Zero retinal vein pulsation amplitude extrapolated model in non-invasive intracranial pressure estimation.

Intracranial pressure (ICP) includes the brain, optic nerve, and spinal cord pressures; it influences blood flow to those structures. Pathological elevation in ICP results in structural damage through various mechanisms, which adversely affects outcomes in traumatic brain injury and stroke. Currently, invasive procedures which tap directly into the cerebrospinal fluid are required to measure this pressure. Recent fluidic engineering modelling analogous to the ocular vascular flow suggests that retinal venous pulse amplitudes are predictably influenced by downstream pressures, suggesting that ICP could be estimated by analysing this pulse signal. We used this modelling theory and our photoplethysmographic (PPG) retinal venous pulse amplitude measurement system to measure amplitudes in 30 subjects undergoing invasive ICP measurements by lumbar puncture (LP) or external ventricular drain (EVD). We estimated ICP from these amplitudes using this modelling and found it to be accurate with a mean absolute error of 3.0 mmHg and a slope of 1.00 (r = 0.91). Ninety-four percent of differences between the PPG and invasive method were between - 5.5 and + 4.0 mmHg, which compares favourably to comparisons between LP and EVD. This type of modelling may be useful for understanding retinal vessel pulsatile fluid dynamics and may provide a method for non-invasive ICP measurement.

Inviting others to life in reciprocal space.

Crystallography is an important science that impacts many areas of research. The number of users of crystallographic techniques has increased significantly over the past few decades, as diffractometers have become readily available and many commercial programs with user-friendly interfaces have been developed. The growth in computing power has led to the development of advanced methods that were unthinkable in the past. Yet at the same time, formal crystallography teaching has declined, with many programs no longer offering formal crystallography classes. This combination has resulted in many avoidable errors in data collection, processing, and interpretation of results. Making crystallographic teaching, both of theoretical concepts and hands-on training in data processing and analysis, available to the next generation of crystallographers is a crucial mandate. This paper gives a glimpse at several possible avenues to invite newcomers to a successful life in reciprocal space.

Are viruses associated with disc herniation? A clinical case series.

BACKGROUND: There is some limited evidence for the presence of viruses in herniated disc material including a previous case series that claimed to provide "unequivocal evidence of the presence of herpes virus DNA in intervertebral disc specimens of patients with lumbar disc herniation suggesting the potential role of herpes viruses as a contributing factor to the pathogenesis of degenerative disc disease". This study has not been replicated. The objective of our study was to determine if viruses were present in herniated disc fragments in participants with a prior history of back pain. METHODS: We recruited fifteen participants with a history of prior low-back pain prior to undergoing disc herniation surgery in the lumbar spine. Harvested disc samples were subject to next generation sequencing for detection of both RNA and DNA viral pathogens. Additionally, samples were analysed by a broadly reactive PCR targeting herpesviral DNA. Ethics approval was granted by the Human Research Ethics Committees of both Murdoch University, and St John of God Hospital, Western Australia. RESULTS: Of the fifteen research participants, 8 were female. Mean age was 49.4 years (SD 14.5 yrs) with a range of 24-70 years. All participants had prior back pain with mean time since first ever attack being 8.8 years (SD 8.8 yrs). No samples contained significant DNA sequences relating to known human viral agents. Inconsequential retroviral sequences were commonly found and were a mixture of putative animal and human retroviral protein coding segments. All samples were negative for herpesvirus DNA when analysed by pan-herpesvirus PCR. CONCLUSIONS: This study found no viral pathogens in any intervertebral disc fragments of patients who had previous back pain and underwent discectomy for disc herniation and thus it is unlikely that viruses are associated with disc herniation, however given the contradiction between key studies enhanced replication of this experiment is recommended.

Assessment of genetic diversity and population structure in cultured Australian Pacific oysters.

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (HE ) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low-density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.

Breeding for robustness: investigating the genotype-by-environment interaction and micro-environmental sensitivity of Genetically Improved Farmed Tilapia (Oreochromis niloticus).

Robustness has become a highly desirable breeding goal in the globalized agricultural market. Both genotype-by-environment interaction (G × E) and micro-environmental sensitivity are important robustness components of aquaculture production, in which breeding stock is often disseminated to different environments. The objectives of this study were (i) to quantify the degree of G × E by assessing the growth performance of Genetically Improved Farmed Tilapia (GIFT) across three countries (Malaysia, India and China) and (ii) to quantify the genetic heterogeneity of environmental variance for body weight at harvest (BW) in GIFT as a measure of micro-environmental sensitivity. Selection for BW was carried out for 13 generations in Malaysia. Subsets of 60 full-sib families from Malaysia were sent to China and India after five and nine generations respectively. First, a multi-trait animal model was used to analyse the BW in different countries as different traits. The results indicate a strong G × E. Second, a genetically structured environmental variance model, implemented using Bayesian inference, was used to analyse micro-environmental sensitivity of BW in each country. The analysis revealed the presence of genetic heterogeneity of both BW and its environmental variance in all environments. The presence of genetic variation in residual variance of BW implies that the residual variance can be modified by selection. Incorporating both G × E and micro-environmental sensitivity information may help in selecting robust genotypes with high performance across environments and resilience to environmental fluctuations.

The current role of decompressive craniectomy for severe traumatic brain injury.

There is little doubt that decompressive craniectomy can reduce mortality however, the results of a recent study has provided more evidence to inform the debate regarding clinical and ethical concerns that it merely converts death into survival with severe disability or in a vegetative state. The recently published RESCUEicp trial compared last-tier secondary decompressive craniectomy with continued medical management for refractory intracranial hypertension after severe traumatic brain injury. Patients were randomly assigned to decompressive craniectomy with medical therapy or to receive continued medical therapy with the option of adding barbiturates. The results of the study support the findings of the stroke studies in that the reduction in mortality was almost directly translatable into survival with either severe disability or in a vegetative state. The question remains as to whether there is a subset of patients who obtain benefit from surgical decompression and it is in this regard that the use of observational cohort studies and sophisticated outcome prediction models may be of use. Comparing the percentage prediction with the observed long outcome provides an objective assessment of the most likely outcome can be obtained for patients thought to require surgical intervention. Whilst there will always be limitations when using this type of data they may help prompt appropriate patient-centred discussions regarding realistic outcome expectations. A broader debate is also needed regarding use of a medical intervention that may leave a person in a condition that they may feel to be unacceptable and also places a considerable burden on society.

Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus.

The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.

Malignant cerebral swelling following cranioplasty.

Over the past few years there have been a number of case reports and small cohort studies that have described so called "malignant" cerebral swelling following an uneventful cranioplasty procedure. The pathophysiology remains to be established however it has been suggested that it may be related to a combination of failure of autoregulation and the use of closed vacuum suction drainage. The current study presents three further patients who had had a decompressive hemicraniectomy for ischaemic stroke. If decompressive craniectomy is utilised in the management of neurological emergencies, close attention and wider reporting of this type of complication is required not only to focus attention on possible management strategies, but also to determine which patients are at most risk of this devastating complication.

Impact of incident myocardial infarction on the risk of venous thromboembolism: the Tromsø Study.

UNLABELLED: Essentials Registry-based studies indicate a link between arterial- and venous thromboembolism (VTE). We studied this association in a cohort with confounder information and validated outcomes. Myocardial infarction (MI) was associated with a 4.8-fold increased short-term risk of VTE. MI was associated with a transient increased risk of VTE, and pulmonary embolism in particular. SUMMARY: Background Recent studies have demonstrated an association between venous thromboembolism (VTE) and arterial thrombotic diseases. Objectives To study the association between incident myocardial infarction (MI) and VTE in a prospective population-based cohort. Methods Study participants (n = 29 506) were recruited from three surveys of the Tromsø Study (conducted in 1994-1995, 2001-2002, and 2007-2008) and followed up to 2010. All incident MI and VTE events during follow-up were recorded. Cox regression models with age as the time scale and MI as a time-dependent variable were used to calculate hazard ratios (HRs) of VTE adjusted for sex, body mass index, blood pressure, diabetes mellitus, HDL cholesterol, smoking, physical activity, and education level. Results During a median follow-up of 15.7 years, 1853 participants experienced an MI and 699 experienced a VTE. MI was associated with a 51% increased risk of VTE (HR 1.51; 95% confidence interval [CI] 1.08-2.10) and a 72% increased risk of pulmonary embolism (PE) (HR 1.72; 95% CI 1.07-2.75), but not significantly associated with the risk of deep vein thrombosis (DVT) (HR 1.36; 95% CI 0.86-2.15). The highest risk estimates for PE were observed during the first 6 months after the MI (HR 8.49; 95% CI 4.00-18.77). MI explained 6.2% of the PEs in the population (population attributable risk) and 78.5% of the PE risk in MI patients (attributable risk). Conclusions Our findings indicate that MI is associated with a transient increased VTE risk, independently of traditional atherosclerotic risk factors. The risk estimates were particularly high for PE.

Atlanto-axial infection after acupuncture.

A 67-year-old man presented with neck cellulitis following acupuncture for cervical spondylosis. Blood cultures were positive for methicillin-sensitive Staphylococcus aureus Increased neck pain and bacteraemia prompted MRI, which showed atlanto-axial septic arthritis without signs of infection of the tissues between the superficial cellulitic area and the atlanto-axial joint, thus making direct extension of infection unlikely. It is more likely that haematogenous spread of infection resulted in seeding in the atlanto-axial joint, with the proximity of the arthritis and acupuncture site being coincidental. Acupuncture is a treatment option for some indolent pain conditions. As such, acupuncture services are likely to be more frequently utilised. A history of acupuncture is rarely requested by the admitting doctor and seldom offered voluntarily by the patient, especially where the site of infection due to haematogenous spread is distant from the needling location. Awareness of infectious complications following acupuncture can reduce morbidity through early intervention.

Determining performance characteristics of an NGS-based HLA typing method for clinical applications.

This study presents performance specifications of an in-house developed human leukocyte antigen (HLA) typing assay using next-generation sequencing (NGS) on the Illumina MiSeq platform. A total of 253 samples, previously characterized for HLA-A, -B, -C, -DRB1 and -DQB1 were included in this study, which were typed at high-resolution using a combination of Sanger sequencing, sequence-specific primer (SSP) and sequence-specific oligonucleotide probe (SSOP) technologies and recorded at the two-field level. Samples were selected with alleles that cover a high percentage of HLA specificities in each of five different race/ethnic groups: European, African-American, Asian Pacific Islander, Hispanic and Native American. Sequencing data were analyzed by two software programs, Omixon's target and GenDx's NGSengine. A number of metrics including allele balance, sensitivity, specificity, precision, accuracy and remaining ambiguity were assessed. Data analyzed by the two software systems are shown independently. The majority of alleles were identical in the exonic sequences (third field) with both programs for HLA-A, -B, -C and -DQB1 in 97.7% of allele determinations. Among the remaining discrepant genotype calls at least one of the analysis programs agreed with the reference typing. Upon additional manual analysis 100% of the 2530 alleles were concordant with the reference HLA genotypes; the remaining ambiguities did not exceed 0.8%. The results demonstrate the feasibility and significant benefit of HLA typing by NGS as this technology is highly accurate, eliminates virtually all ambiguities, provides complete sequencing information for the length of the HLA gene and forms the basis for utilizing a single methodology for HLA typing in the immunogenetics labs.

Computer-aided combined movement examination of the lumbar spine and manual therapy implications: Case report.

Combined movement examination (CME) of the lumbar spine has been recommended for clinical examination as it confers information about mechanical pain patterns. However, little quantitative study has been undertaken to validate its use in manual therapy practice. This study used computer aided CME to develop a normal reference range, and to guide provisional diagnosis and management. Two cases were assessed, before and after manual therapy using CME, a pain Visual Analogue Scale, the Roland Morris Low Back Pain and Disability Questionnaire and the Short Form (SF-12) Health Survey. Diagnosis and management were guided by comparing each CME pattern with the age and gender matched reference range. Self-reports data and CME total change scores were markedly improved for both cases, particularly for the most painful and restricted CME directions. This report describes how computer-aided CME and a normal reference range may be used objectively to inform a diagnosis and as an outcome measure in cases of mechanical LBP. Future investigations of cases with specific lumbar pathologies are required to validate this concept.

Atlanto-axial infection after acupuncture.

A 67-year-old man presented with neck cellulitis following acupuncture for cervical spondylosis. Blood cultures were positive for methicillin-sensitive Staphylococcus aureus. Increased neck pain and bacteraemia prompted MRI, which showed atlanto-axial septic arthritis without signs of infection of the tissues between the superficial cellulitic area and the atlanto-axial joint, thus making direct extension of infection unlikely. It is more likely that haematogenous spread of infection resulted in seeding in the atlanto-axial joint, with the proximity of the arthritis and acupuncture site being coincidental. Acupuncture is a treatment option for some indolent pain conditions. As such, acupuncture services are likely to be more frequently utilised. A history of acupuncture is rarely requested by the admitting doctor and seldom offered voluntarily by the patient, especially where the site of infection due to haematogenous spread is distant from the needling location. Awareness of infectious complications following acupuncture can reduce morbidity through early intervention.

Towards allele-level human leucocyte antigens genotyping - assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq.

Human leucocyte antigens (HLA) typing has been a challenge due to extreme polymorphism of the HLA genes and limitations of the current technologies and protocols used for their characterization. Recently, next-generation sequencing techniques have been shown to be a well-suited technology for the complete characterization of the HLA genes. However, a comprehensive assessment of the different platforms for HLA typing, describing the limitations and advantages of each of them, has not been presented. We have compared the Ion Torrent Personal Genome Machine (PGM) and Illumina MiSeq, currently the two most frequently used platforms for diagnostic applications, for a number of metrics including total output, quality score per position across the reads and error rates after alignment which can all affect the accuracy of HLA genotyping. For this purpose, we have used one homozygous and three heterozygous well-characterized samples, at HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1. The total output of bases produced by the MiSeq was higher, and they have higher quality scores and a lower overall error rate than the PGM. The MiSeq also has a higher fidelity when sequencing through homopolymer regions up to 9 bp in length. The need to set phase between distant polymorphic sites was more readily achieved with MiSeq using paired-end sequencing of fragments that are longer than those obtained with PGM. Additionally, we have assessed the workflows of the different platforms for complexity of sample preparation, sequencer operation and turnaround time. The effects of data quality and quantity can impact the genotyping results; having an adequate amount of good quality data to analyse will be imperative for confident HLA genotyping. The overall turnaround time can be very comparable between the two platforms; however, the complexity of sample preparation is higher with PGM, while the actual sequencing time is longer with MiSeq.

Assessing the clinical utility of combined movement examination in symptomatic degenerative lumbar spondylosis.

OBJECTIVES: The aim of this study is to report the development and validation of a low back computer-aided combined movement examination protocol in normal individuals and record treatment outcomes of cases with symptomatic degenerative lumbar spondylosis. DESIGN: Test-retest, following intervention. BACKGROUND: Self-report assessments and combined movement examination were used to record composite spinal motion, before and following neurosurgical and pain medicine interventions. METHODS: 151 normal individuals aged from 20 years to 69 years were assessed using combined movement examination between L1 and S1 spinal levels to establish a reference range. Cases with degenerative low back pain and sciatica were assessed before and after therapeutic interventions with combined movement examination and a battery of self-report pain and disability questionnaires. Change scores for combined movement examination and all outcome measures were derived. FINDINGS: Computer-aided combined movement examination validation and intraclass correlation coefficient with 95% confidence interval and least significant change scores indicated acceptable reliability of combined movement examination when recording lumbar movement in normal subjects. In both clinical cases lumbar spine movement restrictions corresponded with self-report scores for pain and disability. Post-intervention outcomes all showed significant improvement, particularly in the most restricted combined movement examination direction. INTERPRETATION: This study provides normative reference data for combined movement examination that may inform future clinical studies of the technique as a convenient objective surrogate for important clinical outcomes in lumbar degenerative spondylosis. It can be used with good reliability, may be well tolerated by individuals in pain and appears to change in concert with validated measures of lumbar spinal pain, functional limitation and quality of life.

Identification and characterization of a novel HLA-B hybrid allele, B*08:132 with Next Generation Sequencing.

The new allele is a hybrid between B*08:01:01 and B*42:01:01.

Identification of a novel HLA-DQB1*02 variant allele, DQB1*02:01:06.

The new HLA-DQB1 allele most closely resembles DQB1*02:01:01, differing at a single position 141 (exon 2, codon 15.3).

Study of B1 (NaCl-type) to B2 (CsCl-type) pressure-induced structural phase transition in BaS, BaSe and BaTe using ab initio computations.

We have studied the pressure-induced phase transitions from NaCl-type (B1) to CsCl-type (B2) structure in BaS, BaSe and BaTe by using ab initio density functional theory computations in the local density approximation. The Buerger and WTM mechanisms were explored by mapping the enthalpy contours in two- and four-dimensional configuration space for the two mechanisms, respectively. Transition pressures for BaS, BaSe and BaTe were determined to be 5.5 GPa, 4.9 GPa and 3.4 GPa, respectively. From these configuration space landscapes, a low enthalpy barrier path was constructed for the transitions to proceed at three different pressures. We obtained barriers of 0.18, 0.16 and 0.15 eV/pair (17.4, 15.4 and 14.5 kJ mol(-1)) for the Buerger mechanism and 0.13, 0.13 and 0.12 eV/pair (12.5, 12.5 and 11.6 kJ mol(-1)) for the WTM mechanism at the transition pressures for BaS, BaSe and BaTe, respectively, indicating that the WTM mechanism is slightly more favorable in these compounds. We describe the difference between the two mechanisms by differences in their symmetry and atomic coordination.

16(th) IHIW : review of HLA typing by NGS.

Human leucocyte antigen (HLA) genes play an important role in the success of organ transplantation and are associated with autoimmune and infectious diseases. Current DNA-based genotyping methods, including Sanger sequence-based typing (SSBT), have identified a high degree of polymorphism. This level of polymorphism makes high-resolution HLA genotyping challenging, resulting in ambiguous typing results due to an inability to resolve phase and/or defining polymorphisms lying outside the region amplified. Next-generation sequencing (NGS) may resolve the issue through the combination of clonal amplification, which provides phase information, and the ability to sequence larger regions of genes, including introns, without the additional effort or cost associated with current methods. The NGS HLA sequencing project of the 16IHIW aimed to discuss the different approaches to (i) template preparation including short- and long-range PCR amplicons, exome capture and whole genome; (ii) sequencing platforms, including GS 454 FLX, Ion Torrent PGM, Illumina MiSeq/HiSeq and Pacific Biosciences SMRT; (iii) data analysis, specifically allele-calling software. The pilot studies presented at the workshop demonstrated that although individual sequencers have very different performance characteristics, all produced sequence data suitable for the resolution of HLA genotyping ambiguities. The developments presented at this workshop clearly highlight the potential benefits of NGS in the HLA laboratory.