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The North Carolina Wildlife Resources Commission has used coded wire tags to mark fish. We evaluated coded wire tags placed at three different anatomical locations (left cheek, right cheek and snout) in brown trout (Salmo trutta) fingerlings (range of mean annual total lengths = 81.31 – 101.89 mm) prior to stockings (10,000 fish per tagging location). We determined the probability of tag retention at zero, 87 and 176 days posttagging across mean fish lengths. Anatomical tagging location influenced the probability of a fish being tagged. At all evaluation periods and for all mean sizes, brown trout fingerlings tagged in the left cheek had higher probabilities of being tagged than other positions of tags, with snout tags performing the worst. Intra-location comparisons revealed a decline in tag retention across temporal scales. Days posttagging had a negative effect on probability of tag retention, while length had a positive effect on the probability of tag retention. Our results indicated that the likelihood of a tag being present at 176 days was influenced by position of tag and initial tagging success more so than length or days posttagging. Although tag retention was generally high across all tag positions, differences in retention revealed the need to refine the tagging procedure. In addition, the underperformance of coded wire tags placed in the snout suggested that alternative marking locations should be explored.

Skillful marine biogeochemical (BGC) models are required to understand a range of coastal and global phenomena such as changes in nitrogen and carbon cycles. The refinement of BGC models through the assimilation of variables calculated from observed in-water inherent optical properties (IOPs), such as phytoplankton absorption, is problematic. Empirically derived relationships between IOPs and variables such as chlorophyll-a concentration (Chl a), total suspended solids (TSS) and coloured dissolved organic matter (CDOM) have been shown to have errors that can exceed 100 % of the observed quantity. These errors are greatest in shallow coastal regions, such as the Great Barrier Reef (GBR), due to the additional signal from bottom reflectance. Rather than assimilate quantities calculated using IOP algorithms, this study demonstrates the advantages of assimilating quantities calculated directly from the less error-prone satellite remote-sensing reflectance (RSR). To assimilate the observed RSR, we use an in-water optical model to produce an equivalent simulated RSR and calculate the mismatch between the observed and simulated quantities to constrain the BGC model with a deterministic ensemble Kalman filter (DEnKF). The traditional assumption that simulated surface Chl a is equivalent to the remotely sensed OC3M estimate of Chl a resulted in a forecast error of approximately 75 %. We show this error can be halved by instead using simulated RSR to constrain the model via the assimilation system. When the analysis and forecast fields from the RSR-based assimilation system are compared with the non-assimilating model, a comparison against independent in situ observations of Chl a, TSS and dissolved inorganic nutrients (NO3, NH4 and DIP) showed that errors are reduced by up to 90 %. In all cases, the assimilation system improves the simulation compared to the non-assimilating model. Our approach allows for the incorporation of vast quantities of remote-sensing observations that have in the past been discarded due to shallow water and/or artefacts introduced by terrestrially derived TSS and CDOM or the lack of a calibrated regional IOP algorithm.

In contrast to physical processes, biogeochemical processes are inherently patchy in the ocean, which affects both the observational sampling strategy and the representativeness of sparse measurements in data assimilating models. In situ observations from multiple glider deployments are analysed to characterize spatial scales of variability in both physical and biogeochemical properties, using an empirical statistical model. We find that decorrelation ranges are strongly dependent on the balance between local dynamics and mesoscale forcing. The shortest horizontal (5–10 km) and vertical (45 m) decorrelation ranges are for chlorophyll a fluorescence, whereas those variables that are a function of regional ocean and atmosphere dynamics (temperature and dissolved oxygen) result in anisotropic patterns with longer ranges along (28–37 km) than across the shelf (8–19 km). Variables affected by coastal processes (salinity and coloured dissolved organic matter) have an isotropic range similar to the baroclinic Rossby radius (10–15 km).

Observations along the southwestern Atlantic WOCE A17 line made during the Dutch GEOTRACES-NL programme (2010–2011) were compared with historical data from 1994 to quantify the changes in the anthropogenic component of the total pool of dissolved inorganic carbon (ΔCant). Application of the extended multi-linear regression (eMLR) method shows that the ΔCant from 1994 to 2011 has largely remained confined to the upper 1000 dbar. The greatest changes occur in the upper 200 dbar in the Subantarctic Zone (SAZ), where a maximum increase of 37 μmol kg−1 is found. South Atlantic Central Water (SACW) experienced the highest rate of increase in Cant, at 0.99 ± 0.14 μmol kg−1 yr−1, resulting in a maximum rate of decrease in pH of 0.0016 yr−1. The highest rates of acidification relative to ΔCant, however, were found in Subantarctic Mode Water (SAMW) and Antarctic Intermediate Water (AAIW). The low buffering capacity of SAMW and AAIW combined with their relatively high rates of Cant, increase of 0.53 ± 0.11 and 0.36 ± 0.06 μmol kg−1 yr−1, respectively, has lead to rapid acidification in the SAZ, and will continue to do so whilst simultaneously reducing the chemical buffering capacity of this significant CO2 sink.

Water column dissolved inorganic carbon and total alkalinity were measured during five hydrographic sections in the Atlantic Ocean and Drake Passage. The work was funded through the Strategic Funding Initiative of the UK's Oceans2025 programme, which ran from 2007 to 2012. The aims of this programme were to establish the regional budgets of natural and anthropogenic carbon in the North Atlantic, the South Atlantic, and the Atlantic sector of the Southern Ocean, as well as the rates of change of these budgets. This paper describes in detail the dissolved inorganic carbon and total alkalinity data collected along east–west sections at 47° N to 60° N, 24.5° N, and 24° S in the Atlantic and across two Drake Passage sections. Other hydrographic and biogeochemical parameters were measured during these sections, and relevant standard operating procedures are mentioned here. Over 95% of dissolved inorganic carbon and total alkalinity samples taken during the 24.5° N, 24° S, and the Drake Passage sections were analysed onboard and subjected to a first-level quality control addressing technical and analytical issues. Samples taken along 47° N to 60° N were analysed and subjected to quality control back in the laboratory. Complete post-cruise second-level quality control was performed using cross-over analysis with historical data in the vicinity of measurements, and data were submitted to the CLIVAR and Carbon Hydrographic Data Office (CCHDO), the Carbon Dioxide Information Analysis Center (CDIAC) and and will be included in the Global Ocean Data Analyses Project, version 2 (GLODAP 2), the upcoming update of Key et al. (2004).

The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO2 values) and extended data coverage (from 1968–2007 to 1968–2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models. Data coverage Repository-References: Individual data set files and synthesis product: doi:10.1594/PANGAEA.811776 Gridded products: doi:10.3334/CDIAC/OTG.SOCAT_V2_GRID Available at: http://www.socat.info/ Coverage: 79° S to 90° N; 180° W to 180° E Location Name: Global Oceans and Coastal Seas Date/Time Start: 16 November 1968 Date/Time End: 26 December 2011

Introduction: Unilateral tonsillar enlargement is often seen in the out-patient setting. Frequently, these patients are listed for tonsillectomy for the purpose of ruling out malignant histology. This study aims to determine the necessity for tonsillectomy.Method: This retrospective case-note review looks at all the tonsillectomies performed for histological examination at our institution over a five year period, and analyses the histological findings in those with unilateral tonsillar enlargement (UTE) alone, and those with UTE with other clinical features (history of chronic pain, dysphagia, the presence of tonsillar or peritonsillar mucosal abnormality, those with cervical lymphadenopathy). All patients who underwent tonsillectomy for the purpose of histological examination from 1 June 1998 to 30 May 2003 were identified and their notes reviewed. Exclusion criteria included cases where there were no pre-operative out-patient notes, those patients where the specimens had been sent from other hospitals, those patients who had malignancy already diagnosed, and those cases where tonsillectomy had been performed by other surgical specialties (e.g. maxillofacial, plastics). There were 1475 tonsillectomies, of which 181 performed over this period were sent for histological analysis. After excluding those patients that did not meet our criteria, we were left with 53 patients who had UTE. The primary outcome measure was the rate of malignancy in the two groups.Results: Of these, 33 had UTE alone, 20 had associated clinical features. In the former group, none of the patients were found to have malignancy. In the latter, nine (45 per cent) had a malignancy. Fisher''s exact test was used to test for differences between the UTE alone group versus the UTE plus other features group (p<0.001).Discussion: The prevalence of malignancy in tonsils which exhibit asymmetry with no other clinical features is very low; in our study it was zero. However, other studies have found a small percentage representing underlying malignancy. In view of this, we feel that a ‘watch and wait’ policy is initially more appropriate, and if symptoms or signs are progressive, tonsillectomy should then be advised. [ABSTRACT FROM AUTHOR]

Background: A prospective audit of specialist registrars'' (SRs'') training in tympanomastoid surgery for chronic otitis media within the Anglia Regional Training Scheme is described. This audit recorded the surgical activity of the trainees and their contribution to operative procedures, and assessed the results of the procedures. This type of systematic approach to the audit of surgical training is important in light of the current shortened training programmes and increased accountability of trainers.Objectives: The study aimed to establish the levels of exposure to, supervision of and outcome of ear operations for chronic otitis media performed by ENT trainees in the East Anglia region.Method: A prospective, region-wide, minimum otology dataset-based proforma audit was undertaken, with compulsory SR participation. Proformas were completed at the time of operation (form one) and at a minimum interval of nine months post-operatively (form two). Data on form one included hospital, supervising consultant, name and training year of SR, contribution of SR (based on England Royal College of Surgeons guidelines interpreted by the SR), pre-operative audiology average (air conduction/bone conduction over 0.5, 1, 2 and 4 kHz), the pathology and the state of the ear at the time of surgery, and a breakdown of the procedure(s) undertaken. Form two recorded data relevant to form one as well as information regarding patient satisfaction and the operative result obtained, graded as ‘gold’ (no disease, dry ear and hearing average < 25 dB), ‘silver’ (two of these three) and ‘bronze’ (one of these three). All completed forms were analysed using Microsoft Access software.;> 3;  3;Results: Completed copies of 409 form ones and 156 form twos were analysed. With advancing years, SRs'' contributions to procedures increased without significant effect on the graded outcome, which appeared to be independent of SR year of training. Different regional hospitals were compared. Data collected also provided an otology training portfolio for SRs, forming part of their registrar in-training assessment (RITA).Conclusion: The East Anglia SR audit of SRs'' training in tympanomastoid surgery for chronic otitis media was a powerful training tool. It demonstrated the safe progression of SR training in supervised ear surgery, with SRs'' results being comparable to those for consultant-performed procedures. [ABSTRACT FROM AUTHOR]

The investigation of a complaint of unilateral right sensorineural hearing loss led to the identification of a right 3 mm vestibular schwannoma arising from the inferior division of the right vestibular nerve. On investigation the patient was found to have normal caloric function, this being mediated by the superior vestibular nerve. Both transient and distortion product otoacoustic emissions were absent in the right ear, and ABR was abnormal on this side. These findings are of interest as they indicate that this small lesion produced a hearing loss that was both cochlear and retrocochlear. The anatomical finding that the medial auditory efferents run within the inferior vestibular nerve is considered. This patient did not experience tinnitus or hyperacusis despite the site of the lesion arising from the inferior vestibular nerve. [ABSTRACT FROM AUTHOR]

Abstract The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclature Committee, to approve gene nomenclature in vertebrate species without an existing dedicated nomenclature committee. The VGNC aims to harmonize gene nomenclature across selected vertebrate species in line with human gene nomenclature, with orthologs assigned the same nomenclature where possible. This article presents an overview of the VGNC project and discussion of key findings resulting from this work to date. VGNC-approved nomenclature is accessible at https://vertebrate.genenames.org and is additionally displayed by the NCBI, Ensembl, and UniProt databases.

Abstract Background Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

Summary Primordial germ cell (PGC) formation in holometabolous insects like Drosophila melanogaster relies on maternally synthesised germ cell determinants that are asymmetrically localised to the oocyte posterior cortex. Embryonic nuclei that inherit this “germ plasm” acquire PGC fate. In contrast, historical studies of basally branching insects (Hemimetabola) suggest that a maternal requirement for germ line genes in PGC specification may be a derived character confined principally to Holometabola. However, there have been remarkably few investigations of germ line gene expression and function in hemimetabolous insects. Here we characterise PGC formation in the milkweed bug Oncopeltus fasciatus, a member of the sister group to Holometabola, thus providing an important evolutionary comparison to members of this clade. We examine the transcript distribution of orthologues of 19 Drosophila germ cell and/or germ plasm marker genes, and show that none of them localise asymmetrically within Oncopeltus oocytes or early embryos. Using multiple molecular and cytological criteria, we provide evidence that PGCs form after cellularisation at the site of gastrulation. Functional studies of vasa and tudor reveal that these genes are not required for germ cell formation, but that vasa is required in adult males for spermatogenesis. Taken together, our results provide evidence that Oncopeltus germ cells may form in the absence of germ plasm, consistent with the hypothesis that germ plasm is a derived strategy of germ cell specification in insects.