A national survey of diagnostic tests reported by UK community optometrists for the detection of chronic open angle glaucoma

Purpose:  In the UK, the majority of cases of chronic open angle glaucoma are detected by community optometrists following a routine sight test. However, there is potential for variability in case finding strategies used. The aim of this study was to carry out a national web-based survey to determine current diagnostic tests used by optometrists in glaucoma case finding. / Methods:  Optometrists on the Association of Optometrists (AOP) electronic database were invited to participate. The survey was open for 16 weeks between April and July 2008. / Results:  A total of 1875 optometrists were eligible to enter the survey, of which 1264 answered the questions relating to diagnostic equipment. Respondents were asked to indicate their usual method of examining the optic nerve head. Direct ophthalmoscopy only was used by 25% with the majority (62%) using a combination of direct and slit-lamp binocular indirect methods. The vast majority of optometrists (78%) used non-contact tonometry to measure intraocular pressure, with only 16% routinely using a Goldmann or Perkins applanation tonometer. The perimeter most frequently used was either one of the Henson range of instruments (39%) or the Humphrey Field Analyser (22%). A smaller number of optometrists (<5%) had access to more specialised imaging equipment, such as HRT, GDx or OCT. / Conclusions:  The results of the survey demonstrate that UK optometrists are well equipped to carry out case finding for chronic open angle glaucoma, although there is a lack of standardisation with respect to equipment used

A survey of current and anticipated use of standard and specialist equipment by UK optometrists

Purpose: To investigate current and anticipated use of equipment and information technology (IT) in community optometric practice in the UK, and to elicit optometrists' views on adoption of specialist equipment and IT. Methods: An anonymous online questionnaire was developed, covering use of standard and specialist diagnostic equipment, and IT. The survey was distributed to a random sample of 1300 UK College of Optometrists members. Results: Four hundred and thirty-two responses were received (response rate = 35%). Enhanced (locally commissioned) or additional/separately contracted services were provided by 73% of respondents. Services included glaucoma repeat measures (30% of respondents), glaucoma referral refinement (22%), fast-track referral for wet age-related macular degeneration (48%), and direct cataract referral (40%). Most respondents (88%) reported using non-contact/pneumo tonometry for intra-ocular pressure measurement, with 81% using Goldmann or Perkins tonometry. The most widely used item of specialist equipment was the fundus camera (74% of respondents). Optical Coherence Tomography (OCT) was used by 15% of respondents, up from 2% in 2007. Notably, 43% of those anticipating purchasing specialist equipment in the next 12 months planned to buy an OCT. ‘Paperless’ records were used by 39% of respondents, and almost 80% of practices used an electronic patient record/practice management system. Variations in responses between parts of the UK reflect differences in the provision of the General Ophthalmic Services contract or community enhanced services. There was general agreement that specialised equipment enhances clinical care, permits increased involvement in enhanced services, promotes the practice and can be used as a defence in clinico-legal cases, but initial costs and ongoing maintenance can be a financial burden. Respondents generally agreed that IT facilitates administrative flow and secure exchange of health information, and promotes a state-of-the-art practice image. However, use of IT may not save examination time; its dynamic nature necessitates frequent updates and technical support; the need for adequate training is an issue; and security of data is also a concern. Conclusion: UK optometrists increasingly employ modern equipment and IT services to enhance patient care and for practice management. While the clinical benefits of specialist equipment and IT are appreciated, questions remain as to whether the investment is cost-effective, and how specialist equipment and IT may be used to best advantage in community optometric practice

SSE: a nucleotide and amino acid sequence analysis platform

<p>Abstract</p> <p>Background</p> <p>There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes.</p> <p>Finding</p> <p>A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes, mono-, di- and higher order nucleotide compositional biases and codon usage.</p> <p>Association Index calculations, GroupScans, Bootscanning and TreeOrder scans perform phylogenetic analyses that reconcile group membership with tree branching orders and provide powerful methods for examining segregation of alleles and detection of recombination events. Phylogeny changes across alignments and scoring of branching order differences between trees using the Robinson-Fould algorithm allow effective visualisation of the sites of recombination events.</p> <p>RNA secondary and tertiary structures play important roles in gene expression and RNA virus replication. For the latter, persistence of infection is additionally associated with pervasive RNA secondary structure throughout viral genomic RNA that modulates interactions with innate cell defences. SSE provides several programs to scan alignments for RNA secondary structure through folding energy thermodynamic calculations and phylogenetic methods (detection of co-variant changes, and structure conservation between divergent sequences). These analyses complement methods based on detection of sequence constraints, such as suppression of synonymous site variability.</p> <p>For each program, results can be plotted in real time during analysis through an integrated graphics package, providing publication quality graphs. Results can be also directed to tabulated datafiles for import into spreadsheet or database programs for further analysis.</p> <p>Conclusions</p> <p>SSE combines sequence editor functions with analytical tools in a comprehensive and user-friendly package that assists considerably in bioinformatic and evolution research.</p

Primary vs. Secondary Antibody Deficiency: Clinical Features and Infection Outcomes of Immunoglobulin Replacement

<div><p>Secondary antibody deficiency can occur as a result of haematological malignancies or certain medications, but not much is known about the clinical and immunological features of this group of patients as a whole. Here we describe a cohort of 167 patients with primary or secondary antibody deficiencies on immunoglobulin (Ig)-replacement treatment. The demographics, causes of immunodeficiency, diagnostic delay, clinical and laboratory features, and infection frequency were analysed retrospectively. Chemotherapy for B cell lymphoma and the use of Rituximab, corticosteroids or immunosuppressive medications were the most common causes of secondary antibody deficiency in this cohort. There was no difference in diagnostic delay or bronchiectasis between primary and secondary antibody deficiency patients, and both groups experienced disorders associated with immune dysregulation. Secondary antibody deficiency patients had similar baseline levels of serum IgG, but higher IgM and IgA, and a higher frequency of switched memory B cells than primary antibody deficiency patients. Serious and non-serious infections before and after Ig-replacement were also compared in both groups. Although secondary antibody deficiency patients had more serious infections before initiation of Ig-replacement, treatment resulted in a significant reduction of serious and non-serious infections in both primary and secondary antibody deficiency patients. Patients with secondary antibody deficiency experience similar delays in diagnosis as primary antibody deficiency patients and can also benefit from immunoglobulin-replacement treatment.</p></div

Molecular characterisation of protist parasites in human-habituated mountain gorillas (Gorilla beringei beringei), humans and livestock, from Bwindi impenetrable National Park, Uganda

Over 60 % of human emerging infectious diseases are zoonotic, and there is growing evidence of the zooanthroponotic transmission of diseases from humans to livestock and wildlife species, with major implications for public health, economics, and conservation. Zooanthroponoses are of relevance to critically endangered species; amongst these is the mountain gorilla (Gorilla beringei beringei) of Uganda. Here, we assess the occurrence of Cryptosporidium, Cyclospora, Giardia, and Entamoeba infecting mountain gorillas in the Bwindi Impenetrable National Park (BINP), Uganda, using molecular methods. We also assess the occurrence of these parasites in humans and livestock species living in overlapping/adjacent geographical regions

Author correction : a global database for metacommunity ecology, integrating species, traits, environment and space

Correction to: Scientific Data https://doi.org/10.1038/s41597-019-0344-7, published online 08 January 202

Author correction : a global database for metacommunity ecology, integrating species, traits, environment and space

Correction to: Scientific Data https://doi.org/10.1038/s41597-019-0344-7, published online 08 January 202

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

<p>Abstract</p> <p>Background</p> <p>Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.</p> <p>Results</p> <p>We present a new method of multiple sequence alignment, called MISHIMA (Method for Inferring Sequence History In terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm is used to quickly find rare oligonucleotide sequences shared by all sequences. Divide and conquer approach is then applied to break the sequences into fragments that can be aligned independently by an external alignment program. These partial alignments are assembled together to form a complete alignment of the original sequences.</p> <p>Conclusions</p> <p>MISHIMA provides improved performance compared to the commonly used multiple alignment methods. As an example, six complete genome sequences of bacteria species <it>Helicobacter pylori </it>(about 1.7 Mb each) were successfully aligned in about 6 hours using a single PC.</p

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

<p>Abstract</p> <p>Background</p> <p>Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields.</p> <p>Results</p> <p>We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores.</p> <p>Conclusion</p> <p>MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at <url>http://sysbio.rnet.missouri.edu/multicom_toolbox/</url>.</p