VIDA: a virus database system for the organization of animal virus genome open reading frames

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships, Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus-database/ VIDA.html

Microbial load in instruments used in surgeries classified as clean

Introduction / objectives The number of orthopedic surgery, especially surgery of total hip and knee, have been more frequent due to technological advances. This study aims to determine the microbial load in the instruments used in clean surgeries, quantifying and identifying the genus and species of microbial growth.Methods\ud Orthopedic surgical instruments were immersed, after use, in sterile water, sonicated in ultrasonic washer and consecutively shaken. Then, the lavage was filtered through a 0.45micron membrane, the result was incubated in aerobic medium, anaerobic medium and medium for fungi and yeasts. Results In clean surgeries, results showed that 47% of used instruments had microbiological growth in the range of 1 to 100 CFU/instrument. The most prevalent organism was Staphylococcus coagulase negative (28%), followed by Bacillus subtilis (11%).This study refuted the hypothesis that clean surgeries happen in micro-organismsfree surgery field. Conclusion The microbiological findings reinforce the importance of antibiotic prophylaxis, practice already well established for this category of surgical procedure

Late Eocene to middle Miocene (33 to 13 million years ago) vegetation and climate development on the North American Atlantic Coastal Plain (IODP Expedition 313, Site M0027)

ArticleWe investigated the palynology of sediment cores from Site M0027 of IODP (Integrated Ocean Drilling Program) Expedition 313 on the New Jersey shallow shelf to examine vegetation and climate dynamics on the east coast of North America between 33 and 13 million years ago and to assess the impact of over-regional climate events on the region. Palynological results are complemented with pollen-based quantitative climate reconstructions. Our results indicate that the hinterland vegetation of the New Jersey shelf was characterized by oak–hickory forests in the lowlands and conifer-dominated vegetation in the highlands from the early Oligocene to the middle Miocene. The Oligocene witnessed several expansions of conifer forest, probably related to cooling events. The pollen-based climate data imply an increase in annual temperatures from ∼11.5 °C to more than 16 °C during the Oligocene. The Mi-1 cooling event at the onset of the Miocene is reflected by an expansion of conifers and mean annual temperature decrease of ∼4 °C, from ∼16 °C to ∼12 °C around 23 million years before present. Relatively low annual temperatures are also recorded for several samples during an interval around ∼20 million years before present, which may reflect the Mi-1a and the Mi-1aa cooling events. Generally, the Miocene ecosystem and climate conditions were very similar to those of the Oligocene. Miocene grasslands, as known from other areas in the USA during that time period, are not evident for the hinterland of the New Jersey shelf, possibly reflecting moisture from the proto-Gulf Stream. The palaeovegetation data reveal stable conditions during the mid-Miocene climatic optimum at ∼15 million years before present, with only a minor increase in deciduous–evergreen mixed forest taxa and a decrease in swamp forest taxa. Pollen-based annual temperature reconstructions show average annual temperatures of ∼14 °C during the mid-Miocene climatic optimum, ∼2 °C higher than today, but ∼1.5 °C lower than preceding and following phases of the Miocene. We conclude that vegetation and regional climate in the hinterland of the New Jersey shelf did not react as sensitively to Oligocene and Miocene climate changes as other regions in North America or Europe due to the moderating effects of the North Atlantic. An additional explanation for the relatively low regional temperatures reconstructed for the mid-Miocene climatic optimum could be an uplift of the Appalachian Mountains during the Miocene, which would also have influenced the catchment area of our pollen record.We thank the entire IODP Expedition 313 Scientific Party for input, and the IODP staff for support. We thank M. Drljepan, R. Zanatta, V. Menke, K. Reichel, and S. Namyslo for their assistance with preparing and processing the samples, and during photographing. Discussions with C. Bjerrum, J. Browning, T. Donders, L. Fang, M. Katz, Y. Milker, K. Miller, and P. Sugarman are gratefully acknowledged. Input from K. Dybkjær and anonymous reviewers was very much appreciated and contributed to a significant condensing of the manuscript. The German Science Foundation supported the research (DFG project KO 3944/3-1 to U. Kotthoff). Funding was also provided by NSERC Discovery Grants to F. M. G. McCarthy and to D. R. Greenwood respectively. NERC supported work by S. P. Hesselbo. This research used samples and/or data provided by the Integrated Ocean Drilling Program (IODP)

Quality research in healthcare: are researchers getting enough statistical support?

BACKGROUND: Reviews of peer-reviewed health studies have highlighted problems with their methodological quality. As published health studies form the basis of many clinical decisions including evaluation and provisions of health services, this has scientific and ethical implications. The lack of involvement of methodologists (defined as statisticians or quantitative epidemiologists) has been suggested as one key reason for this problem and this has been linked to the lack of access to methodologists. This issue was highlighted several years ago and it was suggested that more investments were needed from health care organisations and Universities to alleviate this problem. METHODS: To assess the current level of methodological support available for health researchers in England, we surveyed the 25 National Health Services Trusts in England, that are the major recipients of the Department of Health's research and development (R&D) support funding. RESULTS AND DISCUSSION: The survey shows that the earmarking of resources to provide appropriate methodological support to health researchers in these organisations is not widespread. Neither the level of R&D support funding received nor the volume of research undertaken by these organisations showed any association with the amount they spent in providing a central resource for methodological support for their researchers. CONCLUSION: The promotion and delivery of high quality health research requires that organisations hosting health research and their academic partners put in place funding and systems to provide appropriate methodological support to ensure valid research findings. If resources are limited, health researchers may have to rely on short courses and/or a limited number of advisory sessions which may not always produce satisfactory results

The combinatorics of resource sharing

We discuss general models of resource-sharing computations, with emphasis on the combinatorial structures and concepts that underlie the various deadlock models that have been proposed, the design of algorithms and deadlock-handling policies, and concurrency issues. These structures are mostly graph-theoretic in nature, or partially ordered sets for the establishment of priorities among processes and acquisition orders on resources. We also discuss graph-coloring concepts as they relate to resource sharing.Comment: R. Correa et alii (eds.), Models for Parallel and Distributed Computation, pp. 27-52. Kluwer Academic Publishers, Dordrecht, The Netherlands, 200

Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index

BACKGROUND: Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-based information. Improved DomainDiscovery uses a Support Vector Machine (SVM) approach and a unique training dataset built on the principle of consensus among experts in defining domains in protein structure. The SVM was trained using a PSSM (Position Specific Scoring Matrix), secondary structure, solvent accessibility information and inter-domain linker index to detect possible domain boundaries for a target sequence. RESULTS: Improved DomainDiscovery is compared with other methods by benchmarking against a structurally non-redundant dataset and also CASP5 targets. Improved DomainDiscovery achieves 70% accuracy for domain boundary identification in multi-domains proteins. CONCLUSION: Improved DomainDiscovery compares favourably to the performance of other methods and excels in the identification of domain boundaries for multi-domain proteins as a result of introducing support vector machine with benchmark_2 dataset

Response to Merritts et al. (2023): The Anthropocene is complex. Defining it is not

Merritts et al. (2023) misrepresent Paul Crutzen's Anthropocene concept as encompassing all significant anthropogenic impacts, extending back many millennia. Crutzen's definition reflects massively enhanced, much more recent human impacts that transformed the Earth System away from the stability of Holocene conditions. His concept of an epoch (hence the ‘cene’ suffix) is more consistent with the strikingly distinct sedimentary record accumulated since the mid-20th century. Waters et al. (2022) highlighted a Great Acceleration Event Array (GAEA) of stratigraphic event markers that are indeed diverse and complex but also tightly clustered around 1950 CE, allowing ultra-high resolution characterization and correlation of a clearly recognisable Anthropocene chronostratigraphic base. The ‘Anthropocene event’ offered by Merritts et al., following Gibbard et al. (2021, 2022), is a highly nuanced concept that obfuscates the transformative human impact of the chronostratigraphic Anthropocene. Waters et al. (2022) restricted the meaning of the term ‘event’ in geology to conform with usual Quaternary practice and improve its utility. They simultaneously recognized an evidence-based Anthropogenic Modification Episode that is more explicitly defined than the highly interpretive interdisciplinary ‘Anthropocene event’ of Gibbard et al. (2021, 2022). The advance of science is best served through clearly developed concepts supported by tightly circumscribed terminology; indeed, improvements to stratigraphy over recent decades have been achieved through increasingly precise definitions, especially for chronostratigraphic units, and not by retaining vague terminology