Development of a compressed FCN architecture for semantic segmentation using Particle Swarm Optimization.

Researchers have adapted the conventional deep learning classification networks to generate Fully Conventional Networks (FCN) for carrying out accurate semantic segmentation. However, such models are expensive both in terms of storage and inference time and not readily employable on edge devices. In this paper, a compressed version of VGG16-based Fully Convolution Network (FCN) has been developed using Particle Swarm Optimization. It has been shown that the developed model can offer tremendous saving in storage space and also faster inference time, and can be implemented on edge devices. The efficacy of the proposed approach has been tested using potato late blight leaf images from publicly available PlantVillage dataset, street scene image dataset and lungs X-Ray dataset and it has been shown that it approaches the accuracies offered by standard FCN even after 851× compression.

Population dynamics of Citrus tristeza virus (CTV) in single aphid-transmitted sub-isolates of the South African GFMS12 isolate.

Grapefruit trees in South Africa have been cross protected against severe stem pitting genotypes of Citrus tristeza virus (CTV) since the 1920s using a mild strain initially called 'Nartia' but later referred to as grapefruit mild strain 12 (GFMS12). In the current study, the GFMS12 isolate was used as the source for single aphid transmissions (SAT) using Toxoptera citricida, commonly called the brown citrus aphid (BrCA). The BrCA-transmitted CTV sub-isolates were analyzed by the heteroduplex mobility assay (HMA), serological assays, genetic marker analysis (GMA), and selected sub-isolates were biologically indexed. Reverse transcription PCR of genomic regions was conducted using universal primers followed by cloning the PCR products, HMA and sequence analysis; nine genotypes of CTV were identified in the complex of GFMS12, including both severe and mild genotypes. A single BrCA transmitted up to six CTV genotypes simultaneously in one sub-isolate. The HMA was found to be a rapid, reliable tool for the identification of genotypes and can be useful in the development of CTV management strategies and budwood certification programs.

Advances in Nanotechnology as a Potential Alternative for Plant Viral Disease Management.

Plant viruses cause enormous losses in agricultural production accounting for about 47% of the total overall crop losses caused by plant pathogens. More than 50% of the emerging plant diseases are reported to be caused by viruses, which are inevitable or unmanageable. Therefore, it is essential to devise novel and effective management strategies to combat the losses caused by the plant virus in economically important crops. Nanotechnology presents a new tendency against the increasing challenges in the diagnosis and management of plant viruses as well as plant health. The application of nanotechnology in plant virology, known as nanophytovirology, includes disease diagnostics, drug delivery, genetic transformation, therapeutants, plant defense induction, and bio-stimulation; however, it is still in the nascent stage. The unique physicochemical properties of particles in the nanoscale allow greater interaction and it may knock out the virus particles. Thus, it opens up a novel arena for the management of plant viral diseases. The main objective of this review is to focus on the mounting collection of tools and techniques involved in the viral disease diagnosis and management and to elucidate their mode of action along with toxicological concerns.

Fluorescence in situ hybridisation in Carnoy's fixed tonsil tissue.

Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy's fixative, accordingly limiting its application to investigate the pathogenesis of tonsillar hyperplasia. Tonsil tissue from 24 children undergoing tonsillectomy for either recurrent tonsillitis or sleep-disordered breathing were obtained during a previous study. The specificity of each of the five FISH probes (Fusobacterium spp., Bacteroides spp., Streptococcus spp., Haemophilus influenzae and Pseudomonas spp.) were successfully optimised using pure and mixed bacterial isolates, and in Carnoy's fixed tonsil tissue. Bacteroides spp. were present in 100% of patients with microcolonies. In comparison, the prevalence of Fusobacterium spp. was 93.8%, Streptococcus spp. 85.7%, H. influenzae 82.35% and Pseudomonas spp. 76.5%. Notable differences in the organisation of bacterial taxa within a single microcolony were also observed. This is the first study to establish a robust FISH protocol identifying multiple aerobic and anaerobic bacteria in Carnoy's fixed tonsil tissue. This protocol provides a strong foundation for combining histological and microbiological analyses of Carnoy's fixed tonsil samples. It may also have important implications on the analysis of microorganisms in other human tissues prepared using the same techniques.

A multiplex polymerase chain reaction for the simultaneous detection of the virus and satellite components associated with cotton leaf curl begomovirus disease complex.

Cotton leaf curl disease (CLCuD) is caused by a complex of several whiteflies (Bemisia tabaci Genn.)-transmitted begomovirus species, Cotton leaf curl Multan virus (CLCuMuV), Cotton leaf curl Kokhran virus (CLCuKoV) and Cotton leaf curl Alabad virus (CLCuAlV) by individual of mixed infection, associated with Cotton leaf curl Multan betasatellite (CLCuMB) and several alphasatellites. The disease causes major economic losses in cotton in the Indian subcontinent. For monitoring of epidemiology and development of management strategies of CLCuD, a quick, sensitive and effective method capable of detecting all the begomovirus, betasatellite and alphasatellite components associated with CLCuD is required. With this objective, a multiplex polymerase chain reaction (mPCR) assay was developed for the simultaneous detection of these three viral components associated with CLCuD of cotton. Primers for each component were designed based on the retrieved reference sequences from the GenBank. Each pair of primers, designed for each of the respective component, was evaluated for its sensitivity and specificity in both the component-specific simplex polymerase chain reaction (sPCR) and mPCR assay. This report identified three viral component-specific pairs of primers which, in all combinations, amplified simultaneously the CP gene (780 nts) of the begomovirus, the ßC1gene (375 nts) of the betasatellite and the Rep gene (452 nts) of the alphasatellite associated with CLCuD in the mPCR assays. The amplified products specific to each component produced by these assays were identified based on their amplicon sizes, and the identities of the viral components amplified were confirmed by cloning and sequencing the amplicons obtained in the mPCR. The mPCR assay was validated using naturally CLCuD-affected cotton plants of the fields. This assay will be useful for rapid detection of CLCuD-associated begomovirus, betasatellite and alphasatellite DNA in field samples, extensive resistance screening in resistance breeding programme, and also monitoring epidemiology for detection of virus and its components when symptoms are mild or absent in the plant.

The in vitro efficacy of neutral electrolysed water and povidone-iodine against CRS-associated biofilms.

BACKGROUND: Despite best medical and surgical practice, some cases of chronic rhinosinusitis (CRS) can remain recalcitrant. Bacterial biofilms have been associated with the recalcitrance of sinonasal inflammation. Biofilms are highly resistant to commonly prescribed antibiotics. Accordingly, more effective antimicrobial treatment options are needed to treat refractory CRS. The aim of this study was to determine the in vitro efficacy of neutral electrolysed water (NEW) and povidone-iodine (PVI) against CRS-associated Staphylococcus aureus biofilms. METHODS: Mature S. aureus biofilms were grown in a Centre for Disease Control (CDC) biofilm reactor. The antimicrobial activity of NEW, PVI and doxycycline was determined for both planktonic and biofilm cultures of a clinical S. aureus isolate using minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and minimum biofilm eradication concentration (MBEC) assays. RESULTS: MICs and MBCs were determined for all antimicrobials. MBC values were similar to MICs for both antiseptics, but doxycycline MBCs were significantly higher than the associated MICs. Biofilms were highly resistant to NEW and doxycycline. The MBEC for doxycycline was between 500 and 1000 Â#181;g/mL. NEW was ineffective against biofilms and no MBEC could be determined. In contrast, a concentration of 10% of the commercial PVI solution (10 mg/mL PVI) led to effective eradication of mature biofilms. CONCLUSION: In this study, only PVI showed promising antibiofilm activity at physiological concentrations. The in vivo efficacy of PVI warrants further investigation of its potential as a treatment for recalcitrant CRS.

The sinonasal mycobiota in chronic rhinosinusitis and control patients.

BACKGROUND: While bacterial associations with chronic rhinosinusitis (CRS) are increasingly well described, fewer studies have examined the fungal component of the sinonasal microbiota. Here we present a study of the sinonasal mycobiota in a cohort of 144 patients (106 patients with CRS and 38 controls). METHODOLOGY: Fungal communities were characterised by analysis of mucosal swab samples of the left and right middle meatuses via ITS2 marker amplicon sequencing on the Illumina MiSeq platform. Fungal associations with previously published bacterial community and inflammatory cytokine and cell data for this cohort (collected at the same intra-operative time point) were also investigated. RESULTS: Malassezia spp. were ubiquitous and often highly predominant. Season of sampling explained more of the variability in the data than any of the clinical parameters. The predominant Malassezia sp. was distinct in patients with cystic fibrosis compared to those without. However, distinctions in the mycobiota were not evident between any other patient groupings assessed, and few fungal-bacterial or fungal-inflammatory associations were observed. CONCLUSIONS: This study confirms the prominent place of Malassezia spp. within the upper respiratory tract. Overall, few distinctions between patient groups were evident, and these data lend further support to the hypothesis that fungal community types may have no direct causative association with idiopathic CRS. Additional studies incorporating a broader array of inflammatory markers are required to assess whether these ubiquitous fungi nonetheless play an exacerbating role in some sensitive individuals.

Moving beyond descriptions of diversity: clinical and research implications of bacterial imbalance in chronic rhinosinusitis.

Chronic rhinosinusitis (CRS) is a debilitating disease which affects 5-16% of the general population and involves long-term inflammation of the sinonasal cavity. While microbial involvement in the pathogenesis of CRS has long been suspected, the exact role of microbes remains unclear. Recent application of cultivation-independent, molecular methods has provided much new information, taking advantage of developments in both laboratory- and bioinformatics-based analyses. The aim of this mini-review is to present a variety of available bioinformatics approaches, such as data classification techniques and network analyses, with proven applications in other aspects of human microbiome health and disease research. The uses of molecular techniques in the clinical setting are still in its infancy, but these tools can further our understanding of microbial imbalance during chronic disease and help guide effective patient treatment. The mini-review emphasises ways in which CRS bacterial gene-targeted sequencing data can progress beyond descriptive summaries and toward unlocking the mechanisms by which bacterial communities can be markers for sinus health.

Toll-like receptor activation by sino-nasal mucus in chronic rhinosinusitis.

BACKGROUND: The sino-nasal disease chronic rhinosinusitis (CRS) is primarily an inflammatory condition that manifests in several ways. However, the aetiology of this complex disease is poorly understood. The aim of this study was to explore the association between toll-like receptor (TLR) activation, host immune response and sino-nasal mucus in healthy and diseased patients. METHODS: The activation of TLR2/1 and TLR4 by sino-nasal mucus from 26 CRS patients and 10 healthy controls was measured. In addition, 7 inflammatory cytokines, bacterial community composition and bacterial abundance within the sino-nasal mucus were measured using molecular and diagnostic tools. RESULTS: TLR activity was observed in 9/36 samples, including 2 healthy controls. There was a strong, positive correlation between members of the Gammaproteobacteria (Haemophilus, Enterobacter, Pseudomonas) and TLR2/1 and TLR4 activity. Bacterial abundance and cytokine (tumour necrosis factor) abundance were also positively correlated with TLR activity. CONCLUSIONS: These findings suggest that a small proportion (20-30%) of individuals in each sub-group are more predisposed to TLR activity, which may be related to bacterial composition, diversity and abundance in the sinuses.

The in vitro effect of xylitol on chronic rhinosinusitis biofilms.

INTRODUCTION: Biofilms have been implicated in chronic rhinosinusitis (CRS) and may explain the limited efficacy of antibiotics. There is a need to find more effective, non-antibiotic based therapies for CRS. This study examines the effects of xylitol on CRS biofilms and planktonic bacteria. METHODS: Crystal violet assay and spectrophotometry were used to quantify the effects of xylitol (5% and 10% solutions) against Staphylococcus epidermidis, Pseudomonas aeruginosa, and Staphylococcus aureus. The disruption of established biofilms, inhibition of biofilm formation and effects on planktonic bacteria growth were investigated and compared to saline and no treatment. RESULTS: Xylitol 5% and 10% significantly reduced biofilm biomass (S. epidermidis), inhibited biofilm formation (S. aureus and P. aeruginosa) and reduced growth of planktonic bacteria (S. epidermidis, S. aureus, and P. aeruginosa). Xylitol 5% inhibited formation of S. epidermidis biofilms more effectively than xylitol 10%. Xylitol 10% reduced S. epidermidis planktonic bacteria more effectively than xylitol 5%. Saline, xylitol 5% and 10% disrupted established biofilms of S. aureus when compared with no treatment. No solution was effective against established P. aeruginosa biofilm. CONCLUSIONS: Xylitol has variable activity against biofilms and planktonic bacteria in vitro and may have therapeutic efficacy in the management of CRS.

Al2O3 influence on structural, elastic, thermal properties of Yb(3+) doped Ba-La-tellurite glass: evidence of reduction in self-radiation trapping at 1µm emission.

Ba-La-tellurite glasses doped with Yb(3+) ions have been prepared through melt quenching technique by modifying their composition with the inclusion of varied concentration of Al2O3 to elucidate its effects on glass structural, elastic, thermal properties and Yb(3+) ion NIR luminescence performance. The FTIR spectral analysis indicates Al2O3 addition is promoting the conversion of BOs from NBOs which have been generated during the process of depolymerisation of main glass forming TeO4 units. The elastic properties of the glass revealed an improved rigidity of the glass network on addition of Al2O3. In concurrence to this, differential thermal analysis showed an increase in glass transition temperature with improved thermal stability factor. Also, Yb(3+) fluorescence dynamics demonstrated that, Al2O3 inclusion helps in restraining the detrimental radiation trapping of ∼1µm emission.

Comparison of Manning, Rome I, II, and III, and Asian diagnostic criteria: report of the Multicentric Indian Irritable Bowel Syndrome (MIIBS) study.

BACKGROUND: Attempts to diagnose and subtype irritable bowel syndrome (IBS) by symptom-based criteria have limitations, as these are developed in the West and might not be applicable in other populations. OBJECTIVES: This study aimed to compare different criteria for diagnosing and subtyping of IBS in India. METHOD: Manning's and the Rome I, II, and III criteria as well as the Asian criteria were applied to 1,618 patients (from 17 centers in India) with chronic lower gastrointestinal (GI) symptoms with no alarm features and negative investigations. RESULTS: Of 1,618 patients (aged 37.5 [SD 12.6] years; 71.2% male), 1,476 (91.2%), 1,098 (67.9%), 649 (40.1%), 849 (52.5%), and 1,206 (74.5%) fulfilled Manning's, Rome I, II, and III, and the Asian criteria, respectively. The most common reason for not fulfilling the criteria was absence of the following symptoms: "more frequent stools with onset of pain," "loose stool with onset of pain," "relief of pain with passage of stool," "other abdominal discomfort/bloating," and, in a minority, not meeting the duration criterion of 3 months/12 weeks. By stool frequency, constipation-predominant IBS (<3 stools/week) was diagnosed in 319 (19.7%), diarrhea-predominant IBS (>3 stools/day) in 43 (2.7%), and unclassified in 1,256 (77.6%). By Bristol stool form, constipation, diarrhea, and unclassified were diagnosed in 655 (40.5%), 709 (43.8%), and 254 (15.7%) patients, respectively. By their own perception, 462 (28.6%), 541 (33.4%), and 452 (27.9%) patients reported constipation-predominant, diarrhea-predominant, and alternating types, respectively. CONCLUSION: By Manning's and the Asian criteria, a diagnosis of IBS was made frequently among Indian patients with chronic functional lower GI symptoms with no alarm features; the Rome II criteria gave the lowest yield. By the stool frequency criteria, a majority of patients had unclassified pattern, unlike by the stool form and patients' perception of their symptoms.

Distribution, genetic diversity and recombination analysis of Citrus tristeza virus of India.

Citrus tristeza virus (CTV) isolates representing all the citrus-growing geographical zones of India were analyzed for nucleotide sequence of the 5'ORF1a fragments of the partial LProI domain and for the coat protein (CP) gene. The nucleotide sequences were compared with previously reported Indian and CTV genotypes from GenBank. The Indian isolates had 80-99 % sequence identity for the 5'ORF1a and 89-99 % identity for the CP genes. In phylogenetic tree analysis, all the Indian and previously reported isolates segregated into eight clades or groups for the 5'ORF1a region. Indian CTV isolates were clustered in all the clades, four of which, D13, K5, BAN-1, and B165, consisted of only Indian isolates. Phylogenetic tree analysis of the CP genes resulted in seven clades. Indian CTV isolates clustered in six of them, and clades I and VI consisted of only Indian isolates. In the phylogenetic tree the Indian CTV isolates clustered in different groups regardless their geographical origin. Diversities in CTV isolates within individual citrus farms were highlighted. Because incongruent phylogenetic relationships were observed for both of the genomic regions, 5'ORF1a and CP gene, recombination analysis was performed using program RDP3. This analysis detected potential recombination events among the CTV isolates which involved exchange of sequences between divergent CTV variants. The SplitsTree analysis showed evidence of phylogenetic conflicts in evolutionary relationships among CTV isolates.

Product quality of parenteral vancomycin products in the United States.

In response to concerns raised about the quality of parenteral vancomycin products, the U.S. Food and Drug Administration (FDA) is investigating the product quality of all FDA-approved parenteral vancomycin products available in the United States. Product quality was evaluated independently at two FDA Office of Testing and Research (FDA-OTR) sites. In the next phase of the investigation, being done in collaboration with the National Institute of Allergy and Infectious Diseases, the in vivo activity of these products will be evaluated in an appropriate animal model. This paper summarizes results of the FDA investigation completed thus far. One site used a validated ultrahigh-pressure liquid chromatography method (OTR-UPLC), and the second site used the high-performance liquid chromatography (HPLC) method for related substances provided in the British Pharmacopeia (BP) monograph for vancomycin intravenous infusion. Similar results were obtained by the two FDA-OTR laboratories using two different analytical methods. The products tested had 90 to 95% vancomycin B (active component of vancomycin) by the BP-HPLC method and 89 to 94% vancomycin by OTR-UPLC methods. Total impurities were 5 to 10% by BP-HPLC and 6 to 11% by OTR-UPLC methods. No single impurity was >2.0%, and the CDP-1 level was ≤ 2.0% across all products. Some variability in impurity profiles of the various products was observed. No adverse product quality issues were identified with the six U.S. vancomycin parenteral products. The quality parameters of all parenteral vancomycin products tested surpassed the United States Pharmacopeia acceptance criteria. Additional testing will characterize in vivo performance characteristics of these products.

Delayed puberty: experience of a tertiary care centre in India.

BACKGROUND: Pubertal delay can be a manifestation of a wide variety of diseases, the proportions of which may vary between developing and industrialised countries. OBJECTIVE: A retrospective study was undertaken to investigate the aetiology of delayed puberty in northern India. SUBJECTS AND METHODS: Follow-up records of patients with delayed puberty presenting to the endocrine clinic between 2003 and 2007 were analysed. RESULTS: Forty-two patients (19 boys, 23 girls, age range 14-27 y) of 46 who initially presented had complete evaluation. The main causes of pubertal delay were chronic systemic illnesses (16), e.g. malnutrition, anaemia and chronic infections, hormone deficiencies (11), hypergonadotrophic hypogonadism (7) and constitutional delay (6). While the majority of girls (11/23) were found to have underlying systemic disorders, endocrinopathies (6/19) were the major causes of pubertal delay in boys. CONCLUSION: Chronic systemic illnesses are the major cause of pubertal delay in developing countries. Social awareness and education leading to early detection and treatment can prevent pubertal delay in a large proportion of cases.

Molecular characterization of Citrus tristeza virus isolates from the Northeastern Himalayan region of India.

Citrus tristeza virus (CTV) isolates from the Darjeeling hills of the Northeastern Himalayan region of India were characterized by biological indexing, multiple molecular marker (MMM) analysis, heteroduplex mobility assay (HMA) and sequence analysis. Variability was studied using the CP gene and a 5' ORF1a fragment of the CTV genome. HMA and sequence analysis of the 5' ORF1a fragment classified Darjeeling isolates into two groups, whereas CP gene analysis provided evidence for three different groups. Darjeeling CTV isolates shared nucleotide sequence identities of 89-97 and 91-92% in the 5' ORF1a fragment and CP gene, respectively, suggesting extensive diversity among CTV isolates from this Indian region.

A study of tubular potassium secretory capacity in older patients with hyperkalaemia.

OBJECTIVES: Sustained hyperkalaemia usually indicates a defect in renal potassium (K+) excretion and can be due to severe impairment of glomerular filtration rate (GFR). The major determinants of renal K+ secretion were studied in hyperkalaemic and normokalaemic elderly subjects to probe the major determinants of hyperkalaemia in this setting. DESIGN: The transtubular potassium gradient (TTKG) provides an index of tubular K+ secretion and normally rises in patients with significant hyperkalaemia. Both GFR(glomerular filtration rate) and TTKG were assessed at baseline and repeated after 3 hours following ingestion of 0.1mg of fludrocortisone in three groups. SETTING: An acute general hospital in the West of Ireland. PARTICIPANTS: 23 subjects in total; 8 older patients with unexplained hyperkalaemia (OHK), 8 older patients with normokalaemia (ONK) and 9 young normokalaemic controls (YNK). MEASUREMENTS: The GFR was either measured by 24 hour creatinine clearance estimation or calculated using the Cockroft and Gault formula.TTKG was calculated using a specific formula. RESULTS: Mean baseline TTKG was similar in all three groups and consequently inappropriately low in hyperkalaemic subjects. Three hours post fludrocortisone, the TTKG had risen significantly from baseline levels in the young subjects only (from 7.5+/-0.09 to 11.6+/-1.1, p<0.05). No significant increase was noted in either older group at this timepoint. CONCLUSIONS: The inappropriately low baseline TTKG in the OHK group as well as the absence of a response to fludrocortisone indicate tubular insensitivity to aldosterone. GFR values in both OHK (40.06+/-2.31) and ONK (55.58+/-6.1) groups were significantly lower than those in the YNK group (101.66+/-6.9). In aggregate, these findings indicate that older hyperkalaemic patients typically have both impairment of glomerular filtration and renal tubular K+ secretion and highlights the requirement for vigilance in elderly patients when using medications which interfere with tubular function.

Recurrent lymphocytic hypophysitis in a woman 27 years after subtotal adrenalectomy for hypercortisolism possibly of autoimmune origin.

Lymphocytic hypophysitis commonly occurs in females in peripartum period but several unusual presentations have been reported. Here we report a rare case of recurrent lymphocytic hypophysitis in a woman who had subtotal adrenalectomy for hypercortisolism 27 years back. Polyglandular autoimmune endocrinopathy with an uncommon combination of Cushing's syndrome and recurrent hypophysitis is a strong possibility in this case. Treatment with steroids has been found to have beneficial effect.