Genetic and morphological variation of the lanternfish Lampanyctodes hectoris (Myctophiformes: Myctophidae) off southern Africa

Genetic and morphological variation within the southern African population of Lampanyctodes hectoris was analysed. A total of 15 enzymes, encoding 22 isozyme loci, was examined (n = 327); seven were polymorphic. The percentage of polymorphic loci ranged from 13.6 to 27.3%. The mean heterozygosity was generally low and ranged from 0.003 to 0.005. Genetic divergences between specimens from four areas along the west coast of southern Africa were negligible, genetic distance values (D) ranging from 0 to 0.00011. The results showed the population of L. hectoris to be genetically invariant. Principal Component Analysis was performed separately on ratios of 13 morphometric and 6 meristic variables (n = 446), and there was evidence of extensive overlap between fish from all areas. However, discriminant analysis suggested some morphological variability within this population. Although genetically the population of L. hectoris seems to be homogenous, morphologically it appears to be variable. A combination of these results suggests that there is no clear genetic basis for the slight morphological differentiation within the population. Keywords: Agulhas Bank, Benguela Current, lanternfish, Namibia, population geneticsAfrican Journal of Marine Science 2002, 24: 193–20

Are infestations of Cymomelanodactylus killing Acropora cytherea in the Chagos archipelago?

Associations between branching corals and infaunal crabs are well known, mostly due to the beneficial effects of Trapezia and Tetralia crabs in protecting host corals from crown-of-thorns starfish (e.g., Pratchett et al. 2000) and/or sedimentation (Stewart et al. 2006). These crabs are obligate associates of live corals and highly prevalent across suitable coral hosts, with 1–2 individuals per colony (Patton 1994). Cymo melanodactylus (Fig. 1) are also prevalent in branching corals, mostly Acropora, and are known to feed on live coral tissue, but are generally found in low abundance (<3 per colony) and do not significantly affect their host corals (e.g., Patton 1994). In the Chagos archipelago, however, infestations of Cymo melanodactylus were found on recently dead and dying colonies of Acropora cytherea

What is the real impact of acute kidney injury?

Background: Acute kidney injury (AKI) is a common clinical problem. Studies have documented the incidence of AKI in a variety of populations but to date we do not believe the real incidence of AKI has been accurately documented in a district general hospital setting. The aim here was to describe the detected incidence of AKI in a typical general hospital setting in an unselected population, and describe associated short and long-term outcomes. Methods: A retrospective observational database study from secondary care in East Kent (adult catchment population of 582,300). All adult patients (18 years or over) admitted between 1st February 2009 and 31st July 2009, were included. Patients receiving chronic renal replacement therapy (RRT), maternity and day case admissions were excluded. AKI was defined by the acute kidney injury network (AKIN) criteria. A time dependent risk analysis with logistic regression and Cox regression was used for the analysis of in-hospital mortality and survival. Results: The incidence of AKI in the 6 month period was 15,325 pmp/yr (adults) (69% AKIN1, 18% AKIN2 and 13% AKIN3). In-hospital mortality, length of stay and ITU utilisation all increased with severity of AKI. Patients with AKI had an increase in care on discharge and an increase in hospital readmission within 30 days. Conclusions: This data comes closer to the real incidence and outcomes of AKI managed in-hospital than any study published in the literature to date. Fifteen percent of all admissions sustained an episode of AKI with increased subsequent short and long term morbidity and mortality, even in those with AKIN1. This confers an increased burden and cost to the healthcare economy, which can now be quantified. These results will furnish a baseline for quality improvement projects aimed at early identification, improved management, and where possible prevention, of AKI

Multi-domain clinical natural language processing with MedCAT: The Medical Concept Annotation Toolkit

Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of information extraction (IE) technologies to enable clinical analysis. We present the open source Medical Concept Annotation Toolkit (MedCAT) that provides: (a) a novel self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT; (b) a feature-rich annotation interface for customizing and training IE models; and (c) integrations to the broader CogStack ecosystem for vendor-agnostic health system deployment. We show improved performance in extracting UMLS concepts from open datasets (F1:0.448-0.738 vs 0.429-0.650). Further real-world validation demonstrates SNOMED-CT extraction at 3 large London hospitals with self-supervised training over ∼8.8B words from ∼17M clinical records and further fine-tuning with ∼6K clinician annotated examples. We show strong transferability (F1 > 0.94) between hospitals, datasets and concept types indicating cross-domain EHR-agnostic utility for accelerated clinical and research use cases

Binding of Transcription Factor GabR to DNA Requires Recognition of DNA Shape at a Location Distinct from its Cognate Binding Site

Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR–DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR–DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites

Phenotypic Variation and Bistable Switching in Bacteria

Microbial research generally focuses on clonal populations. However, bacterial cells with identical genotypes frequently display different phenotypes under identical conditions. This microbial cell individuality is receiving increasing attention in the literature because of its impact on cellular differentiation, survival under selective conditions, and the interaction of pathogens with their hosts. It is becoming clear that stochasticity in gene expression in conjunction with the architecture of the gene network that underlies the cellular processes can generate phenotypic variation. An important regulatory mechanism is the so-called positive feedback, in which a system reinforces its own response, for instance by stimulating the production of an activator. Bistability is an interesting and relevant phenomenon, in which two distinct subpopulations of cells showing discrete levels of gene expression coexist in a single culture. In this chapter, we address techniques and approaches used to establish phenotypic variation, and relate three well-characterized examples of bistability to the molecular mechanisms that govern these processes, with a focus on positive feedback.

Symptom Dimensions in OCD: Item-Level Factor Analysis and Heritability Estimates

To reduce the phenotypic heterogeneity of obsessive-compulsive disorder (OCD) for genetic, clinical and translational studies, numerous factor analyses of the Yale-Brown Obsessive Compulsive Scale checklist (YBOCS-CL) have been conducted. Results of these analyses have been inconsistent, likely as a consequence of small sample sizes and variable methodologies. Furthermore, data concerning the heritability of the factors are limited. Item and category-level factor analyses of YBOCS-CL items from 1224 OCD subjects were followed by heritability analyses in 52 OCD-affected multigenerational families. Item-level analyses indicated that a five factor model: (1) taboo, (2) contamination/cleaning, (3) doubts, (4) superstitions/rituals, and (5) symmetry/hoarding provided the best fit, followed by a one-factor solution. All 5 factors as well as the one-factor solution were found to be heritable. Bivariate analyses indicated that the taboo and doubts factor, and the contamination and symmetry/hoarding factor share genetic influences. Contamination and symmetry/hoarding show shared genetic variance with symptom severity. Nearly all factors showed shared environmental variance with each other and with symptom severity. These results support the utility of both OCD diagnosis and symptom dimensions in genetic research and clinical contexts. Both shared and unique genetic influences underlie susceptibility to OCD and its symptom dimensions.Obsessive Compulsive FoundationTourette Syndrome AssociationAnxiety Disorders Association of AmericaAmerican Academy of Child and Adolescent Psychiatr

The relationship between quality of life and compliance to a brace protocol in adolescents with idiopathic scoliosis: a comparative study

<p>Abstract</p> <p>Background</p> <p>Corrective bracing for adolescent idiopathic scoliosis (AIS) has favourable outcomes when patients are compliant. However, bracing may be a stressful and traumatic experience and compliance with a bracing protocol is likely to be dependent upon patients' physical, emotional and social wellbeing. The Brace Questionnaire (BrQ), a recently-developed, condition-specific tool to measure quality of life (QOL) has enabled clinicians to study relationships between QOL and compliance.</p> <p>Methods</p> <p>The BrQ was administered to 31 AIS patients after a minimum of 1 year of wearing a brace. Subjects were 13–16 year old South African girls with Cobb angles of 25–40 degrees. Participants were divided into two groups according to their level of compliance with the bracing protocol. Brace Questionnaire sub- and total scores were compared between the two groups using the t-test for comparison of means.</p> <p>Results</p> <p>Twenty participants were classified as compliant and 11 as non-compliant. Mean total BrQ scores (expressed as a percentage) were 83.7 for the compliant group and 64.4 for the non-compliant group (p < 0.001), and on analysis of the 8 domains that make up the BrQ, the compliant group scored significantly higher in the 6 domains that measured vitality and social, emotional and physical functioning.</p> <p>Conclusion</p> <p>Poor compliance with a brace protocol is associated with poorer QOL, with non-compliant patients lacking vitality and functioning poorly physically, emotionally and socially. Quality of life for adolescents with idiopathic scoliosis may relate more to psychosocial coping mechanisms than to physical deformity and its consequences. It is important to establish whether remedial programmes are capable of addressing personal, group and family issues, improving QOL and promoting compliance.</p

PLA2G6-associated neurodegeneration (PLAN): Further expansion of the clinical, radiological and mutation spectrum associated with infantile and atypical childhood-onset disease

Phospholipase A2 associated neurodegeneration (PLAN) is a major phenotype of autosomal recessive Neurodegeneration with Brain Iron Accumulation (NBIA). We describe the clinical phenotypes, neuroimaging features and PLA2G6 mutations in 5 children, of whom 4 presented with infantile neuroaxonal dystrophy (INAD). One other patient was diagnosed with the onset of PLAN in childhood, and our report highlights the diagnostic challenges associated with this atypical PLAN subtype. In this series, the neuroradiological relevance of classical PLAN features as well as apparent claval hypertrophy' is explored. Novel PLA2G6 mutations were identified in all patients. PLAN should be considered not only in patients presenting with a classic INAD phenotype but also in older patients presenting later in childhood with non-specific progressive neurological features including social communication difficulties, gait disturbance, dyspraxia, neuropsychiatric symptoms and extrapyramidal motor features. © 2014 Elsevier Inc