Aligning distant sequences to graphs using long seed sketches

Sequence-to-graph alignment is crucial for applications such as variant genotyping, read error correction, and genome assembly. We propose a novel seeding approach that relies on long inexact matches rather than short exact matches, and show that it yields a better time-accuracy trade-off in settings with up to a [Formula: see text] mutation rate. We use sketches of a subset of graph nodes, which are more robust to indels, and store them in a k-nearest neighbor index to avoid the curse of dimensionality. Our approach contrasts with existing methods and highlights the important role that sketching into vector space can play in bioinformatics applications. We show that our method scales to graphs with 1 billion nodes and has quasi-logarithmic query time for queries with an edit distance of [Formula: see text] For such queries, longer sketch-based seeds yield a [Formula: see text] increase in recall compared with exact seeds. Our approach can be incorporated into other aligners, providing a novel direction for sequence-to-graph alignment.

Lossless indexing with counting de Bruijn graphs

Sequencing data are rapidly accumulating in public repositories. Making this resource accessible for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated (or colored) de Bruijn graphs for efficiently indexing k-mer sets. However, approaches for representing quantitative attributes such as gene expression or genome positions in a general manner have remained underexplored. In this work, we propose counting de Bruijn graphs, a notion generalizing annotated de Bruijn graphs by supplementing each node-label relation with one or many attributes (e.g., a k-mer count or its positions). Counting de Bruijn graphs index k-mer abundances from 2652 human RNA-seq samples in over eightfold smaller representations compared with state-of-the-art bioinformatics tools and is faster to construct and query. Furthermore, counting de Bruijn graphs with positional annotations losslessly represent entire reads in indexes on average 27% smaller than the input compressed with gzip for human Illumina RNA-seq and 57% smaller for Pacific Biosciences (PacBio) HiFi sequencing of viral samples. A complete searchable index of all viral PacBio SMRT reads from NCBI's Sequence Read Archive (SRA) (152,884 samples, 875 Gbp) comprises only 178 GB. Finally, on the full RefSeq collection, we generate a lossless and fully queryable index that is 4.6-fold smaller than the MegaBLAST index. The techniques proposed in this work naturally complement existing methods and tools using de Bruijn graphs, and significantly broaden their applicability: from indexing k-mer counts and genome positions to implementing novel sequence alignment algorithms on top of highly compressed graph-based sequence indexes.

28 Review of Operative and Non-Operative Time-Use During General Anaesthetic Cases in a Busy Surgical Oncology Service

Aim

To review theatre running times of all general anaesthetic cases performed in a single theatre during a set six-week period. We intend to assess the division of theatre time between operative and non-operative tasks and review areas of improvement in our department.

Method

The data was collected concurrently by a member of the surgical team (AB) at the time of surgery. Date, surgical procedure, and time elapsed from knife-to-skin (KTS) to skin closure were monitored between the hours 08:30–17:00. Results were reviewed and presented graphically using Microsoft Excel. Instances of theatre over-running were identified, and these outliers were reviewed in more detail.

Results

We identified two main time management issues in our department. The first occurs prior to the first procedure which highlighted significant delays with only one instance of KTS at 08:30 during the period of data collection. The second notable issue is the pattern of delays. There was a trend toward longer delays between cases as the day proceeds.

Conclusions

Upon review of our data, we were able to identify possible areas of improvement in the time management of our theatre group. These improvements will allow for accurate theatre planning which should be a priority for all stakeholders given the significant waiting lists created by the COVID19 pandemic. There are many peer-reviewed methods of improving the efficiency of departments such as ours. Further work is required to discuss targets for improvement with relevant stakeholders and to implement PDSA cycles to assess the impact of implemented changes in our theatre.

24 Mediastinal Ectopic Parathyroid Adenoma Causing Malignant Hypercalcaemia in a Young Female - a Case Report and Review of Literature

Ectopic parathyroid tissue can pose difficulties in diagnosis and management of patients with hyperparathyroidism. Due to the embryological origins of the inferior parathyroid glands from the 3rd pharyngeal arch where they develop with the thymus; they can have variable anatomical locations, including the anterior mediastinum. While the incidence of ectopic parathyroid glands varies in the literature mediastinal parathyroid tissue is extremely rare. This anatomical variation has important diagnostic and surgical ramifications for patients and is an important topic for trainees in medical endocrinology, endocrine surgery, and cardiothoracic surgery to be aware of.

We present the case of a 22-year-old woman who presented as an emergency with severe hypercalcaemia. Who was subsequently found to have an ectopic mediastinal parathyroid adenoma. She underwent surgery within days of her initial presentation providing her with an immediate cure and restoring her calcium homeostasis. Despite diagnostic and operative challenges, combined care from our endocrine and cardio-thoracic surgical teams ensured an uneventful post-operative recovery for this patient.

Induction of periodontal disease via retentive ligature, lipopolysaccharide injection, and their combination in a rat model

Periodontitis is a highly prevalent, chronic immune-inflammatory disease of the periodontium that results in the periodontium and alveolar bone loss's progressive destruction. In this study, the induction of periodontal disease via retentive ligature, lipopolysaccharide, and their combination at three different times were compared in a rat model. Seventy-two Sprague Dawley rats were distributed into four treatment groups: 1) control group with no treatment; 2) application of 4/0 nylon ligature around second maxillary molars; 3) combination of ligature and LPS injection (ligature-LPS); 4) intragingival injection of Porphyromonas gingivalis lipopolysaccharide (Pg-LPS) to the palatal mucosa of the second maxillary molars. Six rats were sacrificed from each group after 7, 14, and 30 days of periodontal disease induction. Alveolar bone loss, attachment loss, number of inflammatory cells, and blood vessels were evaluated histologically. A micro-CT scan was used as a parameter to know the rate of alveolar bone loss. Parametric data were analyzed using two-way ANOVA followed by Bonferroni correction with a significance set at 5%. Non-parametric data were analyzed using Kruskal-Wallis, followed by multiple comparisons with Bonferroni correction. The histological results revealed significant destructive changes in the periodontal tissues and alveolar bone following the ligature and ligature-LPS induction techniques. These changes were evident as early as seven days, maintained until 14 days post-treatment, and declined with time. The ligature technique was effective in inducing acute periodontal disease. The LPS injection technique did not induce alveolar bone loss, and its combination to ligature added insignificant effects.

Topology-based sparsification of graph annotations

Motivation

Since the amount of published biological sequencing data is growing exponentially, efficient methods for storing and indexing this data are more needed than ever to truly benefit from this invaluable resource for biomedical research. Labeled de Bruijn graphs are a frequently-used approach for representing large sets of sequencing data. While significant progress has been made to succinctly represent the graph itself, efficient methods for storing labels on such graphs are still rapidly evolving.

Results

In this article, we present RowDiff, a new technique for compacting graph labels by leveraging expected similarities in annotations of vertices adjacent in the graph. RowDiff can be constructed in linear time relative to the number of vertices and labels in the graph, and in space proportional to the graph size. In addition, construction can be efficiently parallelized and distributed, making the technique applicable to graphs with trillions of nodes. RowDiff can be viewed as an intermediary sparsification step of the original annotation matrix and can thus naturally be combined with existing generic schemes for compressed binary matrices. Experiments on 10 000 RNA-seq datasets show that RowDiff combined with multi-BRWT results in a 30% reduction in annotation footprint over Mantis-MST, the previously known most compact annotation representation. Experiments on the sparser Fungi subset of the RefSeq collection show that applying RowDiff sparsification reduces the size of individual annotation columns stored as compressed bit vectors by an average factor of 42. When combining RowDiff with a multi-BRWT representation, the resulting annotation is 26 times smaller than Mantis-MST.

Availability and implementation

RowDiff is implemented in C++ within the MetaGraph framework. The source code and the data used in the experiments are publicly available at https://github.com/ratschlab/row_diff.

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

P9: MANAGEMENT OF ESOPHAGEAL FOOD BOLUS OBSTRUCTION AT A UNIVERSITY TEACHING HOSPITAL – A RETROSPECTIVE ANALYSIS

Introduction

Despite the fact that esophageal food bolus obstruction is a common surgical problem, there are no clear guidelines on its management. Medical treatment with Buscopan and Glucagon is mostly in-effective, requiring a therapeutic Oesophago-Gastro-Duodenoscopy (OGD).

Method

All consecutive cases of food bolus obstructions (FBO) presenting to the Emergency Department (ED) for 18 month period between 01/01/2018 and 30/06/2019 were retrospectively reviewed.

Result

A total of 30 patients were admitted with food bolus obstruction via ED (1.67 per month). Females (67%) constituted most of these patients. Average age was 55 with range of 19-83. 84% of patients presented with Dysphagia, while Odynophagia (10%) and chest pain (6%) were other presenting symptoms. Average duration of symptoms was 17 hours (Range 2 – 48 hours). 44% of patients had OGD done under sedation while others (56%) had under General Anaesthesia (GA). In 70% of cases, food bolus was pushed into stomach, while it was retrieved out in 20%. In 10%, it had already spontaneously passed in stomach on OGD. The etiology of FBO was inflammatory in 60% cases, while an esophageal stricture was seen in 10% only. In 30% cases no cause of FBO was identified. Post-OGD length of stay was on average 1.15 days (range 12 hours – 7 days). 2 patients had aspiration pneumonia prolonging their hospital stay, there was no esophageal perforation or mortality.

Conclusion

Esophageal food bolus obstruction is a common surgical problem, OGD under GA is a safe recommended procedure, which often picks up an underlying pathology.

Take-home message

Esophageal food bolus obstruction is a common surgical problem, OGD under GA is a safe recommended procedure, which often picks up an underlying pathology.

Sparse Binary Relation Representations for Genome Graph Annotation

High-throughput DNA sequencing data are accumulating in public repositories, and efficient approaches for storing and indexing such data are in high demand. In recent research, several graph data structures have been proposed to represent large sets of sequencing data and to allow for efficient querying of sequences. In particular, the concept of labeled de Bruijn graphs has been explored by several groups. Although there has been good progress toward representing the sequence graph in small space, methods for storing a set of labels on top of such graphs are still not sufficiently explored. It is also currently not clear how characteristics of the input data, such as the sparsity and correlations of labels, can help to inform the choice of method to compress the graph labeling. In this study, we present a new compression approach, Multi-binary relation wavelet tree (BRWT), which is adaptive to different kinds of input data. We show an up to 29% improvement in compression performance over the basic BRWT method, and up to a 68% improvement over the current state-of-the-art for de Bruijn graph label compression. To put our results into perspective, we present a systematic analysis of five different state-of-the-art annotation compression schemes, evaluate key metrics on both artificial and real-world data, and discuss how different data characteristics influence the compression performance. We show that the improvements of our new method can be robustly reproduced for different representative real-world data sets.

Short Communication: Effect of dietary protein level on growth and body condition score of male Beetal goats during summer

The effects of feeding various dietary protein levels on the fattening of male Beetal goats were investigated. Twenty-seven bucks (initial bodyweight 35 ± 0.5 kg) between 12 and 16 months old were randomly assigned to one of three treatments The treatments, which were provided as isocaloric supplements to 5 kg fresh sorghum fodder, differed in the amount of crude protein (CP), namely i) 18% CP (LP) ii) 25.5% CP (MP) and iii) 31.6% CP (HP). Feed intake and faecal score were recorded daily. Live bodyweight was recorded every 14 days. Wither height, heart girth, body length and body condition score were recorded monthly. Dry matter intake and average daily gain increased linearly with the level of CP in the diet. The average body condition score, wither height and heart girth were significantly greater in for goats in the HP group compared with those in LP and MP groups. However, dietary protein did not affect body length. Thus, feeding higher levels of CP linearly increased the growth, feed intake and feed efficiency of growing Beetal goats. The mean faecal score was lower for goats in the HP group compared with goats in the LP group.Keywords: average daily gain, body measurements, faecal consistency

Dynamic compression schemes for graph coloring

Motivation

Technological advancements in high-throughput DNA sequencing have led to an exponential growth of sequencing data being produced and stored as a byproduct of biomedical research. Despite its public availability, a majority of this data remains hard to query for the research community due to a lack of efficient data representation and indexing solutions. One of the available techniques to represent read data is a condensed form as an assembly graph. Such a representation contains all sequence information but does not store contextual information and metadata.

Results

We present two new approaches for a compressed representation of a graph coloring: a lossless compression scheme based on a novel application of wavelet tries as well as a highly accurate lossy compression based on a set of Bloom filters. Both strategies retain a coloring even when adding to the underlying graph topology. We present construction and merge procedures for both methods and evaluate their performance on a wide range of different datasets. By dropping the requirement of a fully lossless compression and using the topological information of the underlying graph, we can reduce memory requirements by up to three orders of magnitude. Representing individual colors as independently stored modules, our approaches can be efficiently parallelized and provide strategies for dynamic use. These properties allow for an easy upscaling to the problem sizes common to the biomedical domain.

Availability and implementation

We provide prototype implementations in C++, summaries of our experiments as well as links to all datasets publicly at https://github.com/ratschlab/graph_annotation.

Supplementary information

Supplementary data are available at Bioinformatics online.

Data on laser induced preferential crystal (re)orientation by picosecond laser ablation of zinc in air

Laser ablation of zinc is performed with a 6.7 ps pulsed laser source to investigate the ablation mechanism and resulting morphology of the irradiated surface. The data shows the changes in crater morphology, as well as chemical composition, for different number of pulses and laser fluence levels. We observed Laser Induced Preferential Crystal Orientation (LIPCO), as a result of ultra-short pulsed laser processing of Zn at a wavelength of 515 nm. Crystallographic data for other laser wavelengths, namely 343 and 1030 nm, as well as for Zn coated steel are also provided in support of this observation. Data presented in this article are related to the research article “Investigation of the ultrashort pulsed laser processing of zinc at 515 nm: morphology, crystallography and ablation threshold” [1].

Picosecond-pulsed laser ablation of zinc: crater morphology and comparison of methods to determine ablation threshold

Ablation of bulk polycrystalline zinc in air is performed with single and multiple picosecond laser pulses at a wavelength of 1030 nm. The relationships between the characteristics of the ablated craters and the processing parameters are analyzed. Morphological changes of the ablated craters are characterized by means of scanning electron microscopy and confocal laser scanning microscopy. Chemical compositions of both the treated and untreated surfaces are quantified with X-ray photoelectron spectroscopy. A comparative analysis on the determination of the ablation threshold using three methods, based on ablated diameter, depth and volume is presented along with associated incubation coefficients. The single pulse ablation threshold value is found to equal 0.21 J/cm². Using the calculated incubation coefficients, it is found that both the fluence threshold and energy penetration depth show lesser degree of incubation for multiple laser pulses.

Sequence-based prediction of permissive stretches for internal protein tagging and knockdown

BACKGROUND

Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool.

METHODS

We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins.

RESULTS

We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability.

CONCLUSIONS

Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.

Knowledge of diabetes among patients in the United Arab Emirates and trends since 2001: a study using the Michigan Diabetes Knowledge Test

Knowledge of diabetes among patients with the disease in the United Arab Emirates is essential for effective self-management. We assessed the level of diabetes-related knowledge among patients and compared it with that found in previous studies in the same city. A cross-sectional study, using an interviewer-administered questionnaire, was conducted at two clinics in Al Ain, United Arab Emirates. The Michigan Diabetes Knowledge Test, translated into Arabic, was used to assess knowledge of diabetes. Of 165 participants with diabetes, 130 (78.8%) were women. The mean knowledge score was low at 55% (6.6 out of a maximum possible score of 12, standard deviation 1.8). This is comparable to levels found in previous studies: 55.5% in 2001 and 68.2% in 2006. Misconceptions about the diabetic diet and blood testing were common. The level of diabetes-related knowledge has remained low since 2001. These results are of concern in view of the substantial investments made in diabetes care and health education in the region.

Epidemiology of tuberculosis and evaluation of treatment outcomes in the national tuberculosis control programme, River Nile state, Sudan, 2011-2013

Tuberculosis is a major health problem in Sudan, a country that carries 11-15% of the tuberculosis burden in the Eastern Mediterranean Region. This study aimed to describe the epidemiology of tuberculosis in River Nile State and to compare treatment outcomes with WHO recommended indicators. A descriptive study was conducted on data collected from records of 1221 patients registered at tuberculosis management units over the 3 years 2011-2013. The mean age of cases was 37.7 (SD 21.5) years and 65.9% were males; 76.3% were pulmonary tuberculosis and 36.9% were sputum smear-positive cases. Average values for all outcome indicators were suboptimal, notably rates of case notification (30.8 per 100 000), case detection (10.3%), treatment success (79.6%), treatment failure (3.0%), default (8.1%) and death (8.0%). Of the 264 patients tested for HIV, 3.8% were positive. Outcome indicators for the national tuberculosis control programme are lagging behind the required targets.

Assembly and characterization of novel Alu inserts detected from next-generation sequencing data

Repetitive elements generally, and Alu inserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of novel Alu inserts using their respective subfamily consensus sequences as references, we found an exponential decay in the Alu subfamily call enrichment with increased number of sequence variants (Pearson correlation [Formula: see text], [Formula: see text]). By mapping the sequences of these inserts to a human reference genome, we infer the reference Alu sources of a subset of the novel Alus, of which 85% were previously shown to be active. We also evaluate relationships between the loci of the novel inserts and their inferred sources.

Delayed aorto-right atrial fistula following percutaneous closure of atrial septal defect

We present the case of a 27-year-old man who underwent percutaneous atrial septal defect (ASD) repair using the Amplatzer(®) (St Jude Medical, St Paul, MN, US) septal occluder (ASO). Six weeks later, he presented with heart failure and was found to have an aorto-right atrial fistulation. He required urgent surgical device explantation and repair of the existing ASD using a pericardial patch repair technique. This is the first case to be reported from the UK describing a delayed aorto-right atrial fistula following percutaneous closure using ASO.

Detecting Alu insertions from high-throughput sequencing data

High-throughput sequencing technologies have allowed for the cataloguing of variation in personal human genomes. In this manuscript, we present alu-detect, a tool that combines read-pair and split-read information to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data while also identifying insertions directly in the vicinity of existing Alus. To set the parameters of our method, we use simulation of a faux reference, which allows us to compute the precision and recall of various parameter settings using real sequencing data. Applying our method to 100 bp paired Illumina data from seven individuals, including two trios, we detected on average 1519 novel Alus per sample. Based on the faux-reference simulation, we estimate that our method has 97% precision and 85% recall. We identify 808 novel Alus not previously described in other studies. We also demonstrate the use of alu-detect to study the local sequence and global location preferences for novel Alu insertions.

Surface plasmon resonance in CdSe semiconductor coated with gold nanoparticles

We have grown CdSe semiconductor films on glass substrates and the films were coated with Au nanoparticles of 10 nm in size by the pulsed-laser deposition technique. The films demonstrate a large enhancement of Raman intensity and photoluminescence of CdSe semiconductor via excitation of surface plasmon resonances in proximate gold metal nanoparticles deposited on the surface of CdSe film. These observations suggest a variety of approaches for improving the performance of devices such as photodetectors, photovoltaics, and related devices, including biosensors.

Epidemiology of astrovirus infection in young children hospitalized with acute gastroenteritis in Melbourne, Australia, over a period of four consecutive years, 1995 to 1998

The incidence of astrovirus infection in children less than 5 years of age hospitalized with acute gastroenteritis in Melbourne, Australia, from 1995 to 1998 was determined. Astrovirus was detected in 40 of 449 specimens tested by Northern hybridization, and astrovirus infection was confirmed by reverse transcription-PCR with or without culture in CaCO-2 cells. This represented 3.0% (40 of 1, 327) of all children tested for enteric pathogens, including viral, bacterial, and parasitic pathogens, over the survey period. The incidences of astrovirus infection in each year were 4.4% (1995), 2. 2% (1996), 3.9% (1997), and 1.4% (1998). In 1995 and 1997, the incidences of astrovirus infection were greater than the incidence of infection with all individual bacterial pathogens and were either greater than or equal to the incidence of adenovirus infection. Astrovirus exhibited an unusual biennial winter peak of incidence that correlated with a greater incidence of serotype 1 virus and an increased rate of hospitalization of children aged 6 to 12 months. Uncommon (serotype 2 and 4) and rare (serotype 8) serotypes were detected during the survey period. Genetic analysis of ORF2 (which encodes the astrovirus capsid precursor) of Melbourne isolates showed nucleotide sequence variation from year to year. This was not accompanied by significant amino acid substitutions. However, geographical variation was apparent by comparison of Melbourne astrovirus isolates with prototype strains identified in the United Kingdom.

Detection of astrovirus gastroenteritis in children

A commercial enzyme immunoassay (EIA) for the detection of astrovirus antigen was used to detect the virus during a 12-month survey of enteric pathogens in children in outpatient (n = 238) and hospital (n = 176) settings. It was found to have a 100% sensitivity and 98.6% specificity. Nineteen astrovirus isolates were detected and confirmed by northern hybridization, cell culture, and RT-PCR. The virus was detected mainly amongst outpatients although a comparison of the detection rate with that in hospitalised children did not demonstrate a statistically significant difference (p = 0.1347). In contrast, there was a strong association between hospitalization and rotavirus infection (p = 0.0371), and a strong association between infection detected in outpatients and adenovirus infection (p = 0.0193). Strains of astrovirus were sequenced, genotyped and shown to be: type 1 (n = 11), type 3 (n = 1), and type 4 (n = 7). Maximum genetic variation in type 1 isolates was 8.6% and type 4 was 7.8%. Changes did not result in amino acid substitutions.

Microsurgical management of a complicated aneurysmal endovascular embolisation with GDC coil: a case report

We present a case involving a microsurgical approach to solving the problem of a medial cerebral artery (MCA) occlusion occurring after GDC coiling of an internal cerebral artery (ICA) bifurcation aneurysm in a 40 year old woman. We describe the clinical course of the case and discuss technical possibilities and risks of clipping a coiled aneurysm. One key to success is awareness of changes in the aneurysm's properties after coiling. With loss of elasticity the aneurysm had the effect of a tumor fixed on the vessel. The apposition of the aneurysm to the wall of the vessel, as well as the aneurysm's rigidity and increase of intracranial pressure after subarachnoideal hemorrhage (SAH), may lead to occlusion of the vessel. In cases of an mandatory operation due to the occlusion of a main arterial stem after coiling, it is primarily crucial to perforate the aneurysm's fundus, remove the coils, and, finally, to clip the slack neck of the aneurysm. An attempt to precisely prepare and clip the aneurysmal neck without removing the coils could result in the rupture of the aneurysm's neck.

Improved sensitivity of astrovirus-specific RT-PCR following culture of stool samples in CaCo-2 cells

BACKGROUND

During an epidemiological study on the incidence of astrovirus infection in children hospitalized with acute gastroenteritis, a Northern hybridization method was used to screen stool samples for astrovirus RNA. Positive results were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR), which showed surprisingly low sensitivity. The low sensitivity of the RT-PCR method was considered likely to be due to the presence of non-specific inhibitors.

OBJECTIVE

To develop and use a simple culture method to improve the sensitivity of diagnosis of astrovirus in clinical stool samples using RT-PCR.

STUDY DESIGN

Stool samples from children hospitalized with acute gastroenteritis were screened for astrovirus using Northern hybridization. The presence of astrovirus RNA was then confirmed using an astrovirus-specific RT-PCR. Hybridization positive samples that failed to generate an RT-PCR product were cultured in CaCO-2 cells for 48 h. RNA was isolated from cultures and re-tested using the same RT-PCR method.

RESULTS

Using Northern hybridization, human astroviruses were detected in the stools of 31 patients and confirmed by RT-PCR in 16 samples. RNA extracted directly from 15 faecal specimens could not be amplified by RT-PCR. After culture for 48 h in CaCO-2 cells, RNA extracted from these samples could be amplified and confirmed the presence of astrovirus in all 15 specimens.

CONCLUSIONS

Development of a simplified culture method for astrovirus positive faecal specimens improved the sensitivity of astrovirus-specific RT-PCR from 52 to 100%. The technique should be of value as a confirmatory test in surveys of human astrovirus infection.

[Hyperthyroidism caused by TSH producing hypophyseal adenoma]

Thyrotropin (TSH-)producing adenomas of the anterior pituitary gland are the least frequently encountered ones and constitute a very rare cause of hyperthyroidism. The case is presented of a 58 year old male patient with a well-known history of hyperthyroidism over a period of at least 9 years growing goiter. Despite different forms of medical treatment he presented a constant clinical pattern consisting of restlessness and paroxysmal tachycardial atrial fibrillation. Laboratory findings revealed elevated levels of circulating thyroid hormones despite inadequately high levels of TSH. MRI scan revealed an adenoma of the pituitary measuring 9 mm in diameter. After microsurgery, consisting of transphenoidal resection of the tumor, the patient recorded no clinical symptoms. Histological examination revealed positive immunohistochemical staining, with antibodies to TSH, but a negative reaction against the GH, PRL, FSH, LH and ACTH hormone antibodies. Moreover, the levels of circulating hormones (GH, PRL, FSH, LH and ACTH) were normal. TSH-alpha subunits were not elevated. Before the correct diagnosis was reached, this patient was treated for nine years with antithyroid drugs. Five months after the operation the patient showed normal values of circulating thyroid hormones and TSH and thus no thyroid-specific medication was necessary.

Analysis and potential of excretory-secretory antigens of Setaria cervi for immunodiagnosis of human filariasis

The excretory-secretory (E-LS) products released by the adult Setaria cervi, a bovine filarial parasite, were used to raise polyvalent hyperimmune serum in rabbits. Analysis of E-S products, using anti-E-S serum showed the presence of 10-14 immunogenic proteins, the rabbit anti-E-S serum showed reciprocal antibody titres in the range of 100,000-250,000 by enzyme linked immunosorbent assay. The anti-E-S antibodies could detect circulating antigen in filarial patients sera by Counter immunoelectrophoresis.

Endoscopic-guided clipping of cerebral aneurysms

An endoscopic probe has been used intraoperatively to facilitate the obliteration of cerebral aneurysms. This method has been used in 24 patients with 30 arterial aneurysms. There were 13 males and 11 females. They ranged in age from 22 to 73 years (mean age 48 years). The mean time of surgery was 7.3 days after subarachnoid haemorrhage (ranging from 2 to 24 days). In three cases there was intraoperative rupture of the aneurysm and with one patient the operation had to be abandoned because of severe brain oedema. The follow-up ranged from 12 to 48 weeks (average 31.8 weeks). The overall outcome was good in 14 cases (58.3%), eight patients (33.3%) showed moderate disability, severe disability occurred in one patient (4%) and one patient (4%) died. In all cases when the endoscope was used, there was a striking improvement in the visualisation of the anatomy of the aneurysm and surrounding structures. Furthermore, the position of the clip and the state of the vessels leading to and from the aneurysm could be easily examined.

Radionuclide study of the blood ocular barrier

The purpose of this study was to investigate the permeability and clinical significance of the blood-ocular barrier. A new technique using systemic, subtenon, and retrobulbar injections was applied to the study of intraocular penetration of labelled steroid compound. The study was carried out in normal rabbits and in animals with artificially induced intraventional inflammation. It is concluded that there is no blood-vitreous barrier, a vague concept in any case, in the anterior region of the vitreous where free diffusion was observed between the anterior and posterior segments of the eye. High concentration of the labelled steroids was found in the cornea with the peak of activity usually at 30 minutes. However, traces of activity were detectable for up to 4 hours. This indicates the need for a depot long term respiratory form of corticosteroid that would deliver a high concentration of the medication. Local subtenon's and retrobulbar injections resulted in a relatively higher ocular I-125 Cortisol concentration than obtained by systemic route. It is concluded therefore that a high concentration of steroids applied locally will give better and less deletrious effects than systemic administration. Subtenon injection resulted in higher activity in various ocular tissues especially aqueous and vitreous. However, the I-125 Cortisol was rapidly cleared regardless of the route of administration.