Multi-scale Hierarchical Vision Transformer with Cascaded Attention Decoding for Medical Image Segmentation

Transformers have shown great success in medical image segmentation. However, transformers may exhibit a limited generalization ability due to the underlying single-scale self-attention (SA) mechanism. In this paper, we address this issue by introducing a Multi-scale hiERarchical vIsion Transformer (MERIT) backbone network, which improves the generalizability of the model by computing SA at multiple scales. We also incorporate an attention-based decoder, namely Cascaded Attention Decoding (CASCADE), for further refinement of multi-stage features generated by MERIT. Finally, we introduce an effective multi-stage feature mixing loss aggregation (MUTATION) method for better model training via implicit ensembling. Our experiments on two widely used medical image segmentation benchmarks (i.e., Synapse Multi-organ, ACDC) demonstrate the superior performance of MERIT over state-of-the-art methods. Our MERIT architecture and MUTATION loss aggregation can be used with downstream medical image and semantic segmentation tasks.Comment: 19 pages, 4 figures, MIDL 202

G-CASCADE: Efficient Cascaded Graph Convolutional Decoding for 2D Medical Image Segmentation

In recent years, medical image segmentation has become an important application in the field of computer-aided diagnosis. In this paper, we are the first to propose a new graph convolution-based decoder namely, Cascaded Graph Convolutional Attention Decoder (G-CASCADE), for 2D medical image segmentation. G-CASCADE progressively refines multi-stage feature maps generated by hierarchical transformer encoders with an efficient graph convolution block. The encoder utilizes the self-attention mechanism to capture long-range dependencies, while the decoder refines the feature maps preserving long-range information due to the global receptive fields of the graph convolution block. Rigorous evaluations of our decoder with multiple transformer encoders on five medical image segmentation tasks (i.e., Abdomen organs, Cardiac organs, Polyp lesions, Skin lesions, and Retinal vessels) show that our model outperforms other state-of-the-art (SOTA) methods. We also demonstrate that our decoder achieves better DICE scores than the SOTA CASCADE decoder with 80.8% fewer parameters and 82.3% fewer FLOPs. Our decoder can easily be used with other hierarchical encoders for general-purpose semantic and medical image segmentation tasks.Comment: 13 pages, IEEE/CVF Winter Conference on Applications of Computer Vision (WACV 2024

Typing of Erwinia Chrysanthemi isolated from josapine pineapple in Malaysia using antimicrobial susceptibility, plasmid profiles, ERIC-PCR and RFLP analysis

Ninety one leaf samples of Josapine pineapple cultivar (Kelantan, n=8; Pahang, n=20; Perak, n=11; Sabah, n=15; Johor, n=37) showing symptoms of heart rot disease were collected to determine the incidence of Erwinia chrysanthemi. Sixteen strains of E. chrysanthemi were isolated from 13 leaf samples from Pahang (n=4), Sabah (n=2) and Johor (n=7). All of the E. chrysanthemi strains displayed resistance to bacitracin with two strains showing resistance to sulfamethoxazole. None of the E. chrysanthemi strains were resistant toward ampicillin, carbenicillin, cephalothin, ceftriaxone, cefuroxime, gentamicin, kanamycin, nalidixic acid, penicillin G, streptomycin and tetracycline. All of the E. chrysanthemi strains were plasmidless. The dendrogram generated from the ERIC-PCR fingerprinting showed that the E. chrysanthemi strains formed 4 clusters and 7 single isolates at 80% similarity level. The restriction fragment length polymorphism (RFLP) analysis for 16 strains of E. chrysanthemi with HinfI and HaeIII endonuclease, 2 and 4 restriction profiles were obtained, respectively. The combinations of the four techniques were able to differentiate the 16 E. chrysanthemi strains into 14 genome types, suggesting a wide diversity of strains examined. ERICPCR fingerprinting method is found to be more discriminating and useful for the determination of the E. chrysanthemi strains relatedness

Lagrangian Reachtubes: The Next Generation

We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball's volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the "wrapping effect" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG's superior performance compared to LRT, CAPD, and Flow*.Comment: 12 pages, 14 figure

Prevalence of Salmonella in broilers at retail outlets, processing plants and farms in Malaysia

A study was conducted to estimate the prevalence of Salmonella among broilers retailed at wet-markets and processing plants. Litter and feed samples obtained from both broiler and breeder farms were also examined for Salmonella. A total of 158 out of 445 (35.5%) and 52 out of 104 (50.0%) broiler carcasses obtained from wet-markets and processing plants were contaminated with Salmonella, respectively. Salmonella was isolated from 14 out of 98 (14.3%) samples of intestinal content. Litter samples from broiler and breeder farms were positive for Salmonella, 8/40 (20%) and 2/10 (20%), respectively. Salmonella isolates (230) belonging to 15 different serovars were isolated. Predominant serovars were S. enteritidis, S. muenchen, S. kentucky and S. blockley

The Use of Mechanical Suture in the Treatment of Hirschsprung's Disease: Experience of 17 Cases

Rezumat Folosirea suturii mecanice în tratamentul bolii Hirschsprung -o experienåã de 17 cazuri Introducere: Boala Hirschsprung sau megacolonul congenital este o malformaåie caracterizatã prin absenåa celulelor ganglionare la nivelul intestinului distal. Zona de aganglionozã cuprinde cel mai frecvent rectul aei o parte din sigmoid, dar ea se poate întinde pe lungimi variabile. În ultimii ani tratamentul chirurgical al acestei afecåiuni s-a îmbunãtãåit semnificativ, atât prin introducerea procedeului de coborare a colonului pe cale perinealã transanalã, asistat sau nu laparoscopic, cât aei prin dezvoltarea tehnicilor de sutura mecanicã. Scop: Lucrarea îaei propune sã analizeze rezultatele noastre cu procedeul Duhamel modificat, folosind sutura mecanicã pentru realizarea anastomozei colo-rectale latero-laterale. Materiale aei metode: Au fost analizate 17 cazuri de megacolon congenital operate în departamentul nostru între anii 2007 aei 2011 de cãtre aceeaaei echipa de chirurgi pediatri, utilizând tehnica Duhamel modificatã prin folosirea suturii mecanice. Este prima serie operatã în åara noastrã prin acest procedeu. 2 pacienåi au avut forma întinsã de aganglionozã colonicã, 2 au prezentat segment aganglionotic scurt, iar 13 pacienåi au avut forma comunã a bolii. Am urmãrit detaliile tehnice, perioada de spitalizare, precum aei complicaåiile imediate aei cele la distanåã. Rezultate: Perioada medie de spitalizare a fost de 9 zile. Mortalitatea în seria analizatã a fost 0. Complicaåiile postoperatorii au constat în: rectoragie minorã (5 cazuri), ocluzie prin bride (1 caz) aei sindrom subocluziv determinat de prezenåa unui sept restant cu dezvoltarea consecutivã de fecalom în ampula rectalã (4 cazuri). Toate cazurile operate din aceastã serie au avut în final o continenåã de materii fecale foarte bunã. Concluzii: În opinia noastrã folosirea dispozitivelor de suturã mecanicã în cadrul unui procedeu Duhamel într-o singurã etapa este deosebit de beneficã, atât în ceea ce priveaete rata complicaåiilor, cât aei durata de spitalizare. Aceastã tehnicã este sigurã, simplã aei eficientã. Cuvinte cheie: boala Hirschsprung, procedeul Duhamel, dispozitive de sutura mecanicã Abstract Introduction: Hirschsprung's disease, or congenital megacolon, is a malformation characterised by the absence of ganglion cells in the distal bowel. Most often, the aganglionic segment includes the rectosigmoid, but it may extend proximally to variable length. In late years, significant improvements regarding the surgical treatment of Hirschsprung's disease were made, by the introduction of both one-stage transanal endorectal pull-through -laparoscopically assisted or not -and mechanical suture devices Aim: The purpose of this paper is to analyse our results with modified Duhamel procedure by using mechanical sutures for construction of a side-to-side colo-rectal anastomosis Materials and Method: We analysed 17 congenital megacolon cases operated in our department between 2007 -2011 by the same pediatric surgical team, using the modified Duhamel technique performed with mechanical suture. It is the first series operated in our country using this procedure. 2 patients had a long colonic aganglionosis, 2 patients had a short aganglionotic segment and 13 patients had the common form Results: The mean hospitalization period was of 9 days. Mortality in our series was 0. Postoperative complications consisted in minor bleeding (5 cases), adhesions and mechanical occlusion (1 case), and subocclusive symptoms due to remnant septum with subsequent fecaloma formation in the rectal ampula (4 cases). All of our operated cases had consequently a very good fecal continence. Conclusions: We think that usage of mechanical suture devices in a single stage Duhamel procedure is extremely beneficial regarding both complication rate and hospitalisation time. This technique is safe, simple and efficient

Identification and characterization of actinomycetes for biological control of bacterial wilt of Ralstonia solanacearum isolated from tomato

Five actinomycetes which showed antimicrobial activity towards Ralstonia solanacearum were identified using specific polymerase chain reaction (PCR) of 16S rDNA gene. Strain C1 and Strain G10 were identified as Streptomyces aureofaciens and S. roseoflavus respectively. All actinomycetes were then characterized using antimicrobial and extracellular enzyme activity, metabolic and restriction fragment length polymorphism (RFLP) profiles. Strain A3 showed positive reaction to three bacteria namely Xanthomonas campestris, Staphylococcus aureus and Listeria monocytogenes. Strain C1 and Strain I15 showed positive reaction towards S. aureus and X. campestris respectively. Strains A3, C1 and I15 were able to metabolize xylan and cellulose, while Strain G10 and Strain L8 were able to use all substrates (xylan, mannan and cellulose) as carbon sources. All the Streptomyces strains were positive towards more than 25 carbon sources and can be differentiated into five distinct strains. These results were consistent and confirmed with DNA analysis of RFLP profiles. The specific amplification of 16S rDNA PCR restriction profiles for the strains using three restriction endonucleases, resulted two restriction profiles produced from the digested 16S rDNA product using HaeIII (H1–H2) and HinfI (Hf1–Hf2), while PstI produced three restriction profiles (P1–P3). No profiles were produced from restriction endonuclases of XbaI, SpeI and BamHI