Content Based Image Retrieval by Convolutional Neural Networks

Hamreras S., Benítez-Rochel R., Boucheham B., Molina-Cabello M.A., López-Rubio E. (2019) Content Based Image Retrieval by Convolutional Neural Networks. In: Ferrández Vicente J., Álvarez-Sánchez J., de la Paz López F., Toledo Moreo J., Adeli H. (eds) From Bioinspired Systems and Biomedical Applications to Machine Learning. IWINAC 2019. Lecture Notes in Computer Science, vol 11487. Springer.In this paper, we present a Convolutional Neural Network (CNN) for feature extraction in Content based Image Retrieval (CBIR). The proposed CNN aims at reducing the semantic gap between low level and high-level features. Thus, improving retrieval results. Our CNN is the result of a transfer learning technique using Alexnet pretrained network. It learns how to extract representative features from a learning database and then uses this knowledge in query feature extraction. Experimentations performed on Wang (Corel 1K) database show a significant improvement in terms of precision over the state of the art classic approaches.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Bardeen black holes in the novel 4D4D Einstein-Gauss-Bonnet gravity

In this paper, following the idea of Glavan and Lin [Phys. Rev. Lett. 124, 081301 (2020)] of re-scaling the Gauss-Bonnet (GB) coupling constant to $\alpha/(D-4)$, we obtain the Bardeen black hole solution of $4D$ Einstein-Gauss-Bonnet gravity. We analyze the horizon structure to determine the effect of GB parameter $\alpha$ on the minimum and maximum cutoff values of mass, $M_0$, and magnetic monopole charge, $g_0$, for the existence of a black hole horizon. The analytical expressions for thermodynamical quantities, namely Hawking temperature $T_+$, entropy $S_+$, Gibbs free energy $F_+$ and specific heat $C_+$ associated with the black hole horizon are determined. In the analysis of heat capacity, we find that there exists a critical value of horizon radius, $r_+^{c}$, corresponding to the local maximum of Hawking temperature, at which heat capacity diverges, confirming the second-order phase transition.Comment: 15 pages and 4 figure

Dual-Camera Joint Deblurring-Denoising

Recent image enhancement methods have shown the advantages of using a pair of long and short-exposure images for low-light photography. These image modalities offer complementary strengths and weaknesses. The former yields an image that is clean but blurry due to camera or object motion, whereas the latter is sharp but noisy due to low photon count. Motivated by the fact that modern smartphones come equipped with multiple rear-facing camera sensors, we propose a novel dual-camera method for obtaining a high-quality image. Our method uses a synchronized burst of short exposure images captured by one camera and a long exposure image simultaneously captured by another. Having a synchronized short exposure burst alongside the long exposure image enables us to (i) obtain better denoising by using a burst instead of a single image, (ii) recover motion from the burst and use it for motion-aware deblurring of the long exposure image, and (iii) fuse the two results to further enhance quality. Our method is able to achieve state-of-the-art results on synthetic dual-camera images from the GoPro dataset with five times fewer training parameters compared to the next best method. We also show that our method qualitatively outperforms competing approaches on real synchronized dual-camera captures.Comment: Project webpage: http://shekshaa.github.io/Joint-Deblurring-Denoising

Evaluating the effectiveness of a sodium butyrate feed additive for the control of Salmonella carriage in finishing pigs

This study aimed to investigate the effectiveness of commercially available sodium butyrate to control the shedding of Salmonella on two Irish pig farms with a history of high Salmonella seroprevalence. On both farms, pens (12-17 pigs/pen) were randomly assigned to a control (finisher feed without additives) or an acid treatment (the same feed supplemented with 0.03% sodium butyrate) for 24-26 days prior to slaughter. On Farm A, Salmonella shedding was reduced in the acid group compared to the control group at the end of the treatment period (30% vs. 57% probability of detecting Salmonella in faeces, respectively; p\u3c0.05). However no effect of treatment was observed on Farm B, which could perhaps be explained by a concomitant infection by Lawsonia intracellularis. No significant differences in Salmonella recovery rates were observed from caecal digesta or ileocaecal/mesenteric lymph nodes collected at slaughter in either of the trials. Furthermore, feed intake, weight gain and feed conversion efficiency did not differ significantly between control and treatment groups on either farm

Insights into the Regulatory Characteristics of the Mycobacterial Dephosphocoenzyme A Kinase: Implications for the Universal CoA Biosynthesis Pathway

Being vastly different from the human counterpart, we suggest that the last enzyme of the Mycobacterium tuberculosis Coenzyme A biosynthetic pathway, dephosphocoenzyme A kinase (CoaE) could be a good anti-tubercular target. Here we describe detailed investigations into the regulatory features of the enzyme, affected via two mechanisms. Enzymatic activity is regulated by CTP which strongly binds the enzyme at a site overlapping that of the leading substrate, dephosphocoenzyme A (DCoA), thereby obscuring the binding site and limiting catalysis. The organism has evolved a second layer of regulation by employing a dynamic equilibrium between the trimeric and monomeric forms of CoaE as a means of regulating the effective concentration of active enzyme. We show that the monomer is the active form of the enzyme and the interplay between the regulator, CTP and the substrate, DCoA, affects enzymatic activity. Detailed kinetic data have been corroborated by size exclusion chromatography, dynamic light scattering, glutaraldehyde crosslinking, limited proteolysis and fluorescence investigations on the enzyme all of which corroborate the effects of the ligands on the enzyme oligomeric status and activity. Cysteine mutagenesis and the effects of reducing agents on mycobacterial CoaE oligomerization further validate that the latter is not cysteine-mediated or reduction-sensitive. These studies thus shed light on the novel regulatory features employed to regulate metabolite flow through the last step of a critical biosynthetic pathway by keeping the latter catalytically dormant till the need arises, the transition to the active form affected by a delicate crosstalk between an essential cellular metabolite (CTP) and the precursor to the pathway end-product (DCoA)

Surveillance Data Highlights Feed Form, Biosecurity, and Disease Control as Significant Factors Associated with Salmonella Infection on Farrow-to-Finish Pig Farms

Copyright © 2018 Argüello, Manzanilla, Lynch, Walia, Leonard, Egan, Duffy, Gardiner and Lawlor. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.[EN] Among the zoonotic pathogens affecting pigs, Salmonella stands out due to the high number of human cases linked to pork consumption. In the last two decades many countries have put considerable effort into the control of the infection by surveillance and control strategies on farm. Despite this effort, many herds still have a high Salmonella prevalence and they require guidance to address this problem. The present study, using the serological surveillance data of finishing pigs from the Irish National pig Salmonella Control Programme, aimed to highlight factors associated with increased risk or that might mitigate Salmonella occurrence on farm. A questionnaire with 33 questions regarding herd characteristics, management, feeding, biosecurity, and health was completed for 61 individual herds. After the multivariate analysis by linear regression, nine variables were retained in the final model and linked to herd seroprevalence. Home produced-feed linked to the use of meal showed an eight points reduction in Salmonella prevalence compared to purchased feed (p = 0.042). Different biosecurity measures were associated to lower seroprevalence. Changing of footwear from outside to inside the farm decreased seroprevalence nearly 20 units (p = 0.014) and policies not permitting access to the farmyard to feed trucks (p = 0.048) or avoiding the presence of cats on the farm (p = 0.05) were estimated in 10 units less of seroprevalence. In contrast, the lack of perimeter fence increased the chance to have higher seroprevalence in five units (p = 0.05). Finally, intestinal diseases such as swine dysentery (p = 0.044) and E. coli diarrhea (p = 0.1) were estimated to increase Salmonella prevalence in ~20 and 10 units, respectively, demonstrating the importance of controlling other enteric pathogens in an on-farm Salmonella control programme. These results show the usefulness of surveillance data to improve on-farm control and confirm that Salmonella infection in pigs is multi-factorial and the approach to its control should be multifaceted.SIThis study was funded by the Food Institutional Research Measure (FIRM) administered by the Department of Agriculture Food and the Marine (DAFM) (FIRM/RSF/CoFoRD 2011 Project 11/SF/329).The authors gratefully acknowledge the staff at Longtown Research Farm and the Central Veterinary Research Laboratory (CVRL) Backweston for their expert help in the serological analyses of the study

Transition metal oxides - Thermoelectric properties

Transition metal oxides (TMOs) are a fascinating class of materials due to their wide ranging electronic, chemical and mechanical properties. Additionally, they are gaining increasing attention for their thermoelectric (TE) properties due to their high temperature stability, tunable electronic and phonon transport properties and well established synthesis techniques. In this article, we review TE TMOs at cryogenic, ambient and high temperatures. An overview of strategies used for morphological, compositing and stoichiometric tuning of their key TE parameters is presented. This article also provides an outlook on the current and future prospects of implementing TMOs for a wide range of TE applications

Novel Vector Design and Hexosaminidase Variant Enabling Self-Complementary Adeno-Associated Virus for the Treatment of Tay-Sachs Disease

GM2 gangliosidosis is a family of three genetic neurodegenerative disorders caused by the accumulation of GM2 ganglioside (GM2) in neuronal tissue. Two of these are due to the deficiency of the heterodimeric (α–β), “A” isoenzyme of lysosomal β-hexosaminidase (HexA). Mutations in the α-subunit (encoded by HEXA) lead to Tay-Sachs disease (TSD), whereas mutations in the β-subunit (encoded by HEXB) lead to Sandhoff disease (SD). The third form results from a deficiency of the GM2 activator protein (GM2AP), a substrate-specific cofactor for HexA. In their infantile, acute forms, these diseases rapidly progress with mental and psychomotor deterioration resulting in death by approximately 4 years of age. After gene transfer that overexpresses one of the deficient subunits, the amount of HexA heterodimer formed would empirically be limited by the availability of the other endogenous Hex subunit. The present study used a new variant of the human HexA α-subunit, μ, incorporating critical sequences from the β-subunit that produce a stable homodimer (HexM) and promote functional interactions with the GM2AP– GM2 complex. We report the design of a compact adeno-associated viral (AAV) genome using a synthetic promoter–intron combination to allow self-complementary (sc) packaging of the HEXM gene. Also, a previously published capsid mutant, AAV9.47, was used to deliver the gene to brain and spinal cord while having restricted biodistribution to the liver. The novel capsid and cassette design combination was characterized in vivo in TSD mice for its ability to efficiently transduce cells in the central nervous system when delivered intravenously in both adult and neonatal mice. This study demonstrates that the modified HexM is capable of degrading long-standing GM2 storage in mice, and it further demonstrates the potential of this novel scAAV vector design to facilitate widespread distribution of the HEXM gene or potentially other similar-sized genes to the nervous system

Automated IMT estimation and BMI correlation using a low-quality carotid ultrasound image database from India.

This paper presents AtheroEdgeLowRes (AELR), an extention of AtheroEdge™ from AtheroPoint™, and a solution to carotid ultrasound IMT measurement in low-resolution and overall low quality images. The images were collected using a low-end ultrasound machine during a screening study in India. We aim to demonstrate the accuracy and reproducibility of the AELR system by benchmarking it against an expert Reader's manual tracing and to show the correlation between the automatically measured intima media thickness (IMT) and the subjects' cardiovascular risk factors (i.e. body mass index - BMI). We introduced an innovative penalty function (PF) to our dual-snake segmentation technique, necessary due to the low image resolution. We processed 512 images from 256 patients, and correlated the AELR IMT values with the patients' age and BMI. AELR processed all 512 images, and the IMT measurement error was 0.011±0.099 mm with the PF correction and 0.173±0.127 mm without. AELR IMT values correlated with the Reader's values (r = 0.883) and also correlated with the subject's BMI and age. The AELR system showed accuracy and reproducibility levels that make it suitable to be used in large epidemiological and screening studies in emerging countries

Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs

[EN] Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animalsSIThis study was funded by the Food Institutional Research Measure (FIRM) administered by the Department of Agriculture Food and the Marine (DAFM). H.A. is a postdoctoral researcher supported by the Juan de la Cierva Postdoctoral Trainee Program of the Spanish Ministry of Economy and Competitiveness (IJCI-2016-30795). H.A. was funded by the PiGutNet COST action (FA1401) for a Short-Term Scientific Mission at INRA’s GABI laboratory (Jouy-en-Josas, France). We gratefully acknowledge the Central Veterinary Research Laboratory (CVRL) Backweston for their expert help with the serological analyses. H.A. participated in the study design, sample collection and processing, data analysis, and manuscript writing. F.C.L. participated in study design and manuscript correction. J.E. participated in data analysis and manuscript revision. P.D.C. and F.C. participated in microbiome sequencing and manuscript revision. O.O. performed part of the data analysis and manuscript revision. H.L. and K.W. participated in sample collection and processing. G.D. and P.G.L. participated in the study design and manuscript correction. G.E.G. participated in the study design, data analysis, and manuscript writin