Rare presentation of sepsis caused by necrotizing scalp infection.

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is a rising cause of skin and soft tissue infections over the last decade with potentially serious complications. In this article, we describe a case of a large scalp and post-auricular abscess complicated by bacteremia. This is a case of a 73-year-old female who presented with altered mental status was found to have two fluctuant scalp abscesses, bacteremia with necrosis. The patient was promptly treated with intravenous antibiotics, multiple operative debridements without calvarial periosteum involvement defects requiring split-thickness skin grafts for wound closure. This case highlights the severity of a CA-MRSA skin infection in an atypical location.

Management of Incidental Hernia Discovered During Abdominal Contouring in Post-Bariatric Surgery Patients.

PURPOSE: An increase in bariatric surgery has led to a rise in postbariatric contouring procedures. Despite a comprehensive preoperative assessment, body habitus in these patients may significantly limit the abdominal exam. Abdominal contouring procedures typically elevate large portions of the skin and fat off the abdominal wall, and unexpected hernia may be discovered intraoperatively. No study to date has characterized such hernia discovery at the time of body contouring surgery. We reviewed our experience of management of incidental hernia found during abdominoplasty or panniculectomy after laparoscopic bariatric surgery. METHODS: Records of all post-bariatric surgery patients undergoing abdominal contouring procedures between 2007 and 2017 were reviewed to identify patients with incidental hernias discovered intraoperatively. These patients were further examined by reviewing operative details, patient-specific factors, and outcomes. RESULTS: Six hundred eighty-one post-bariatric surgery patients underwent abdominal body contouring procedures with incidental ventral hernia discovered in 36 patients (5.3% [45 hernias]). At the time of plastic surgery, average age was 49 years (range, 25-64 years), and body mass index was 30.7 kg/m (range 25-43 kg/m). Of 36 patients with incidental hernia, 26 patients (72.2%) had a single hernia, and the remainder had multiple (27.8%). Mean hernia size was 4.1 cm (range, 0.25-24 cm). Most hernias were located paraumbilical/umbilical (46.7%) or epigastric (37.8%). Ninety-eight percent of hernias were repaired primarily (n = 44) by the plastic surgeon, and in 1 case (2%), mesh repair was performed by a consulting general surgeon. Average follow-up was 1.9 ± 0.3 years. Only 1 patient (2.8%) developed hernia recurrence after 48 months. Other postoperative complications included superficial wound healing problems (19.4%), seroma (16.7%), suture abscess (5.6%), and cellulitis that resolved with antibiotics (5.6%). CONCLUSIONS: This is the first study to characterize incidental hernia discovered at the time of body contouring in the post-bariatric surgery patient. The body contouring surgeon should be aware of this common finding. Hernias typically discovered during panniculectomy or abdominoplasty arise in umbilical or epigastric regions, likely from prior laparoscopic port sites, and can be safely repaired by the plastic surgeon with low overall complication rates.

Complications After Reduction Mammaplasty: A Comparison of Wise Pattern/Inferior Pedicle and Vertical Scar/Superomedial Pedicle.

Reduction mammaplasty is a commonly-performed procedure among plastic surgeons. Although several methods exist, the Wise pattern/inferior pedicle (IP) technique is the most widely used. The vertical scar/superomedial pedicle (SP) technique has gained acceptance for its shorter scar and more durable projection results, but some hesitation remains with its use in larger volume reductions.The incidence of complications in 124 consecutively performed breast reductions (246 breasts) at a single institution using either the Wise pattern/IP technique or vertical scar/SP technique, as well as risk factors associated with them, was determined. Patient demographics, comorbidities, intraoperative details, and major and minor complications were assessed.Ninety (72.6%) patients underwent SP, and 39 patients had IP reductions. Minor infections and wound dehiscence were the most common complications (11 each [8.9%]), followed by minor nonoperative hematomas, 10 (8.1%) and fat necrosis, 7 (5.6%). The mean weight of resected tissue per breast was 692 g. No nipple loss, major complications or reexplorations occurred. Obese, diabetic patients were more likely to undergo IP compared with SP reductions. After adjustment in a multivariate analysis, there was no significant difference in complication rates between the 2 methods (IP vs SP: odds ratio, 2.65; 95% confidence interval, 0.85-8.27; P = 0.09). The results were similar after the analysis was restricted to patients with mean weight of resected tissue per breast greater than 1000 g.There was no significant difference in complications between IP and SP reduction, suggesting that the SP method is a safe alternative to the IP technique, even in macromastia patients undergoing large-volume reductions.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

The Ontology for Biomedical Investigations.

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

A giant phyllodes tumor causing ulceration and severe breast disfigurement: case report and review of giant phyllodes.

Phyllodes tumors are rare fibroepithelial tumors that account for <1% of the breast tumors in women. These tumors are often benign unilateral lesions of the female breast (70%). Less common are malignant phyllodes, which have the potential for hematogenous spread. Phyllodes tumors can be seen in all age groups, and the median age of presentation is 45 years. Surgery is the main form of treatment. Wide excisions with margins of 1cm are suggested. While smaller and moderate size phyllodes may typically be seen, gigantic ones are very rare. These may be seen in neglected tumors. By definition, a giant phyllodes tumor is one larger than 10 cm in diameter. We report a gigantic phyllodes tumor that grew over 7 years period causing significant ulceration and disfigurement and review features of these tumors and management.

Genomic standards consortium projects.

The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently has 18 ongoing projects, with additional projects regularly proposed from within and outside the GSC. Here we describe our recently enacted policy for proposing new activities that are intended to be taken on by the GSC, along with the template for proposing such new activities.

The founding charter of the Genomic Observatories Network.

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

The environment ontology: contextualising biological and biomedical entities.

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; http://www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO's motivation, content, structure, adoption, and governance approach. The ontology is available from http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching the file suffix to "obo".

A decadal view of biodiversity informatics: challenges and priorities.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012.

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.

RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011.

At the GSC11 meeting (4-6 April 2011, Hinxton, England, the GSC's genomic biodiversity working group (GBWG) developed an initial model for a data management testbed at the interface of biodiversity with genomics and metagenomics. With representatives of the Global Biodiversity Information Facility (GBIF) participating, it was agreed that the most useful course of action would be for GBIF to collaborate with the GSC in its ongoing GBWG workshops to achieve common goals around interoperability/data integration across (meta)-genomic and species level data. It was determined that a quick comparison should be made of the contents of the Darwin Core (DwC) and the GSC data checklists, with a goal of determining their degree of overlap and compatibility. An ad-hoc task group lead by Renzo Kottman and Peter Dawyndt undertook an initial comparison between the Darwin Core (DwC) standard used by the Global Biodiversity Information Facility (GBIF) and the MIxS checklists put forward by the Genomic Standards Consortium (GSC). A term-by-term comparison showed that DwC and GSC concepts complement each other far more than they compete with each other. Because the preliminary analysis done at this meeting was based on expertise with GSC standards, but not with DwC standards, the group recommended that a joint meeting of DwC and GSC experts be convened as soon as possible to continue this joint assessment and to propose additional work going forward.

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.

Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of 'fitness for use' for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC's standard checklists for genomics and metagenomics and (b) TDWG's Darwin Core standard, used primarily in taxonomy and systematic biology.

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012).

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27-29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database.

Composite fat and skin grafting for the management of chronic sickle cell ulcers.

 Lower extremity ulcers affect 8%-10% of individuals with sickle cell disease. The pathogenesis of this condition is poorly understood, and a good option for the long-term management of these lesions does not exist. Skin grafting and local wound care remain the mainstay of treatment; however, even short-term success often leads to long-term failure, as the wound might once again breakdown. The authors postulated that successful long-term healing of a chronic sickle cell leg ulcer would require a permanent alteration of the wound bed with recruitment of a new cell population. To this end, a skin graft, in conjunction with fat grafting, was performed for the treatment of a chronic sickle cell ulcer that had previously failed under local wound care and skin grafting treatments. .

RCN4GSC Meeting Report: Initiating a Testbed for Managing Data at the Interface of Biodiversity and Genomics/Metagenomics, May 2011.

Following up on efforts from two earlier workshops, a meeting was convened in San Diego to (a) establish working connections between experts in the use of the Darwin Core and the GSC MIxS standards, (b) conduct mutual briefings to promote knowledge exchange and to increase the understanding of the two communities' approaches, constraints, community goals, subtleties, etc., (c) perform an element-by-element comparison of the two standards, assessing the compatibility and complementarity of the two approaches, (d) propose and consider possible use cases and test beds in which a joint annotation approach might be tried, to useful scientific effect, and (e) propose additional action items necessary to continue the development of this joint effort. Several focused working teams were identified to continue the work after the meeting ended.