Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade

Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade (MRC). Using the model bacterium Ruegeria pomeroyi, we confirm that the betA, betB and betC genes, encoding choline dehydrogenase, betaine aldehyde dehydrogenase and choline sulfatase, respectively, are involved in choline metabolism. The betT gene, encoding an organic solute transporter, was essential for the rapid uptake of choline but not glycine betaine (GBT). Growth of choline and GBT as a sole carbon source resulted in the re-mineralization of these nitrogen-rich compounds into ammonium. Oxidation of the methyl groups from choline requires formyltetrahydrofolate synthetase encoded by fhs in R.pomeroyi, deletion of which resulted in incomplete degradation of GBT. We demonstrate that this was due to an imbalance in the supply of reducing equivalents required for choline catabolism, which can be alleviated by the addition of formate. Together, our results demonstrate that choline metabolism is ubiquitous in the MRC and reveal the role of Fhs in methyl group oxidation in R.pomeroyi

Financial conservatism, firm value and international business risk: Evidence from emerging economies around the global financial crisis

The increase in debt-free or under-levered firms (financial conservatism) is one of the most recent stylized puzzles that cannot be explained within the context of extant capital structure theories. In this paper, we exploit the 2008–09 contractions in credit supply in a quasi-natural experiment to examine whether financial conservatism affects firm value. Using a large sample of firms from seven African countries over the period 2003–2012, we find strong evidence that financial conservatism mitigates the adverse effect of contractions in credit supply on firm value for both local and international firms. Our results suggest that financial conservatism is an effective strategy for managing risks arising from contractions in credit supply and international business exposure. These findings provide novel empirical evidence on the value relevance of financial conservatism which shields firms from the adverse and far-reaching effects of contractions in credit supply

Vegetable Classification Using Deep Learning

Abstract: Vegetables are an essential component of a healthy diet and play a critical role in promoting overall health and well- being. Vegetables are rich in important vitamins and minerals, including vitamin C, folate, potassium, and iron. They also provide fiber, which helps maintain digestive health and prevent chronic diseases. We are proposing a deep learning model for the classification of vegetables. A dataset was collected from Kaggle depository for Vegetable with 15000 images for 15 different classes. The data was preprocessed, normalized and split into three sets (train, valid, test). The proposed model was trained and validated using the train and valid sets and accuracy of both training and validation was very high. For the evaluation of the proposed model we utilized these metrics: accuracy, F1-score, precision, Recall and time required for testing. We then tested the proposed model using the test set. The result of the testing was accuracy (99.95%), F1-score (99.95%), precision (99.95%), Recall (99.95%) and time required for testing the test set was 1.38 seconds

Diversity, Prevalence, and Longitudinal Occurrence of Type II Toxin-Antitoxin Systems of Pseudomonas aeruginosa Infecting Cystic Fibrosis Lungs

Type II toxin-antitoxin (TA) systems are most commonly composed of two genes encoding a stable toxin, which harms the cell, and an unstable antitoxin that can inactivate it. TA systems were initially characterized as selfish elements, but have recently gained attention for regulating general stress responses responsible for pathogen virulence, formation of drug-tolerant persister cells and biofilms—all implicated in causing recalcitrant chronic infections. We use a bioinformatics approach to explore the distribution and evolution of type II TA loci of the opportunistic pathogen, Pseudomonas aeruginosa, across longitudinally sampled isolates from cystic fibrosis lungs. We identify their location in the genome, mutations, and gain/loss during infection to elucidate their function(s) in stabilizing selfish elements and pathogenesis. We found (1) 26 distinct TA systems, where all isolates harbor four in their core genome and a variable number of the remaining 22 on genomic islands; (2) limited mutations in core genome TA loci, suggesting they are not under negative selection; (3) no evidence for horizontal transmission of elements with TA systems between clone types within patients, despite their ability to mobilize; (4) no gain and limited loss of TA-bearing genomic islands, and of those elements partially lost, the remnant regions carry the TA systems supporting their role in genomic stabilization; (5) no significant correlation between frequency of TA systems and strain ability to establish as chronic infection, but those with a particular TA, are more successful in establishing a chronic infection

Skeletal changes after midface surgery in patients with craniofacial deformities:a threedimensional quantification method

To determine the skeletal changes after midface surgery in patients with syndromic craniosynostosis who underwent Le Fort III (LFIII), monobloc (MB), or facial bipartition (FB). This was a retrospective study including 75 patients: 33 treated by LFIII, 29 by MB, and 13 by FB. Twenty-five had a diagnosis of Apert, 39 Crouzon, and 11 craniofrontonasal syndrome. A three-dimensional mesh was created from the preoperative scan and registered to the postoperative scan to visualise the advancement. LFIII at age 7–12 years effectuated a higher mean advancement in the maxillary (15.5 mm) and zygomatic (7.6 mm) regions when compared to ≥13 years (10.2 mm and 5.5 mm). After MB, mean advancement of the fronto-orbital region was higher at &lt;7 years (16.4 mm), and similarly lower at ages 7–12 (13.8 mm) and ≥13 (12.5 mm). The mean preoperative inter-dacryon distance (34.4 ± 4.4 mm) was reduced by 8.7 ± 4.2 mm after FB without distraction (n = 10). More advancement was seen when midface surgery was performed at a younger age, due to more severe cases and a desire for overcorrection. The highest mean advancement was observed in the fronto-orbital region. Antero-inferior rotational movement was seen after all three techniques.</p

Bacteriocin-mediated competition in cystic fibrosis lung infections

Bacteriocins are toxins produced by bacteria to kill competitors of the same species. Theory and laboratory experiments suggest that bacteriocin production and immunity play a key role in the competitive dynamics of bacterial strains. The extent to which this is the case in natural populations, especially human pathogens, remains to be tested. We examined the role of bacteriocins in competition using Pseudomonas aeruginosa strains infecting lungs of humans with cystic fibrosis (CF). We assessed the ability of different strains to kill each other using phenotypic assays, and sequenced their genomes to determine what bacteriocins (pyocins) they carry. We found that (i) isolates from later infection stages inhibited earlier infecting strains less, but were more inhibited by pyocins produced by earlier infecting strains and carried fewer pyocin types; (ii) this difference between early and late infections appears to be caused by a difference in pyocin diversity between competing genotypes and not by loss of pyocin genes within a lineage over time; (iii) pyocin inhibition does not explain why certain strains outcompete others within lung infections; (iv) strains frequently carry the pyocin-killing gene, but not the immunity gene, suggesting resistance occurs via other unknown mechanisms. Our results show that, in contrast to patterns observed in experimental studies, pyocin production does not appear to have a major influence on strain competition during CF lung infections

Growth patterns and shape development of the paediatric mandible – A 3D statistical model

BACKGROUND/AIM: To develop a 3D morphable model of the normal paediatric mandible to analyse shape development and growth patterns for males and females. METHODS: Computed tomography (CT) data was collected for 242 healthy children referred for CT scan between 2011 and 2018 aged between 0 and 47 months (mean, 20.6 ± 13.4 months, 59.9% male). Thresholding techniques were used to segment the mandible from the CT scans. All mandible meshes were annotated using a defined set of 52 landmarks and processed such that all meshes followed a consistent triangulation. Following this, the mandible meshes were rigidly aligned to remove translation and rotation effects, while size effects were retained. Principal component analysis (PCA) was applied to the processed meshes to construct a generative 3D morphable model. Partial least squares (PLS) regression was also applied to the processed data to extract the shape modes with which to evaluate shape differences for age and sex. Growth curves were constructed for anthropometric measurements. RESULTS: A 3D morphable model of the paediatric mandible was constructed and validated with good generalisation, compactness, and specificity. Growth curves of the assessed anthropometric measurements were plotted without significant differences between male and female subjects. The first principal component was dominated by size effects and is highly correlated with age at time of scan (Spearman's r = 0.94, p < 0.01). As with PCA, the first extracted PLS mode captures much of the size variation within the dataset and is highly correlated with age (Spearman's r = −0.94, p < 0.01). Little correlation was observed between extracted shape modes and sex with either PCA or PLS for this study population. CONCLUSION: The presented 3D morphable model of the paediatric mandible enables an understanding of mandibular shape development and variation by age and sex. It allowed for the construction of growth curves, which contains valuable information that can be used to enhance our understanding of various disorders that affect the mandibular development. Knowledge of shape changes in the growing mandible has potential to improve diagnostic accuracy for craniofacial conditions that impact the mandibular morphology, objective evaluation, surgical planning, and patient follow-up

Loss of Social Behaviours in Populations of Pseudomonas aeruginosa Infecting Lungs of Patients with Cystic Fibrosis

Pseudomonas aeruginosa, is an opportunistic, bacterial pathogen causing persistent and frequently fatal infections of the lung in patients with cystic fibrosis. Isolates from chronic infections differ from laboratory and environmental strains in a range of traits and this is widely interpreted as the result of adaptation to the lung environment. Typically, chronic strains carry mutations in global regulation factors that could effect reduced expression of social traits, raising the possibility that competitive dynamics between cooperative and selfish, cheating strains could also drive changes in P. aeruginosa infections. We compared the expression of cooperative traits - biofilm formation, secretion of exo-products and quorum sensing (QS) - in P. aeruginosa isolates that were estimated to have spent different lengths of time in the lung based on clinical information. All three exo-products involved in nutrient acquisition were produced in significantly smaller quantities with increased duration of infection, and patterns across four QS signal molecules were consistent with accumulation over time of mutations in lasR, which are known to disrupt the ability of cells to respond to QS signal. Pyocyanin production, and the proportion of cells in biofilm relative to motile, free-living cells in liquid culture, did not change. Overall, our results confirm that the loss of social behaviour is a consistent trend with time spent in the lung and suggest that social dynamics are potentially relevant to understanding the behaviour of P. aeruginosa in lung infections

Detecting Mandible Fractures in CBCT Scans Using a 3-Stage Neural Network

After nasal bone fractures, fractures of the mandible are the most frequently encountered injuries of the facial skeleton. Accurate identification of fracture locations is critical for effectively managing these injuries. To address this need, JawFracNet, an innovative artificial intelligence method, has been developed to enable automated detection of mandibular fractures in cone-beam computed tomography (CBCT) scans. JawFracNet employs a 3-stage neural network model that processes 3-dimensional patches from a CBCT scan. Stage 1 predicts a segmentation mask of the mandible in a patch, which is subsequently used in stage 2 to predict a segmentation of the fractures and in stage 3 to classify whether the patch contains any fracture. The final output of JawFracNet is the fracture segmentation of the entire scan, obtained by aggregating and unifying voxel-level and patch-level predictions. A total of 164 CBCT scans without mandibular fractures and 171 CBCT scans with mandibular fractures were included in this study. Evaluation of JawFracNet demonstrated a precision of 0.978 and a sensitivity of 0.956 in detecting mandibular fractures. The current study proposes the first benchmark for mandibular fracture detection in CBCT scans. Straightforward replication is promoted by publicly sharing the code and providing access to JawFracNet on grand-challenge.org