Neisseria gonorrhoeae false-positive result obtained from a pharyngeal swab by using the roche cobas 4800 CT/NG assay in New Zealand in 2012

The Roche cobas 4800 CT/NG assay is a commonly used commercial system for screening for Neisseria gonorrhoeae infection, and previous studies have shown the method to be highly sensitive and specific for urogenital samples. We present the first confirmed clinical N. gonorrhoeae false-positive result using the cobas 4800 NG assay, obtained from testing a pharyngeal swab sample and caused by cross-reaction with a commensal Neisseria strain

Acceptability of human papillomavirus self-sampling for cervical-cancer screening in under-screened Māori and Pasifika women: a pilot study.

AIM: To assess whether self-sampling for cervical-cancer screening is acceptable to New Zealand women. METHODS: Māori, Pacific and Asian un- or under-screened women aged 30-69 years were asked to: 1) examine three self-sampling devices; 2) complete a questionnaire on demographics and experiences with the devices; and 3) take a self-sample. Samples were tested 'off-label' using the cobas® 4800 human papillomavirus (HPV) test (Roche Diagnostics NZ). RESULTS: Thirty-one Pacific, 12 Māori, nine Asian and four women of other ethnicities participated (mean age, 39.5 years). Before trying any devices, 78% indicated a preference to self-sample, compared to 22% who preferred a physician-collected sample (PCS). After trying a device (HerSwab™, 91%; Delphi Screener™, 14%; cobas Swab, 13%; 12.5% used >1 device), fewer women (66%) preferred to self-sample next time, fewer (16%) preferred a PCS, while 18% expressed no preference. One of 32 samples with valid results (35 were tested) was positive for HPV 'other' oncogenic types. CONCLUSIONS: This was the first New Zealand study to invite women, including Māori women, to take a self-sample for cervical-cancer screening. The pilot study suggests that un- and under-screened women generally find self-sampling acceptable and all sample types are suitable for use with the cobas HPV test

Mutations in RAB39B Cause X-Linked Intellectual Disability and Early-Onset Parkinson Disease with alpha-Synuclein Pathology

Advances in understanding the etiology of Parkinson disease have been driven by the identification of causative mutations in families. Genetic analysis of an Australian family with three males displaying clinical features of early-onset parkinsonism and intellectual disability identified a approximately 45 kb deletion resulting in the complete loss of RAB39B. We subsequently identified a missense mutation (c.503C>A [p.Thr168Lys]) in RAB39B in an unrelated Wisconsin kindred affected by a similar clinical phenotype. In silico and in vitro studies demonstrated that the mutation destabilized the protein, consistent with loss of function. In vitro small-hairpin-RNA-mediated knockdown of Rab39b resulted in a reduction in the density of alpha-synuclein immunoreactive puncta in dendritic processes of cultured neurons. In addition, in multiple cell models, we demonstrated that knockdown of Rab39b was associated with reduced steady-state levels of alpha-synuclein. Post mortem studies demonstrated that loss of RAB39B resulted in pathologically confirmed Parkinson disease. There was extensive dopaminergic neuron loss in the substantia nigra and widespread classic Lewy body pathology. Additional pathological features included cortical Lewy bodies, brain iron accumulation, tau immunoreactivity, and axonal spheroids. Overall, we have shown that loss-of-function mutations in RAB39B cause intellectual disability and pathologically confirmed early-onset Parkinson disease. The loss of RAB39B results in dysregulation of alpha-synuclein homeostasis and a spectrum of neuropathological features that implicate RAB39B in the pathogenesis of Parkinson disease and potentially other neurodegenerative disorders

Comparison of the cobas 4800 CT/NG test with culture for detecting neisseria gonorrhoeae in genital and nongenital specimens in a low-prevalence population in New Zealand

To assess the clinical utility of replacing microbial culture for Neisseria gonorrhoeae with a nucleic acid amplification test (NAAT), we compared N. gonorrhoeae culture with the cobas 4800 CT/NG test for 18,247 urogenital and 666 nongenital samples. For urogenital specimens, the sensitivity, specificity, and positive and negative predictive values of the cobas N. gonorrhoeae PCR were 98.7%, 100%, 95.6%, and 100%, respectively, and for nongenital specimens, the values were 100%, 99.8%, 92.9%, and 100%, respectively. In our test population, 37% (10,185) of patients tested over the study period were screened for C. trachomatis by PCR but were not screened for gonorrhea by culture. Of these, 43 were N. gonorrhoeae positive by PCR and therefore went undiagnosed. The cobas 4800 CT/NG test diagnosed 33% (n=30) more urogenital and 25% (n=3) more rectal gonorrhea infections than culture and, based on the above performance indicators, does not require supplementary testing for urogenital or rectal specimens. The ability to test noninvasive specimens (such as urine and self-taken vulvovaginal swabs) for N. gonorrhoeae will enable more patients to be screened for infection, thus offering significant positive public health benefits. Copyrigh

Spatial and Sex-Specific Variation in Growth of Albacore Tuna (Thunnus alalunga) across the South Pacific Ocean

Spatial variation in growth is a common feature of demersal fish populations which often exist as discrete adult sub-populations linked by a pelagic larval stage. However, it remains unclear whether variation in growth occurs at similar spatial scales for populations of highly migratory pelagic species, such as tuna. We examined spatial variation in growth of albacore Thunnus alalunga across 90° of longitude in the South Pacific Ocean from the east coast of Australia to the Pitcairn Islands. Using length-at-age data from a validated ageing method we found evidence for significant variation in length-at-age and growth parameters (L∞ and k) between sexes and across longitudes. Growth trajectories were similar between sexes up until four years of age, after which the length-at-age for males was, on average, greater than that for females. Males reached an average maximum size more than 8 cm larger than females. Length-at-age and growth parameters were consistently greater at more easterly longitudes than at westerly longitudes for both females and males. Our results provide strong evidence that finer spatial structure exists within the South Pacific albacore stock and raises the question of whether the scale of their “highly migratory” nature should be re-assessed. Future stock assessment models for South Pacific albacore should consider sex-specific growth curves and spatial variation in growth within the stock

Where Snow is a Landmark: Route Direction Elements in Alpine Contexts

Route directions research has mostly focused on urban space so far, highlighting human concepts of street networks based on a range of recurring elements such as route segments, decision points, landmarks and actions. We explored the way route directions reflect the features of space and activity in the context of mountaineering. Alpine route directions are only rarely segmented through decision points related to reorientation; instead, segmentation is based on changing topography. Segments are described with various degrees of detail, depending on difficulty. For landmark description, direction givers refer to properties such as type of surface, dimension, colour of landscape features; terrain properties (such as snow) can also serve as landmarks. Action descriptions reflect the geometrical conceptualization of landscape features and dimensionality of space. Further, they are very rich in the semantics of manner of motion

Investigating Behaviour and Population Dynamics of Striped Marlin (Kajikia audax) from the Southwest Pacific Ocean with Satellite Tags

Behaviour and distribution of striped marlin within the southwest Pacific Ocean were investigated using electronic tagging data collected from 2005–2008. A continuous-time correlated random-walk Kalman filter was used to integrate double-tagging data exhibiting variable error structures into movement trajectories composed of regular time-steps. This state-space trajectory integration approach improved longitude and latitude error distributions by 38.5 km and 22.2 km respectively. Using these trajectories as inputs, a behavioural classification model was developed to infer when, and where, ‘transiting’ and ‘area-restricted’ (ARB) pseudo-behavioural states occurred. ARB tended to occur at shallower depths (108±49 m) than did transiting behaviours (127±57 m). A 16 day post-release period of diminished ARB activity suggests that patterns of behaviour were affected by the capture and/or tagging events, implying that tagged animals may exhibit atypical behaviour upon release. The striped marlin in this study dove deeper and spent greater time at ≥200 m depth than those in the central and eastern Pacific Ocean. As marlin reached tropical latitudes (20–21°S) they consistently reversed directions, increased swimming speed and shifted to transiting behaviour. Reversals in the tropics also coincided with increases in swimming depth, including increased time ≥250 m. Our research provides enhanced understanding of the behavioural ecology of striped marlin. This has implications for the effectiveness of spatially explicit population models and we demonstrate the need to consider geographic variation when standardizing CPUE by depth, and provide data to inform natural and recreational fishing mortality parameters

Habitat partitioning and vulnerability of sharks in the Great Barrier Reef Marine Park

Sharks present a critical conservation challenge, but little is known about their spatial distribution and vulnerability, particularly in complex seascapes such as Australia's Great Barrier Reef Marine Park (GBRMP). We review (1) the distribution of shark species among the primary habitats of the GBRMP (coral reefs, inshore/shelf, pelagic and deep-water habitats) (2) the relative exploitation of each species by fisheries, and (3) how current catch rates interact with their vulnerability and trophic index. Excluding rays and chimaeras, we identify a total of 82 shark species in the GBRMP. We find that shark research in the GBRMP has yielded little quantitative information on most species. Reef sharks are largely site-fidelic, but can move large distances and some regularly use non-reef habitats. Inshore and shelf sharks use coastal habitats either exclusively or during specific times in their life cycle (e.g. as nurseries). Virtually nothing is known about the distribution and habitat use of the GBRMP's pelagic and deep-water sharks. At least 46 species (53.5 %) are caught in one or more fisheries, but stock assessments are lacking for most. At least 17 of the sharks caught are considered highly vulnerable to exploitation. We argue that users of shark resources should be responsible for demonstrating that a fishery is sustainable before exploitation is allowed to commence or continue. This fundamental change in management principle will safeguard against stock collapses that have characterised many shark fisheries