T cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach

Gastrointestinal diarrhea is majorly caused by the rotavirus (RV) in the children who generally are under the age group of 5 years. WHO estimates that ∼95% of the children contract RV infection, by this age. The disease is highly contagious; notably in many cases, it is proven fatal with high mortality rates especially in the developing countries. In India alone, an estimated 145,000 yearly deaths occurs due to RV related gastrointestinal diarrhea. WHO pre-qualified vaccines that are available for RV are all live attenuated vaccines with modest efficacy range between 40 and 60%. Further, the risk of intussusceptions has been reported in some children on RV vaccination. Thus, in a quest to develop alternative candidate to overcome challenges associated with these oral vaccines, we chose immunoinformatics approach to design a multi-epitope vaccine (MEV) while targeting the outer capsid viral proteinsVP4 and VP7 of the neonatal strains of rotavirus. Interestingly, ten epitopes, that is, six CD8+T-cells and four CD4+T-cell epitopes were identified which were predicted to be antigenic, non-allergic, non-toxic and stable. These epitopes were then linked to adjuvants, linkers, and PADRE sequences to create a multi-epitope vaccine for RV. The in silico designed RV-MEV and human TLR5 complex displayed stable interactions during molecular dynamics simulations. Further, the immune simulation studies of RV-MEV corroborated that the vaccine candidate emerges as a promising immunogen. Future investigations while performing in vitro and in vivo analyses with designed RV-MEV construct are highly desirable to warrant the potential of this vaccine candidate in protective immunity against different strains of RVs infecting neonates.Communicated by Ramaswamy H. Sarma.

High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics

The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.

Noninvasive Monitoring of Mantle Cell Lymphoma by Immunoglobulin Gene Next-Generation Sequencing in a Phase 2 Study of Sequential Chemoradioimmunotherapy Followed by Autologous Stem-Cell Rescue

Limited information exists in mantle cell lymphoma (MCL) on the performance of next-generation sequencing–based assay of immunoglobulin gene rearrangements for minimal residual disease (MRD) assessment. Posttreatment peripheral blood samples were collected from 16 MCL patients and analyzed with the Adaptive Biotechnologies MRD assay, which identified early molecular relapse. We observed more sensitivity in the cellular versus acellular compartment.

Position paper: recommendations for a digital mammography quality assurance program V4.0

In 2001 the ACPSEM published a position paper on quality assurance in screen film mammography which was subsequently adopted as a basis for the quality assurance programs of both the Royal Australian and New Zealand College of Radiologists (RANZCR) and of BreastScreen Australia. Since then the clinical implementation of digital mammography has been realised and it has become evident that existing screen-film protocols were not appropriate to assure the required image quality needed for reliable diagnosis or to address the new dose implications resulting from digital technology. In addition, the advantages and responsibilities inherent in teleradiology are most critical in mammography and also need to be addressed. The current document is the result of a review of current overseas practice and local experience in these areas. At this time the technology of digital imaging is undergoing significant development and there is still a lack of full international consensus about some of the detailed quality control (QC) tests that should be included in quality assurance (QA) programs. This document describes the current status in digital mammography QA and recommends test procedures that may be suitable in the Australasian environment. For completeness, this document also includes a review of the QA programs required for the various types of digital biopsy units used in mammography. In the future, international harmonisation of digital quality assurance in mammography and changes in the technology may require a review of this document. Version 2.0 represented the first of these updates and key changes related to image quality evaluation, ghost image evaluation and interpretation of signal to noise ratio measurements. In Version 3.0 some significant changes, made in light of further experience gained in testing digital mammography equipment were introduced. In Version 4.0, further changes have been made, most notably digital breast tomosynthesis (DBT) testing and QC have been addressed. Some additional testing for conventional projection imaging has been added in order that sites may have the capability to undertake dose surveys to confirm compliance with diagnostic reference levels (DRLs) that may be established at the National or State level. A key recommendation is that dosimetry calculations are now to be undertaken using the methodology of Dance et al. Some minor changes to existing facility QC tests have been made to ensure the suggested procedures align with those most recently adopted by the Royal Australian and New Zealand College of Radiologists and BreastScreen Australia. Future updates of this document may be provided as deemed necessary in electronic format on the ACPSEM's website ( https://www.acpsem.org.au/whatacpsemdoes/standards-position-papers and see also http://www.ranzcr.edu.au/quality-a-safety/radiology/practice-quality-activities/mqap ).

Clinical outcomes and molecular profile of differentiated thyroid cancers with radioiodine-avid distant metastases

BACKGROUND

Radioiodine (RAI) remains the mainstay of therapy for RAI-avid (RAIA) distant metastatic thyroid carcinoma. We previously demonstrated that RAI-refractory distant metastatic thyroid cancers commonly harbor BRAF mutations. However, the molecular profile of RAIA metastatic thyroid cancer is unknown. Here we describe the mutational profile of thyroid tumors from follicular cell-derived cancer (FCDTC) patients presenting with RAIA distant metastases. In addition, we aimed to correlate clinical outcomes of RAI therapy with clinicopathological factors and tumor mutational status.

METHODS

We retrospectively identified 43 patients with FCDTC who had RAI uptake in the lungs and/or bones on their initial ¹³¹I postablation scan. Primary tumors were genotyped for known mutations in thyroid cancer genes. Structural response to RAI was assessed 6-18 months after each administered RAI activity and at the end of follow-up.

RESULTS

RAS, BRAF, RET/PTC, and PIK3CA mutations were found in 42, 23, 10, and 2% of tumors, respectively, and the remaining 23% were wild type. None of these patients achieved cure after repeat RAI therapies, and most patients (54%) experienced disease progression despite repeated RAI administration. There was an increased prevalence of RAS mutations in these RAIA tumors. RAS-mutant cancers were more likely to concentrate iodine on diagnostic whole body scans. Despite this, structural response to RAI was not influenced by tumor genotype.

CONCLUSIONS

RAIA metastatic FCDTC are overrepresented with RAS mutations, whereas RAI refractory metastatic thyroid cancers are enriched with BRAF mutations. Despite a seemingly preserved ability to concentrate iodine, RAI therapy is ineffective in achieving cure in most patients with RAIA metastatic FCDTC, even in RAS-mutant disease. These poor outcomes may be improved based on recent evidence that pretreatment with MAPK kinase 1/2 inhibitors enhances responses to RAI, particularly in patients with RAS-mutant tumors.

Focal myocardial uptake in a patient with carcinoid tumor by indium-111-pentetreotide on SPECT/CT

We present a case of a 44 year old man with flushing, diarrhea and markedly elevated 24 hour urinary 5-HIAA level, who was referred for an indium-111 pentetreotide study, after the excision of a carcinoid tumor in the terminal ileum. Scan findings revealed focal uptake in the myocardium and liver, suspicious for metastases. Subsequent transthoracic echocardiogram failed to demonstrate a cardiac lesion. Previously, our group has unequivocally demonstrated the usefulness of software fusion of SPECT and CT imaging in the evaluation of a carcinoid metastasizing to the myocardium. This case illustrates that hardware SPECT/CT fusion imaging utilizing indium-111 pentetreotide to evaluate metastatic carcinoid tumors can be useful. In addition, the echocardiogram can yield false negative results, because of a smaller lesion size and the influence of an operator-dependent factor.

Interim recommendations for a digital mammography quality assurance program

In 2001 the ACPSEM published a position paper on quality assurance in screen film mammography which was subsequently adopted as a basis for the quality assurance programs of both the Royal Australian and New Zealand College of Radiologists (RANZCR) and of BreastScreen Australia. Since then the clinical implementation of digital mammography has been realised and it has become evident that existing screen-film protocols were not appropriate to assure the required image quality needed for reliable diagnosis or to address the new dose implications resulting from digital technology. In addition, the advantages and responsibilities inherent in teleradiology are most critical in mammography and also need to be addressed. The current document is the result of a review of current overseas practice and local experience in these areas. At this time the technology of digital imaging is undergoing significant development and there is still a lack of full international consensus about some of the detailed Quality Control tests that should be included in quality assurance (QA) programs. This document describes the current status in digital mammography QA and recommends test procedures that may be suitable in the Australasian environment. For completeness, this document also includes a review of the QA programs required for the various types of digital biopsy units used in mammography. In the future, international harmonisation of digital quality assurance in mammography and changes in the technology may require a review of this document. Accordingly, updates of this document will be provided as deemed necessary in electronic format on the ACPSEM's website (see http://www.acpsem.org.au/au/subgroup/radiology/RadiologySG_index.html).

Comparative evaluation of an II based and a flat panel based cardiovascular fluoroscopy system within a clinical environment

The image quality and dose parameters from a 2004 Siemens Axiom Artis dBC cardiac biplane with flat panel detector were evaluated and compared to similar parameters evaluated for a 1977 Toshiba DPF 2000A biplane cardiac unit with a conventional image intensifier. Image quality assessment was performed with the Westmead test object; using solid water as a patient equivalent absorber. The patient dose comparison of the two systems is based on dose area product meter readings for 1512 patient cases recorded over 6 months following installation of the Siemens flat panel digital unit. The image quality results indicate that: (a) high contrast resolution was better with the digital flat panel unit, (b) low contrast resolution is similar between systems, and (c) the threshold contrast of the flat panel system is the same or inferior to that of the image intensifier system. Input dose to the surface of the flat panel detector showed a strong dependence on field size, similar to the behaviour of image intensifier system. For the most common clinical procedure--Left Heart Study via Judkins--the average total dose area product reading was 64.0 Gy-cm2 against 67.7 Gy-cm2 for the digital and conventional units respectively (p = 0.27) indicating no significant difference in dose performance between the two x-ray machines.

Recommendations for a technical quality control program for diagnostic X-ray equipment

This position paper was produced by a working party set up by the Radiology Special Interest Group of the ACPSEM in 2001. It is designed to give the consensus view of College members in Australia and New Zealand on the nature and frequency of tests which should be performed on diagnostic x-ray equipment to maintain adequate quality control of imaging performance and radiation safety. Tests on mammographic equipment have been excluded having been covered in a previous ACPSEM position paper (Australas Phys Eng Sci Med, 24(3):107-131, 2001). Detailed descriptions of test procedures are not given but it is intended that a series of workbooks should be produced giving College recommended test methods for each imaging modality. The recommendations are produced here in an easy-to-read, tabular form giving the nature and purpose of each test and the implications of non-compliance with regard to image quality and radiation safety.

A study of prevalence of Chlamydia trachomatis infection in women with first trimester pregnancy losses

The study included 125 patients in the first trimester of pregnancy, who were divided into group A (50 control subjects with normal intrauterine pregnancy), Group B (50 patients with spontaneous abortion), group C (25 patients with ectopic pregnancy). All the patients were investigated including routine blood and urine tests and special tests related to the cause of pregnancy loss. The patients were tested for IgG antibodies to Chlamydia trachomatis by ELISA technique and conjunctival smear were tested for presence of inclusion bodies to C. trachomatis. It was concluded that C. trachomatis is one of the important cause of spontaneous abortion and ectopic pregnancy. It is highly prevalent in our population, the prevalence being 10% in group A, 26% in group B, 28% in group C. Conjunctival smear showed presence of inclusion bodies in 0.8% patients. With abortions then risk of lower genital tract chlamydia infection spreading to upper genital tract increases. ELISA for C. trachomatis should be done when women are being investigated for the cause of spontaneous abortion and ectopic pregnancy.

Mutation analysis of oculopharyngeal muscular dystrophy in Hispanic American families

BACKGROUND

Oculopharyngeal muscular dystrophy (OPMD) is a late-onset autosomal dominant muscular dystrophy characterized by progressive ptosis, swallowing difficulties, and proximal limb weakness. Recently, the genetic basis of this disease has been characterized by mutations in the PABP2 gene that involve short expansions of the trinucleotide repeat GCG.

OBJECTIVES

To independently confirm the presence and study the meiotic stability of the GCG expansion mutations in a distinct ethnic population with OPMD.

SETTINGS

Hospital and university research laboratories in Los Angeles, Calif.

SUBJECTS AND METHODS

Three unrelated families of Hispanic American descent were identified in whom OPMD was transmitted in an autosomal dominant pattern. All of these families can trace affected ancestors to the southwestern United States or to the bordering states of Mexico. In these families, 14 persons with OPMD were identified and studied.

RESULTS

Our results confirm that in these families, expansion mutations characterized by a gain of 3 GCG repeats in the wild-type allele result in an abnormal nucleotide length of 9 GCG repeats in the PABP2 gene. In these families, these mutations are associated with the OPMD phenotype. The identical repeat mutation ([GCG]9) is found in all affected members of these unrelated families and shows relative meiotic stability.

CONCLUSIONS

These results support and extend our study of haplotype analysis and suggest that a founder effect may have occurred for OPMD in this Hispanic American population.

Genetic mapping and haplotype analysis of oculopharyngeal muscular dystrophy

Oculopharyngeal muscular dystrophy (OPMD) is an autosomal dominant muscular dystrophy characterized by late onset ptosis, proximal muscle weakness and swallowing difficulties. This disease has been recently linked to chromosome 14q11.2-q13 in French-Canadian pedigrees. We studied three unrelated American families with OPMD of Hispanic descent and our results indicate that in this ethnic group, this disease also maps to chromosome 14q11.2-q13 (marker MYH7.24; Zmax = 3.98; theta max = 0). These results represent an independent demonstration of disease linkage in a second distinct ethnic group. Furthermore, our analysis demonstrates a unique haplotype that is shared by affected individuals from all three families suggesting a founder effect for OPMD in this population. Meiotic recombinants and radiation hybrid mapping permit the narrowing of the critical region to 1 Mb which will facilitate positional cloning of the OPMD disease gene.

Apraclonidine and anterior segment laser surgery. Comparison of 0.5% versus 1.0% apraclonidine for prevention of postoperative intraocular pressure rise

PURPOSE

To compare the efficacy of 0.5% and 1.0% apraclonidine in preventing laser-induced intraocular pressure (IOP) elevation after trabeculoplasty, neodymium: YAG (Nd: YAG) iridotomy, and capsulotomy.

METHODS

This is a prospective, masked, and randomized study of 83 patients undergoing trabeculoplasty, 62 patients undergoing iridotomy, and 57 patients undergoing capsulotomy. Surgical eyes received one drop of 0.5% or 1.0% apraclonidine immediately after surgery.

RESULTS

Intraocular pressure reduced 2 hours after trabeculoplasty in the 0.5% (P = 0.028) and 1.0% (P = 0.004) groups. Intraocular pressure was higher than baseline in a greater number of eyes treated with 0.5% (12 of 39 eyes, 31%) compared with 1.0% apraclonidine (5 of 44 eyes, 11%) (P = 0.032). Intraocular pressure in eyes with a narrow chamber angle was reduced in 16 (85%) of 19 eyes treated with 0.5% and in 10 (84%) of 12 eyes treated with 1.0% apraclonidine after iridotomy. Of patients with chronic angle-closure glaucoma, IOP was similar to prelaser values in 11 (69%) of 16 eyes treated with 0.5% (P > 0.7) and 12 (80%) of 15 eyes treated with 1.0% apraclonidine (P > 0.3). In patients undergoing capsulotomy, pressure was significantly lowered in the 0.5% group (P = 0.04) but not in the 1.0% apraclonidine group. After capsulotomy, both treatment groups had similar (P > 0.3) numbers of eyes with an IOP less than baseline (83% for 0.5% apraclonidine and 81% for 1.0% apraclonidine).

CONCLUSION

The single postoperative administration of 0.5% apraclonidine is as effective as the 1.0% concentration in preventing IOP elevation immediately after trabeculoplasty, iridotomy, or capsulotomy.

A comparative study of ophthalmodynamometry in hypertensive and non-hypertensive cases

Ophthalmodynamometry was done on 100 hypertensive cases and 100 non-hypertensive cases who had clear media and no glaucoma. The ratio of the pressure mean ophthalmic: pressure mean brachial in the non-hypertensive group was 0.71:1.0, which rose to 0.78:1.0 in the hypertensive group. The ophthalmic humeral diastolic ratio increased with the severity of fundus changes. The pressure mean ophthalmic showed higher values with increasing grades of fundus changes. Those cases having a pressure mean opthalmic higher than the expected value in the hypertensive group as compared to the cases having a pressure mean ophthalmic lower than the expected value, were at a greater risk or had a graver prognosis. The importance of ophthalmodynamometry is stressed for the prognosis of hypertension along with the fundus examination.