A Review on Brain Tumor Segmentation Based on Deep Learning Methods with Federated Learning Techniques

Brain tumors have become a severe medical complication in recent years due to their high fatality rate. Radiologists segment the tumor manually, which is time-consuming, error-prone, and expensive. In recent years, automated segmentation based on deep learning has demonstrated promising results in solving computer vision problems such as image classification and segmentation. Brain tumor segmentation has recently become a prevalent task in medical imaging to determine the tumor location, size, and shape using automated methods. Many researchers have worked on various machine and deep learning approaches to determine the most optimal solution using the convolutional methodology. In this review paper, we discuss the most effective segmentation techniques based on the datasets that are widely used and publicly available. We also proposed a survey of federated learning methodologies to enhance global segmentation performance and ensure privacy. A comprehensive literature review is suggested after studying more than 100 papers to generalize the most recent techniques in segmentation and multi-modality information. Finally, we concentrated on unsolved problems in brain tumor segmentation and a client-based federated model training strategy. Based on this review, future researchers will understand the optimal solution path to solve these issues

Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15

Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment

Effectiveness of Azorizobial strains isolated from Sesbania rostrata

Isolation and characterization of bacteria were done from the root nodules of African dhaincha (Sesbania rostrata) to study their effects on growth parameters, nodulation and N uptake. Five isolates were obtained from African dhaincha and were identified them as Azorhizobium on the basis of their colony, morphological and biochemical characteristics. A pot experiments were conducted by using 6 treatments, comprising 5 isolates of Azorhizobium and an uninoculated control to evaluate the performance of the isolates. The experiment was laid out in a Completely Randomized Design (CRD) with 3 replications. Azorhizobium inoculation gave statistically higher values for all the parameters viz. plant height, leaf number plant-1, dry weight of nodule, dry matter yield, N content of shoot (%), total N in shoot over uninoculated control (T1). The highest values of all the parameters except stem nodule number plant-1, root nodule weight and N content of shoot were obtained with the treatment T5 (SR-R-4). The total dry matter yield of African dhaincha ranged from 1217 mg plant-1 noted in the uninoculated control (T1) to 5483 mg plant-1 recorded for the treatment T5 (SR-R-4). The total dry matter yields were increased by 138, 219, 273, 351 and 290 % over control (T1) due to T2 (SR-R-1), T3 (SR-R-2), T4 (SR-R-3), T5 (SR-R-4) and T6 (SR-R-5), respectively. Total N uptake by shoot of African dhaincha had been influenced significantly due to different treatments and the corresponding percent increases in total N uptake by shoot were 359, 496, 429, 629, and 490, respectively, due to T2 (SR-R-1), T3 (SR-R-2), T4 (SR-R-3), T5 (SR-R-4) and T6 (SR-R-5).Considering all the growth parameters, nodulation, dry matter yield, N content of shoot and total N uptake by shoot, it may be inferred that the isolate SR-R-4 showed the best performance. The isolates SR-R-5 and SR-R-3 were also found promising. [Fundam Appl Agric 2018; 3(3.000): 537-544

Evaluation of Commercial Disinfectants against Staphylococcus lentus and Micrococcus spp. of Poultry Origin

Introduction. Effective sanitation strategies for poultry farms require an appropriate selection of the disinfectant based on the contaminants present and their sensitivity to the disinfectants. Aim. The current study investigated the prevalence of streptococci/micrococci in poultry farms of Bangladesh and the efficacy of commercial disinfectants (Savlon, Lysol, Quatovet, Virkon S, and Virocid) along with alcohol against these pathogens to adopt appropriate strategies. Materials and Methods. Conventional approaches and the 16S rRNA gene sequencing were performed to confirm the isolates at the species level along with microtiter biofilm assay to determine their biofilm-forming ability. Efficacy of the disinfectants was tested against those isolates using agar well diffusion and minimum inhibitory concentration (MIC) test by broth dilution method using different dilutions of the disinfectants. Results. Staphylococcus lentus (n = 32), Micrococcus luteus (n = 7), and Micrococcus aloeverae (n = 4) were confirmed among 102 presumptively screened streptococci/micrococci isolates from 43 samples. No single disinfectant showed equally high efficacy against all three bacterial species in agar well diffusion test, although Virocid showed the lowest MIC against all three of them. Lysol was least effective among the commercial disinfectants by both MIC and diffusion method, although each commercial disinfectant was more effective than alcohol. Considering both the average diameter of the inhibition zones and the MIC values, efficacy can be interpreted as Virocid > Quatovet > Savlon > Virkon S > Lysol. Although the efficacy decreased with decreasing concentration, the disinfectants retained a satisfactory level of efficacy at 50% concentration. Among test pathogens, M. aloeverae was the most sensitive to the disinfectants and the weakest biofilm producers, whereas 4/14 S. lentus and 1/5 M. luteus were strong biofilm producers, which may cause more reduction in the efficacy in environmental conditions. Conclusion. As no ideal disinfectant was found in the study, the efficacy of the disinfectants should be routinely evaluated and validated to ensure the sanitation standards in the poultry sector

Circulating Phylotypes of White Spot Syndrome Virus in Bangladesh and Their Virulence

White Spot Syndrome Virus (WSSV) has emerged as one of the most prevalent and lethal viruses globally and infects both shrimps and crabs in the aquatic environment. This study aimed to investigate the occurrence of WSSV in different ghers of Bangladesh and the virulence of the circulating phylotypes. We collected 360 shrimp (Penaeus monodon) and 120 crab (Scylla sp.) samples from the south-east (Cox’s Bazar) and south-west (Satkhira) coastal regions of Bangladesh. The VP28 gene-specific PCR assays and sequencing revealed statistically significant (p 9 copies of WSSV per mL resulted in a median LT50 value of 73 h and 75 h, respectively. The in vivo trial showed higher mean Log WSSV copies (6.47 ± 2.07 per mg tissue) in BD1-challenged shrimp PL compared to BD2 (4.75 ± 0.35 per mg tissue). Crabs infected with BD1 and BD2 showed 100% mortality within 48 h and 62 h of challenge, respectively, with mean Log WSSV copies of 12.06 ± 0.48 and 9.95 ± 0.37 per gram tissue, respectively. Moreover, shrimp antimicrobial peptides (AMPs), penaeidin and lysozyme expression were lower in the BD1-challenged group compared to BD2 challenged shrimps. These results collectively demonstrated that relative virulence properties of WSSV based on mortality rate, viral load and expression of host immune genes in artificially infected shrimp PL could be affected by single aa substitution in VP28

Circulatory white spot syndrome virus in South-West region of Bangladesh from 2014 to 2017: molecular characterization and genetic variation

Abstract White Spot Syndrome Virus (WSSV), the etiological agent of White Spot Disease (WSD) is a major impediment for shrimp aquaculture in the worldwide. A critical threshold level of WSSV load in infected shrimp is an important trait for disease manifestation and WSSV transmission in cultured shrimp and subsequently make outbreaks. The present study investigated 120 naturally infected cultured shrimp samples by SYBR Green based qPCR assay for WSD diagnosis and quantification of WSSV load. Among them, 94 samples resulted a variable count of WSSV load ranging from 2.1 × 108 to 2.64 × 1014 copies/g of shrimp tissue. The severity of WSSV infection was assessed based on the established critical threshold load of WSSV in shrimp tissue. Compared to the established critical threshold value of WSSV load in shrimp tissue, our findings showed the horrifying scenario of the severity of WSSV infection in cultured shrimps of Bangladesh that was found to be above the critical limit to initiate an outbreak in the Bangladeshi shrimp aquaculture industry. The latest phylogenetic pattern was altered from the former monophyletic history among WSSVs of Bangladesh due to a variation at 500th nucleotide of VP28 coding gene. Viruses characterized from recent outbreaks in 2015 and 2017 displayed amino acid substitution at position 167 (G→E) on the surface of VP28 protein which has demonstrated the probable replacement of indigenous virus pool. Therefore, it is imperative to take initiative for the management and prevention of WSSV outbreak to sustain shrimp aquaculture in South-West region of Bangladesh

MOESM2 of Circulatory white spot syndrome virus in South-West region of Bangladesh from 2014 to 2017: molecular characterization and genetic variation

Additional file 2: Figure S1. Wu-Kabat protein variability index showed 13 unique mutations as observed from the protruded peaks’ positioned along with the amino acid residue of VP28 protein