SinEx DB: a database for single exon coding sequences in mammalian genomes

Indexación: Web of Science.Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.https://academic.oup.com/database/article-lookup/doi/10.1093/database/baw09

Influence of Loading Frequency on the Room-Temperature Fatigue of a Carbon-Fiber/SiC-Matrix Composite

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65216/1/j.1151-2916.1993.tb07772.x.pd

Evolutionary History and Attenuation of Myxoma Virus on Two Continents

The attenuation of myxoma virus (MYXV) following its introduction as a biological control into the European rabbit populations of Australia and Europe is the canonical study of the evolution of virulence. However, the evolutionary genetics of this profound change in host-pathogen relationship is unknown. We describe the genome-scale evolution of MYXV covering a range of virulence grades sampled over 49 years from the parallel Australian and European epidemics, including the high-virulence progenitor strains released in the early 1950s. MYXV evolved rapidly over the sampling period, exhibiting one of the highest nucleotide substitution rates ever reported for a double-stranded DNA virus, and indicative of a relatively high mutation rate and/or a continually changing selective environment. Our comparative sequence data reveal that changes in virulence involved multiple genes, likely losses of gene function due to insertion-deletion events, and no mutations common to specific virulence grades. Hence, despite the similarity in selection pressures there are multiple genetic routes to attain either highly virulent or attenuated phenotypes in MYXV, resulting in convergence for phenotype but not genotype. © 2012 Kerr et al

A decision-making framework for restoring riparian zones degraded by invasive alien plants in South Africa

The original publication is available at http://www.sabinet.co.za/?page=open-access-journalsRiparian habitats in many parts of South Africa are severely degraded by invasive alien plants, especially trees. These invasions reduce water yields from catchments and affect riverine functioning and biodiversity. Initiatives are under way countrywide to clear alien plants from watercourses and surrounding catchments. Current understanding of key processes that regulate riparian functioning and define options for restoration is rudimentary. We review the impacts of riparian invasions and identify factors limiting the recovery of natural vegetation following alien clearance. We propose a framework of strategic interventions for optimizing restoration success. The framework identifies abiotic and biotic barriers to restoration at the scales of catchments and local reaches. In highly transformed catchments, interventions at the reach scale may fail if important barriers at the catchment scale are not addressed. The extent to which propagule supply and microsite conditions inhibit vegetation recovery is unknown. We also know little of the relative importance of dispersing vegetative propagules, dispersing seeds and soil-stored seed banks in vegetation dynamics, particularly after severe disturbances such as dense invasion by alien plants. The importance of geomorphological and hydrological factors in mediating recovery of riparian vegetation has not been adequately explored for all climatic areas in South Africa. More research is needed to determine the influence of different alien species and clearing treatments on the recovery of riparian vegetation. The literature strongly suggests that in highly alien-transformed catchments, the re-introduction of riparian species is required to promote recovery and suppress re-invasion. However, such interventions are unlikely to be widely implemented unless the cost:benefit ratios are favourable.Publishers' Versio

Age-related dataset on the mechanical properties and collagen fibril structure of tendons from a murine model

Connective tissues such as tendon, ligament and skin are biological fibre composites comprising collagen fibrils reinforcing the weak proteoglycan-rich ground substance in extracellular matrix (ECM). One of the hallmarks of ageing of connective tissues is the progressive and irreversible change in the tissue mechanical properties; this is often attributed to the underlying changes to the collagen fibril structure. This dataset represents a comprehensive screen of the mechanical properties and collagen fibril structure of tendon from the tails of young to old (i.e. 1.6–35.3 month-old) C57BL6/B mice. The mechanical portion consists of the load-displacement data, as well as the derived tensile properties; the structure data consists of transmission electron micrographs of collagen fibril cross section, as well as the derived cross-sectional parameters. This dataset will allow other researchers to develop and demonstrate the utility of innovative multiscale models and approaches of the extra-cellular and physiological events of ageing of current interest to ageing research, by reducing the current reliance on conducting new mammalian experiments

Coalignment of plasma membrane channels and protrusions (fibripositors) specifies the parallelism of tendon

The functional properties of tendon require an extracellular matrix (ECM) rich in elongated collagen fibrils in parallel register. We sought to understand how embryonic fibroblasts elaborate this exquisite arrangement of fibrils. We show that procollagen processing and collagen fibrillogenesis are initiated in Golgi to plasma membrane carriers (GPCs). These carriers and their cargo of 28-nm-diam fibrils are targeted to previously unidentified plasma membrane (PM) protrusions (here designated “fibripositors”) that are parallel to the tendon axis and project into parallel channels between cells. The base of the fibripositor lumen (buried several microns within the cell) is a nucleation site of collagen fibrillogenesis. The tip of the fibripositor is the site of fibril deposition to the ECM. Fibripositors are absent at postnatal stages when fibrils increase in diameter by accretion of extracellular collagen, thereby maintaining parallelism of the tendon. Thus, we show that the parallelism of tendon is determined by the late secretory pathway and interaction of adjacent PMs to form extracellular channels

SHAPS-C: the Snaith-Hamilton pleasure scale modified for clinician administration

Anhedonia, a diminished or lack of ability to experience and anticipate pleasure represents a core psychiatric symptom in depression. Current clinician assessment of anhedonia is generally limited to one or two all-purpose questions and most well-known psychometric scales of anhedonia are relatively long, self-administered, typically not state sensitive, and are unsuitable for use in clinical settings. A user-friendly tool for a more in-depth clinician assessment of hedonic capacity is needed. The present study assessed the validity and reliability of a clinician administered version of the Snaith-Hamilton Pleasure Scale, the SHAPS-C, in 34 depressed subjects. We compared total and specific item scores on the SHAPS-C, SHAPS (self-report version), Montgomery-Åsberg Depression Rating Scale (MADRS), and the Inventory of Depressive Symptomatology-Self Rating version (IDS-SR). We also examined construct, content, concurrent, convergent, and discriminant validity, internal consistency, and split-half reliability of the SHAPS-C. The SHAPS-C was found to be valid and reliable. The SHAPS and the SHAPS-C were positively correlated with one another, with levels of depression severity, as measured by the MADRS, and the IDS-SR total scores, and with specific items of the MADRS and IDS-SR sensitive to measuring hedonic capacity. Our investigation indicates that the SHAPS-C is a user friendly, reliable, and valid tool for clinician assessment of hedonic capacity in depressed bipolar and unipolar patients

CamDec: Advancing axis P1435-LE video camera security using honeypot-based deception

The explosion of online video streaming in recent years resulted in advanced services both in terms of efficiency and convenience. However, Internet-connected video cameras are prone to exploitation, leading to information security issues and data privacy concerns. The proliferation of video-capable Internet of Things devices and cloud-managed surveillance systems further extend these security issues and concerns. In this paper, a novel approach is proposed for video camera deception via honeypots, offering increased security measures compared to what is available on conventional Internet-enabled video cameras

Restenosis after directional coronary atherectomy: Differences between primary atheromatoes and restenosls lesions and influence of subintimal tissue resection

AbstractRates of restenosis were evaluated in 70 patients (74 lesions) after successful directional coronary atherectomy. The extent of vascular tissue resection was correlated with restenosis rates for coronary (n = 59) and vein bypass graft (n = 15) lesions.After 6 months, the overall restenosis rate was 50% (37 of 74 lesions); it was 42% (15 of 36 lesions) when intima alone was resected, 50% (7 of 14 lesions) when media was resected and 63% (15 of 24 lesions) when adventitia was resected. Subintimal tissue resection increased the restenosis rate for vein grafts (43% with intimal resection versus 100% with subintimal resection, p = 0.01) but not for coronary arteries (50% versus 48%). There was no overall difference in restenosis rates after atherectomy between primary lesions and restenosis lesions that occurred after balloon angioplasty (46% versus 54%). Among postballoon angioplasty restenosis lesions, a higher rate of restenosis after atherectomy was found with subintimal than with intimal resection (78% versus 32%, p = 0.01).Tissues from patients undergoing a second atherectomy for restenosis after initial atherectomy (n = 8) demonstrated neointimal hyperplasia that appeared histotogically identical to restenotic tissue developing after balloon angioplasty (n = 37).These data suggest that the cellular response to directional coronary atherectomy is characterized by neointimal proliferation similar to that which may develop after balloon angioplasty. The extent of fibrous hyperplasia appears to be related to the depth of tissue resection in vein graft lesions and coronary artery restenosis lesions that occur after balloon angioplasty but not in primary atheromatous coronary artery lesions