Domain-general and domain-specific influences on emerging numerical cognition: Contrasting uni-and bidirectional prediction models.

Domain-general skills such as executive functions (EFs), and domain-specific skills such as non-symbolic number sense and symbolic understanding are often pitted against each other as predictors of emerging maths. Here we aimed to investigate early childhood relations between these foundational skills with a balanced, longitudinal design. One hundred and seventy 3- and 4-year-old-children were tested at two time points, 5 months apart, on four domain-general executive and five domain-specific numeracy tasks. A latent EF factor was a strong predictor of symbolic maths and of their growth. In addition, stronger symbolic maths at Time 1 was correlated with later stronger EF, but symbolic maths did not predict EF growth. Our findings provide novel insights into dynamic interplay between general and specific cognitive skills contributing to preschool maths.

A Mycobacterial Systems Resource for the Research Community.

Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulceransIMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.

Privacy rights of human research participants in South Africa must be taken seriously.

Letter by Thaldar and Townsend, following an article by the same authors (Thaldar D, Townsend B. Genomic research and privacy: A response to Staunton et al. S Afr Med J 2020;110(3):172-174. https://doi.org/10.7196/SAMJ.2020.v110i3.14431) and both commenting on an article by Staunton et al. (Staunton C, Adams R, Botes M, et al. Safeguarding the future of genomic research in South Africa: Broad consent and the Protection of Personal Information Act No. 4 of 2013. S Afr Med J 2019;109(7):468-470. https://doi.org/10.7196/SAMJ.2019.v109i7.14148); and response to article and letter by Staunton et al.

Safeguarding the future of genomic research in South Africa: Broad consent and the Protection of Personal Information Act No. 4 of 2013.

Genomic research has been identified in South Africa (SA) as important in developing a strong bio-economy that has the potential to improve human health, drive job creation and offer potential solutions to the disease burden harboured by low- and middle-income countries. Central to the success of genomic research is the wide sharing of biological samples and data, but the true value of data can only be unlocked if there are laws and policies in place that foster the legal and ethical sharing of genomic data. The introduction and entry into force of SA's Protection of Personal Information Act (POPIA) No. 4 of 2013 is to be welcomed, but the wording of POPIA as it pertains to consent for the processing of personal information for research purposes has sparked a debate about the legal status of broad consent. We argue that a purposive interpretation of the legislation would permit broad consent for the processing of personal information for research. Although there are ongoing debates surrounding the ethical use of broad consent in Africa, the objective of this article is not to engage with the ethics of broad consent itself, but rather to focus on the legal status of broad consent for genomic data sharing under POPIA.

Effects of lupin-enriched foods on body composition and cardiovascular disease risk factors: a 12-month randomized controlled weight loss trial.

BACKGROUND: Regular consumption of diets with increased protein or fibre intakes may benefit body weight and composition and cardiovascular disease risk factors. Lupin flour is a novel food ingredient high in protein and fibre. OBJECTIVE: To investigate the effects of a lupin-enriched diet, during and following energy restriction, on body weight and composition and cardiovascular disease risk factors in overweight individuals. DESIGN: Participants (n = 131) were recruited to a 12-month parallel-design trial. They were randomly assigned to consume lupin-enriched foods or matching high-carbohydrate control foods. All participants underwent 3 months of weight loss, 1 month of weight stabilization and 8 months of weight maintenance. Body weight and composition and cardiovascular disease risk factors were assessed at baseline, 4 and 12 months. RESULTS: Lupin, relative to control, did not significantly influence (mean difference (95% CI)) weight loss at 4 months (0.1 kg (-1.2, 1.4)) and 12 months (-0.6 kg (-2.0, 0.8)), maintenance of weight loss from 4 to 12 months (-0.7 kg (-1.83, 0.48)) or measures of body fat and fat-free mass. Relative to control, 24-h ambulatory systolic (-1.3 mm Hg (-2.4, -0.3), P = 0.016) and diastolic (-1.0 mm Hg (-1.9, -0.2), P = 0.021) blood pressures were lower at 12 months but not at 4 months; fasting insulin concentrations and homeostasis model assessment (HOMA) scores were significantly lower at 4 months (-1.2 mU l(-1) (-1.3, -1.1), P = 0.004 and -0.6 units (-1.0, -0.19), P = 0.004) and 12 months (-1.3 mU l(-1) (-1.4, -1.1), P < 0.001 and -0.7 units (-1.1, -0.24), P = 0.002). CONCLUSIONS: A diet higher in protein and fibre derived from lupin-enriched foods does not enhance weight loss or improve the maintenance of weight loss. However, such a diet may provide cardiovascular health benefits in terms of insulin sensitivity and blood pressure.

Locally advanced rectal cancer: histopathological correlation and predictive accuracy of serial MRI after neoadjuvant chemotherapy.

The accuracy of MRI after long-course chemoradiotherapy (CRT) in locally advanced rectal cancer (LARC) has been questioned. We have evaluated our experience of sequential MRI to assess pre-operative downstaging with histopathology correlation. 17 patients with LARC had three MRI scans: MRI 1, before treatment; MRI 2, 6 weeks post-CRT; and MRI 3, pre-operatively. MRI T and N staging were reported, with T3 subdivided into T3a (<5 mm through wall), T3b (1-5 mm), T3c (5-15 mm) and T3d (>15 mm). The maximal wall measurements and a prediction of vascular involvement were also correlated with histopathology. Histopathological agreement with MRI 3 was high: T 82%; N 88% and vascular 73%. Statistically significant (p<0.01) T downstaging was shown in MRI 2 and MRI 3 groups. In the 6 weeks post-CRT scan, T downstaging occurred in 6% of patients, with a further 29.4% showing T3c to T3b downsizing. 41% showed N stage improvement. In the third MRI group pre-surgery, 41.2% showed an MRI T stage improvement, with a further T3 downsizing in 17.6% of patients. 50% of these responders had shown no T stage improvement on their second scan. The sequential scans also showed significant reduction in wall thickness (p<0.01). In conclusion, the pre-operative MRI showed ongoing response to CRT up to 12 weeks post-CRT, which has important clinical implications regarding the most appropriate time to operate. Improved agreement between MRI 3 and histopathology compared with previous studies including only one post-treatment MRI was also demonstrated.

A method for automatic edge detection and volume computation of the left ventricle from ultrafast computed tomographic images.

RATIONALE AND OBJECTIVES: Detection of endocardial and epicardial borders of the left ventricle (LV) using various imaging modalities is time-consuming and prone to interpretive error. An automatic border detection algorithm is presented that is used with ultrafast computed tomographic images of the heart to compute cavity volumes. METHODS: The basal-level slice is identified, and the algorithm automatically detects the endocardial and epicardial borders of images from the basal to the apical levels. From these, the ventricular areas and chamber volumes are computed. The algorithm uses the Fuzzy Hough Transform, region-growing schemes, and optimal border-detection techniques. The cross-sectional areas and the chamber volumes computed with this technique were compared with those from manually traced images using canine hearts in vitro (n = 8) and studies in clinical patients (n = 27). RESULTS: Though the correlation was good (r = .88), the algorithm overestimated the LV epicardial area by 4.8 +/- 6.4 cm2, though this error was not statistically different from zero (P > .05). There was no difference in endocardial areas (r = .95, P > .05). The algorithm tended to underestimate the end-diastolic volume (r = .94) and the end-systolic volume (r = .94), although these errors were not statistically different from zero (P > .05). The algorithm tended to underestimate the ejection fraction (r = .80), although this error was not statistically different from zero (P > .05). CONCLUSIONS: Automatic detection of myocardial borders provides the clinician with a useful tool for calculating chamber volumes and ejection fractions. The algorithm, with the corrections suggested, provides an accurate estimation of areas and volumes. This algorithm may be useful for contour border identification with ultrasound, positron-emission tomography, magnetic resonance imaging, and other imaging modalities in the heart, as well as other structures.

A gradient-layer calorimeter for measurement of energy expenditure of infants.

We have developed and validated a gradient-layer calorimeter for direct measurement of energy expenditure of preterm infants. Infant calorimeters must be operated and tested differently from adult calorimeters, because the calorimeter must be warmed during operation to limit heat loss from the infant, the calorimeter wall temperature (which is selected on the basis of the infant's maturity) must be precisely controlled, and energy expenditure (heat output) is typically < 10 W. We calibrated our calorimeter by varying the heat produced by a dry source (manikin or light bulb) with airflow (n = 42) and without airflow (n = 8) at various water jacket temperatures (n = 7) and by a wet source (combustion of ethyl alcohol) with airflow (n = 9). With no air moving, qc = 0.740 Vc + 0.029 Twj-0.697, where qc (W) is the estimated output of the heat source measured by the calorimeter, Vc (mV) is the gradient-layer voltage of the calorimeter, and Twj (degree C) is the temperature of the water jacket surrounding the walls of the device. From this equation and enthalpy calculations, the slope and intercept of the regression line relating the estimated heat production to the actual heat produced from alcohol combustion are 1.029 +/- 0.046 and -0.549 +/- 0.484 (SE), respectively. The slope is not significantly different from unity, and the intercept is not significantly different from zero. Thus we can accurately estimate the energy expenditure of preterm infants from the equations describing our calorimeter, and we can accurately resolve the total heat output into a dry (nonevaporative) component and a wet (evaporative) component.

The fuzzy Hough transform-feature extraction in medical images.

Identification of anatomical features is a necessary step for medical image analysis. Automatic methods for feature identification using conventional pattern recognition techniques typically classify an object as a member of a predefined class of objects, but do not attempt to recover the exact or approximate shape of that object. For this reason, such techniques are usually not sufficient to identify the borders of organs when individual geometry varies in local detail, even though the general geometrical shape is similar. The authors present an algorithm that detects features in an image based on approximate geometrical models. The algorithm is based on the traditional and generalized Hough Transforms but includes notions from fuzzy set theory. The authors use the new algorithm to roughly estimate the actual locations of boundaries of an internal organ, and from this estimate, to determine a region of interest around the organ. Based on this rough estimate of the border location, and the derived region of interest, the authors find the final (improved) estimate of the true borders with other (subsequently used) image processing techniques. They present results that demonstrate that the algorithm was successfully used to estimate the approximate location of the chest wall in humans, and of the left ventricular contours of a dog heart obtained from cine-computed tomographic images. The authors use this fuzzy Hough transform algorithm as part of a larger procedure to automatically identify the myocardial contours of the heart. This algorithm may also allow for more rapid image processing and clinical decision making in other medical imaging applications.

Automatic detection of myocardial contours in cine-computed tomographic images.

Quantitative evaluation of cardiac function from cardiac images requires the identification of the myocardial walls. This generally requires the clinician to view the image and interactively trace the contours. This method is susceptible to great variability that depends on the experience and knowledge of the particular operator tracing the contours. The particular imaging modality that is used may also add tracing difficulties. Cine-computed tomography (cine-CT) is an imaging modality capable of providing high quality cross-sectional images of the heart. CT images, however, are cluttered, i.e., objects that are not of interest, such as the chest wall, liver, stomach, are also visible in the image. To decrease this variability, investigators have developed computer-assisted or near-automatic techniques for tracing these contours. All of these techniques, however, require some operator intervention to confidently identify myocardial borders. The authors present a new algorithm that automatically finds the heart within the chest, and then proceeds to outline (detect) the myocardial contours. Information at each tomographic slice is used to estimate the contours at the next tomographic slice, thus allowing the algorithm to work in near-apical cross-sectional images where the myocardial borders are often difficult to identify. The algorithm does not require operator input and can be used in a batch mode to process large quantities of data. An evaluation and correction phase is included to allow an operator to view the results and selectively correct portions of contours. The authors tested the algorithm by automatically identifying the myocardial borders of 27 cardiac images obtained from three human subjects and quantitatively comparing these automatically determined borders with those traced by an experienced cardiologist.

Quantitative shape descriptors of left-ventricular cine-CT images.

In order to assess regional diastolic function of the left ventricle (LV), we use LV cine-CT images to build finite element models. To quantitatively evaluate the accuracy of our geometric reconstruction technique used in building these models, we introduce a new measure of shape-similarity, and compare and contrast the results obtained from the new measure to the results obtained from traditional shape-similarity measures. All of these measures are used to compare the endocardial and epicardial LV contours obtained from cine-CT images of canine hearts with those obtained from video images of the same hearts. Our results show that our imaging procedure accurately reproduces shape, and further suggest that the new descriptor has the sensitivity and resolution required to distinguish between images separated by as little as 3 mm.

An in vitro experimental comparison of Edwards-Duromedics and St Jude bileaflet heart valve prostheses.

An in vitro comparison of the hydrodynamic characteristics of the Edwards-Duromedics (DM) and St Jude (SJ) bi-leaflet aortic valve prostheses is presented. Aortic valves 27 mm in diameter were mounted in a pulse duplicator simulating physiological pulsatile flow using a glycerol solution as the blood analogue fluid. Mean trans-valvular pressure difference (TPD) in systole, the per cent regurgitation (PCR) and the projected valve orifice area (VOA) were compared at a range of flow rates and heart rates to reflect the functioning of the valve under resting as well as exercise conditions. Our results showed that the TDP for DM (0.99 +/- 0.28 kPa) valve was slightly larger than the SJ (0.81 +/- 0.19 kPa) valve (mean difference of 0.18 +/- 0.26 kPa, P less than 0.05). However, the PCR for the DM (13.6 +/- 7.8) valve was smaller than the SJ (17.9 +/- 9.0) valve (mean difference of 4.3 +/- 4.2%, P less than 0.01). Moreover, VOA for the DM (2.51 +/- 0.10 cm2) valve was smaller than the SJ (3.13 +/- 0.04 cm2) valve (mean difference of 0.63 +/- 0.10 cm3, P less than 0.001).

Respiratory effects of brief baroreceptor stimuli in the anesthetized dog.

To quantify the immediate isocapnic respiratory response to baroreceptor stimulation, pressure in the isolated externally perfused carotid sinuses (CS) of 24 vagotomized alpha-chloralose-anesthetized dogs was increased selectively during either inspiration or expiration as a step (from time of onset to end of respiratory phase) or a pulse (500 ms). The rise time (150 ms), base-line pressure (80 mmHg), and stimulus magnitude (40 mmHg) were similar for the two stimuli. The time of stimulus onset (delay), expressed as a percent of control time of inspiration (TI) or expiration (TE), was varied. TI, TE, and tidal volume (VT) were expressed as percent changes from control. Stimuli delivered early in inspiration lengthened TI [23.5 +/- 6.4% (SE) for step and 11.7 +/- 6.3% for pulse stimuli at 5% delay] more effectively than late stimuli. VT was essentially unaltered. In contrast, step stimuli delivered during expiration caused a lengthening of TE (32.7 +/- 6.3% at 5% delay) that did not depend on the delay (up to 75%). Very late (85%) pulse stimuli lengthened TE (15.2 +/- 5.7%) more effectively than early stimuli. For both stimuli, the expiratory VT was unaltered. When the responses are compared before and after separation of the blood supply of the carotid bodies from the CS region and when they are compared before and after inhibition of reflex systemic hypotension by ganglionic blockade, the observed responses were shown to be due solely to CS baroreceptor stimulation and not to alterations in carotid body blood flow or reflex changes in systemic cardiovascular variables.