-interferon with anti-interferon antibodies inhibits this effect as well as the binding of interferon to Daudi cells. Diacylglycerol concentrations were unaffected in mouse A9 cells (fibroblasts) incubated with human beta-interferon and in Daudi cells incubated with human gamma-interferon. Mouse A9 cells are insensitive to human interferon and Daudi cells are insensitive to human gamma-interferon. The magnitude of the increase in diacylglycerol concentration stimulated by interferon can be correlated to the interferon-induced inhibition of Daudi cell division in a dose-responsive manner. Phorbol 12-myristate 13-acetate also inhibits Daudi cell division in a dose-responsive manner. It is likely that the sharp and transient increase in diacylglycerol concentration represents one of the early biochemical changes in Daudi cells exposed to interferon.

Reproducibility of microbial mutagenicity assays: II. Testing of carcinogens and noncarcinogens in Salmonella typhimurium and Escherichia coli

A total of 63 chemicals were tested for mutagenicity in Salmonella typhimurium strains TA98, TA100, TA1535, TA1537, and TA1538, and Escherichia coli WP2 uvrA in a four-laboratory study. Sixty of the chemicals had been tested for carcinogenicity by the National Cancer Institute or the National Toxicology Program. All chemicals were tested for mutagenicity without metabolic activation and with liver S-9 preparations from uninduced and Aroclor 1254-induced F344 rats, B6C3F1 mice, and Syrian hamsters. The intra- and interlaboratory reproducibility of the Salmonella assay with regard to the overall judgment of mutagenic or nonmutagenic was good. The results in the E coli strain, however, exhibited a high degree of variability between laboratories. With one or two exceptions, the mutagens were detected with S-9 preparations from all three species. The uninduced liver S-9 preparations did not activate any chemicals to mutagens that were not also activated by induced S-9, but some chemicals were detected as mutagens only when induced S-9 was used. A positive mutagenic response in Salmonella was predictive of carcinogenicity 69% of the time; when equivocal carcinogens and borderline mutagens were included, the predictivity increased to 83%. Conversely, 76% of the carcinogens were mutagens. When the equivocal carcinogens were included, the proportion dropped to 75%. Relatively few chemicals (18%) were mutagenic in E coli. Not all the carcinogens induced tumors in both rats and mice, and the species-specific carcinogenicity could not be predicted from the S-9-specific mutagenicity.

Serum immunoreactive somatomedin levels in normal adults, pregnant women at term, children at various ages, and children with constitutionally delayed growth

Immunoreactive somatomedin (IRSM) levels in term pregnancy material sera (MS) and newborn cord sera (CS) were higher and lower, respectively, than those in normal adults. IRSM levels in MS and CS were not correlated, suggesting that SM dose not cross the placenta. The similar levels of IRSM in arterial and venous CS suggest that the placenta does not produce SM. IRSM levels in CS were higher than those in newborn sera and were correlated with day 1 newborn sera, suggesting that the placenta may regulate fetal serum IRSM levels. Serum IRSM levels in normal children gradually increased from birth to peak levels at puberty. The mean levels of serum IRSM reached peak levels 2 yr earlier in females. Males near pubertal age with constitutionally delayed growth had lower serum IRSM levels than age-matched controls. Diagnostic measurements of serum IRSM in children requires comparison with age- and sex-matched controls. Serum SM levels may only approximately reflect the local concentrations or activities of SM in various tissues.

A new mutagenic and genotoxic response of the flame retardant tris(2,3-dibromopropyl)phosphate. Activation by singlet oxygen

Illumination of tris (2,3-dibromopropyl)phosphate with visible light in the presence of riboflavin resulted in the formation of a stable product with greatly enhanced genetic and DNA-modifying activities. Because illumination of riboflavin results in the formation of short-lived singlet oxygen, it is assumed that the mutagenic and genotoxic chemical results from a reaction between the flame retardant and singlet oxygen. Since the polluted urban atmosphere is conducive to the generation of this species of oxygen, the present results may, therefore, be relevant to an assessment of the health hazard posed by such an environment.

Dissimilation of the lignin model compound veratrylglycerol-beta-(o-methoxyphenyl) ether by Pseudomonas acidovorans: initial transformations

The initial transformadomonas acidovorans are demethylation of the 4-methoxyl group of the 3,4-dimethoxyphenyl portion of the molecule, and a NAD+-linked dehydrogenation of the benzyl alcohol group. Based on these findings and those described before, an overall degradation scheme is postulated.

Degradation of methoxylated benzoic acids by a Nocardia from a lignin-rich environment: significance to lignin degradation and effect of chloro substituents

Strain A81 of Nocardia corallina hydroxylates or demethylates p-anisic acid to p-hydroxybenzoic acid and isovanillic acid. It demethylates veratric acid to a mixture of vanillic and isovanillic acids. These are both demethylated to protocatechuic acid, which undergoes ring cleavage to afford beta-carboxy-cis-cis-muconic acid. The intermediacy of protocatechuic acid in the catabolic pathway of veratric acid was confirmed by blocking ring cleavage with an additional substituent in the ring: 5-chlorovanillic acid was demethylated to 5-chloro-protocatechuic acid, which accumulated. Chloro substituents in the ring of other methoxylated benzoic acids also arrested their normal metabolism by the Nocardia: an ortho-chloro substituent thwarted both demethylation and ring-opening. ortho-Hydroxylation of p-methoxybenzoic acid to isovanillic acid was unaffected by a chlorine ortho to the methoxyl group. Washed whole cells of veratric acid-grown N. corallina A81 produced no detected structural changes in an isolated lignin. The implications of this observation are discussed.

Bacterial cleavage of an arylglycerol- -aryl ether bond

The first known cleavage by a bacterium of an arylglycerol-beta-aryl ether linkage, the most common intermonomer linkage in lignin, is described.

Cellulases of Thermomonospora fusca and Streptomyces thermodiastaticus

The cellulases of Streptomyces thermodiastaticus (strain 2Sts) and thermomonospora fusca (strain 190Th) were produced with carboxymethyl-cellulose (CMC) serving as the carbon source during growth. Both cellulases act by random internal hydrolysis of the CMC chain, producing cellobiose, glucose, and intermediate length oligosaccharides. Cellobiase was not detected in culture filtrates produced under these conditions.

Defined liquid minimal medium for Caryophanon latum

A defined medium has been developed for the trichome-forming bacterium, Caryophanon latum. Acetate is the main carbon and energy source, and either N-glutamate, or N-NH(4) can be used as the nitrogen source.

Survival, transmission, and taxonomy of Pseudomonas syringae van Hall, the causal organism of bacterial brown spot of bean (Phaseolus vulgaris L.)

Pseudomonas syringae van Hall was shown to be transmitted on seed of bean (Phaseolus vulgaris L.). The pathogen survived in bean field soil until April but not until May. Isolates studied were pathogenic to pea, but not to red clover, white dutch clover, ladino clover, alfalfa, or white lupine. Attempts to isolate P. syringae as a pathogen or as an epiphyte from plants in fence lines and wind breaks surrounding diseased bean fields failed. It was concluded that infected seed is a principal source of the bacterial brown spot pathogen in Wisconsin. Routine bacteriological tests including the utilization of 12 carbohydrates, six organic acids, and 30 other diagnostic tests did not differentiate P. syringae and P. pisi Sackett. These two species differed with respect to acrylamide disc-gel electrophoretic protein patterns, electrophoretic peroxidase isozymes, toxin production, and host range. Isolates of P. syringae produced a toxin with characteristics of syringomycin, whereas isolates of P. pisi did not produce such a toxin.

Qualitative analyses of vegetative cell walls and spore walls of some representative species of Streptomyces

Vegetative cell walls and spore walls of seven Streptomyces species representing four types of spore morphology were qualitatively analysed for their components. Amino acid and carbohydrate components (glucose, glucosamine, muramic acid, diaminopimelic acid, glutamic acid, glycine, alanine, arginine, threonine, valine, leucine, and aspartic acid) in both types of walls were identical in all species. Aspartic acid was a major component in spore walls, but a minor component in vegetative cell walls. Although organic phosphate was present in both vegetative- and spore-wall hydrolysates, the other components of teichoic acid were not found nor was teichoic acid extracted from the isolated walls by cold trichloroacetic acid. A portion of the vegetative cell wall was rendered soluble with lysozyme and separated by paper electrophoresis into two fractions detected with ninhydrin. The lysozyme-resistant portion of the vegetative cell wall showed the same major and minor components as the spore walls, which are also lysozyme resistant.

Clostridium botulinum type E in fish from the Great Lakes

Bott, Thomas L. (University of Wisconsin, Madison), Janet S. Deffner, Elizabeth McCoy, and E. M. Foster. Clostridium botulinum type E in fish from the Great Lakes. J. Bacteriol. 91:919-924. 1966.-The intestinal contents of more than 3,000 fish from Lakes Erie, Superior, Huron, and Michigan were examined for Clostridium botulinum type E. Demonstration of the organism was accomplished by identifying its toxin in liquid cultures inoculated with material from the alimentary tract. Incidence figures, expressed as per cent of the fish tested, were: Lake Erie, 1%; Lake Superior, 1%; Lake Huron, 4%; the main body of Lake Michigan, 9%; and Green Bay (on Lake Michigan), 57%. Thus, C. botulinum type E appears to be widely but unevenly distributed in the Great Lakes, and fish from all areas are potential carriers of it.