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.

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.

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. .

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.

Implications of high level pseudogene transcription in Mycobacterium leprae.

BACKGROUND: The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and translational potentials of this genome should increase our understanding of their impact on M. leprae physiology. RESULTS: Gene expression analysis identified transcripts from 49% of all M. leprae genes including 57% of all ORFs and 43% of all pseudogenes in the genome. Transcribed pseudogenes were randomly distributed throughout the chromosome. Factors resulting in pseudogene transcription included: 1) co-orientation of transcribed pseudogenes with transcribed ORFs within or exclusive of operon-like structures; 2) the paucity of intrinsic stem-loop transcriptional terminators between transcribed ORFs and downstream pseudogenes; and 3) predicted pseudogene promoters. Mechanisms for translational "silencing" of pseudogene transcripts included the lack of both translational start codons and strong Shine-Dalgarno (SD) sequences. Transcribed pseudogenes also contained multiple "in-frame" stop codons and high Ka/Ks ratios, compared to that of homologs in M. tuberculosis and ORFs in M. leprae. A pseudogene transcript containing an active promoter, strong SD site, a start codon, but containing two in frame stop codons yielded a protein product when expressed in E. coli. CONCLUSION: Approximately half of M. leprae's transcriptome consists of inactive gene products consuming energy and resources without potential benefit to M. leprae. Presently it is unclear what additional detrimental affect(s) this large number of inactive mRNAs has on the functional capability of this organism. Translation of these pseudogenes may play an important role in overall energy consumption and resultant pathophysiological characteristics of M. leprae. However, this study also demonstrated that multiple translational "silencing" mechanisms are present, reducing additional energy and resource expenditure required for protein production from the vast majority of these transcripts.

An operative approach to the treatment of refractory cutaneous nasal sarcoid: a case report and review of the literature.

The treatment of cutaneous sarcoid is often frustrating, because lesions may be refractory to treatment, or recurrent. There is little information in the literature regarding the surgical treatment of cutaneous sarcoid. Such treatment may become necessary in cases that do not respond to systemic treatments and create functional impairments. We present a 7-year follow-up of a patient with cutaneous nasal sarcoid that was successfully treated surgically.

Habitat-Lite: a GSC case study based on free text terms for environmental metadata.

There is an urgent need to capture metadata on the rapidly growing number of genomic, metagenomic and related sequences, such as 16S ribosomal genes. This need is a major focus within the Genomic Standards Consortium (GSC), and Habitat is a key metadata descriptor in the proposed "Minimum Information about a Genome Sequence" (MIGS) specification. The goal of the work described here is to provide a light-weight, easy-to-use (small) set of terms ("Habitat-Lite") that captures high-level information about habitat while preserving a mapping to the recently launched Environment Ontology (EnvO). Our motivation for building Habitat-Lite is to meet the needs of multiple users, such as annotators curating these data, database providers hosting the data, and biologists and bioinformaticians alike who need to search and employ such data in comparative analyses. Here, we report a case study based on semiautomated identification of terms from GenBank and GOLD. We estimate that the terms in the initial version of Habitat-Lite would provide useful labels for over 60% of the kinds of information found in the GenBank isolation_source field, and around 85% of the terms in the GOLD habitat field. We present a revised version of Habitat-Lite defined within the EnvO Environmental Ontology through a new category, EnvO-Lite-GSC. We invite the community's feedback on its further development to provide a minimum list of terms to capture high-level habitat information and to provide classification bins needed for future studies.

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).

Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.

This meeting report summarizes the proceedings of the fifth Genomic Standards Consortium (GSC) workshop held December 12-14, 2007, at the European Bioinformatics Institute (EBI), Cambridge, UK. This fifth workshop served as a milestone event in the evolution of the GSC (launched in September 2005); the key outcome of the workshop was the finalization of a stable version of the MIGS specification (v2.0) for publication. This accomplishment enables, and also in some cases necessitates, downstream activities, which are described in the multiauthor, consensus-driven articles in this special issue of OMICS produced as a direct result of the workshop. This report briefly summarizes the workshop and overviews the special issue. In particular, it aims to explain how the various GSC-led projects are working together to help this community achieve its stated mission of further standardizing the descriptions of genomes and metagenomes and implementing improved mechanisms of data exchange and integration to enable more accurate comparative analyses. Further information about the GSC and its range of activities can be found at http://gensc.org.

Meeting report: eGenomics: Cataloguing our Complete Genome Collection II.

This article summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection II" workshop held November 10-11, 2005, at the European Bioinformatics Institute. This exploratory workshop, organized by members of the Genomic Standards Consortium (GSC), brought together researchers from the genomic, functional OMICS, and computational biology communities to discuss standardization activities across a range of projects. The workshop proceedings and outcomes are set to help guide the development of the GSC's Minimal Information about a Genome Sequence (MIGS) specification.

Concept of sample in OMICS technology.

Fundamental biological processes can now be studied by applying the full range of OMICS technologies (genomics, transcriptomics, proteomics, metabolomics, and beyond) to the same biological sample. Clearly, it would be desirable if the concept of sample were shared among these technologies, especially as up until the time a biological sample is prepared for use in a specific OMICS assay, its description is inherently technology independent. Sharing a common informatic representation would encourage data sharing (rather than data replication), thereby reducing redundant data capture and the potential for error. This would result in a significant degree of harmonization across different OMICS data standardization activities, a task that is critical if we are to integrate data from these different data sources. Here, we review the current concept of sample in OMICS technologies as it is being dealt with by different OMICS standardization initiatives and discuss the special role that the newly formed Genomic Standards Consortium (GSC) might have to play in this domain.

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.

In this article we present the Reporting Structure for Biological Investigation (RSBI), a working group under the Microarray Gene Expression Data (MGED) Society umbrella. RSBI brings together several communities to tackle the challenges associated with integrating data and representing complex biological investigations, employing multiple OMICS technologies. Currently, RSBI includes environmental genomics, nutrigenomics and toxicogenomics communities, where independent activities are underway to develop databases and establish data communication standards within their respective domains. The RSBI working group has been conceived as a "single point of focus" for these communities, conforming to general accepted view that duplication and incompatibility should be avoided where possible. This endeavour has aimed to synergize insular solutions into one common terminology between biologically driven standardisation efforts and has also resulted in strong collaborations and shared understanding between those in the technological domain. Through extensive liaisons with many standards efforts, several threads have been woven with the hope that ultimately technology-centered standards and their specific extensions into biological domains of interest will not only stand alone, but will also be able to function together, as interchangeable modules.

Development of FuGO: an ontology for functional genomics investigations.

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the "semantic glue" to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans.

Annotation of environmental OMICS data: application to the transcriptomics domain.

Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities.

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.

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

BACKGROUND: maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. RESULTS: maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. CONCLUSION: maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.

A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical pathology and histopathology). A Study is generally an experiment carried out during a period of time for the purpose of obtaining data, and the Study Design Description captures the methods, timing, and organization of the Study. The CEBS Data Dictionary (CEBS-DD) has been designed to define and organize terms in an attempt to standardize nomenclature needed to describe a toxicogenomics Study in a structured yet intuitive format and provide a flexible means to describe a Study as conceptualized by the investigator. The CEBS-DD will organize and annotate information from a variety of sources, thereby facilitating the capture and display of toxicogenomics data in biological context in CEBS, i.e., associating molecular events detected in highly-parallel data with the toxicology/pathology phenotype as observed in the individual Study Subjects and linked to the experimental treatments. The CEBS-DD has been developed with a focus on acute toxicity studies, but with a design that will permit it to be extended to other areas of toxicology and biology with the addition of domain-specific terms. To illustrate the utility of the CEBS-DD, we present an example of integrating data from two proteomics and transcriptomics studies of the response to acute acetaminophen toxicity (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193-202).