Publications by authors named "Norman Morrison"

53 Publications

Rare presentation of sepsis caused by necrotizing scalp infection.

J Surg Case Rep 2020 Mar 18;2020(3):rjaa024. Epub 2020 Mar 18.

Department of General Surgery, Wyckoff Heights Medical Center, New York City, NY, USA.

Community-acquired methicillin-resistant (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.
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http://dx.doi.org/10.1093/jscr/rjaa024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078591PMC
March 2020

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

Ann Plast Surg 2018 11;81(5):591-593

Division of Plastic and Reconstructive Surgery, Department of Surgery, Harlem Hospital, Columbia University, New York, NY.

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.
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http://dx.doi.org/10.1097/SAP.0000000000001546DOI Listing
November 2018

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

Ann Plast Surg 2017 Jul;79(1):13-16

From the *Division of Plastic Surgery, Department of Surgery, Medical University of South Carolina, Charleston, SC; and † Division of Plastic Surgery, Department of Surgery, Columbia University Medical Center/Harlem Hospital, New York, NY.

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.
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http://dx.doi.org/10.1097/SAP.0000000000001059DOI Listing
July 2017

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

BMC Ecol 2016 10 20;16(1):49. Epub 2016 Oct 20.

Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany.

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.
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http://dx.doi.org/10.1186/s12898-016-0103-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073428PMC
October 2016

The Ontology for Biomedical Investigations.

PLoS One 2016 29;11(4):e0154556. Epub 2016 Apr 29.

La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154556PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851331PMC
April 2017

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

J Surg Case Rep 2015 Dec 24;2015(12). Epub 2015 Dec 24.

Division of Breast Surgery, Harlem Hospital Center, Columbia University, New York, NY, USA.

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.
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http://dx.doi.org/10.1093/jscr/rjv162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690487PMC
December 2015

Traumatic thumb amputation: case and review.

Eplasty 2015 24;15:ic18. Epub 2015 Mar 24.

Division of Plastic Surgery, Harlem Hospital Center, Columbia University, New York.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376099PMC
April 2015

Genomic standards consortium projects.

Stand Genomic Sci 2014 Jun 15;9(3):599-601. Epub 2014 Feb 15.

Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA .

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.
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http://dx.doi.org/10.4056/sigs.5559680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148985PMC
June 2014

The founding charter of the Genomic Observatories Network.

Gigascience 2014 Mar 7;3(1). Epub 2014 Mar 7.

Gump South Pacific Research Station, University of California Berkeley, BP 244 98728 Moorea, French Polynesia.

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.
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http://dx.doi.org/10.1186/2047-217X-3-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995929PMC
March 2014

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

PLoS One 2014 3;9(3):e89606. Epub 2014 Mar 3.

University of California San Diego, La Jolla, California, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089606PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940615PMC
January 2015

The environment ontology: contextualising biological and biomedical entities.

J Biomed Semantics 2013 Dec 11;4(1):43. Epub 2013 Dec 11.

HGF-MPG Research Group on Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.

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".
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http://dx.doi.org/10.1186/2041-1480-4-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904460PMC
December 2013

A decadal view of biodiversity informatics: challenges and priorities.

BMC Ecol 2013 Apr 15;13:16. Epub 2013 Apr 15.

School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK.

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.
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http://dx.doi.org/10.1186/1472-6785-13-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843378PMC
April 2013

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

Stand Genomic Sci 2012 Oct 28;7(1):166-70. Epub 2012 Sep 28.

Global Biodiversity Information Facility, GBIF Secretariat, Copenhagen, Denmark.

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.
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http://dx.doi.org/10.4056/sigs.3166513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570805PMC
October 2012

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

Stand Genomic Sci 2012 Oct 28;7(1):159-65. Epub 2012 Jul 28.

University of California San Diego, La Jolla, California, USA.

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.
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http://dx.doi.org/10.4056/sigs.3156511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570804PMC
October 2012

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

Stand Genomic Sci 2012 Oct 24;7(1):153-8. Epub 2012 Sep 24.

University of California San Diego, La Jolla, California, USA.

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.
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http://dx.doi.org/10.4056/sigs.3146509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570803PMC
October 2012

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

Stand Genomic Sci 2012 Oct 28;7(1):171-4. Epub 2012 Sep 28.

University of California San Diego, La Jolla, California USA.

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.
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http://dx.doi.org/10.4056/sigs.3176515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558955PMC
October 2012

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

Stand Genomic Sci 2012 May 4;6(2):276-86. Epub 2012 May 4.

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.
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http://dx.doi.org/10.4056/sigs.2876184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387801PMC
May 2012

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

Wounds 2012 Mar;24(3):51-4

Harlem Hospital Medical Center, New York, NY.

 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. .
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March 2012

The role of the novel exopolyphosphatase MT0516 in Mycobacterium tuberculosis drug tolerance and persistence.

PLoS One 2011 21;6(11):e28076. Epub 2011 Nov 21.

Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

Inorganic polyphosphate (poly P) has been postulated to play a regulatory role in the transition to bacterial persistence. In bacteria, poly P balance in the cell is maintained by the hydrolysis activity of the exopolyphosphatase PPX. However, the Mycobacterium tuberculosis PPX has not been characterized previously. Here we show that recombinant MT0516 hydrolyzes poly P, and an MT0516-deficient M. tuberculosis mutant exhibits elevated intracellular levels of poly P and increased expression of the genes mprB, sigE, and rel relative to the isogenic wild-type strain, indicating poly P-mediated signaling. Deficiency of MT0516 resulted in decelerated growth during logarithmic-phase in axenic cultures, and tolerance to the cell wall-active drug isoniazid. The MT0516-deficient mutant showed a significant survival defect in activated human macrophages and reduced persistence in the lungs of guinea pigs. We conclude that exopolyphosphatase is required for long-term survival of M. tuberculosis in necrotic lung lesions.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028076PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221697PMC
April 2012

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

Stand Genomic Sci 2011 Apr;4(2):286-92

In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources.
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http://dx.doi.org/10.4056/sigs.1344279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111990PMC
April 2011

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Nat Biotechnol 2011 May;29(5):415-20

Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
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http://dx.doi.org/10.1038/nbt.1823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367316PMC
May 2011

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.

Stand Genomic Sci 2010 Dec 4;3(3):216-24. Epub 2010 Dec 4.

This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.
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http://dx.doi.org/10.4056/sigs.1353455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035308PMC
December 2010

Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.

AoB Plants 2010 27;2010:plq008. Epub 2010 May 27.

IRRI-CIMMYT Crop Research Informatics Laboratory (CRIL), Centro Internacional de Mejoramiento de Máiz y Trigo (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F. , Mexico.

Background And Aims: Agricultural crop databases maintained in gene banks of the Consultative Group on International Agricultural Research (CGIAR) are valuable sources of information for breeders. These databases provide comparative phenotypic and genotypic information that can help elucidate functional aspects of plant and agricultural biology. To facilitate data sharing within and between these databases and the retrieval of information, the crop ontology (CO) database was designed to provide controlled vocabulary sets for several economically important plant species.

Methodology: Existing public ontologies and equivalent catalogues of concepts covering the range of crop science information and descriptors for crops and crop-related traits were collected from breeders, physiologists, agronomists, and researchers in the CGIAR consortium. For each crop, relationships between terms were identified and crop-specific trait ontologies were constructed following the Open Biomedical Ontologies (OBO) format standard using the OBO-Edit tool. All terms within an ontology were assigned a globally unique CO term identifier.

Principal Results: The CO currently comprises crop-specific traits for chickpea (Cicer arietinum), maize (Zea mays), potato (Solanum tuberosum), rice (Oryza sativa), sorghum (Sorghum spp.) and wheat (Triticum spp.). Several plant-structure and anatomy-related terms for banana (Musa spp.), wheat and maize are also included. In addition, multi-crop passport terms are included as controlled vocabularies for sharing information on germplasm. Two web-based online resources were built to make these COs available to the scientific community: the 'CO Lookup Service' for browsing the CO; and the 'Crops Terminizer', an ontology text mark-up tool.

Conclusions: The controlled vocabularies of the CO are being used to curate several CGIAR centres' agronomic databases. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases will be important steps in comparative phenotypic and genotypic studies across species and gene-discovery experiments.
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http://dx.doi.org/10.1093/aobpla/plq008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000699PMC
August 2012

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

Ann Plast Surg 2009 Dec;63(6):685-7

Division of Plastic Surgery, Harlem Hospital, Columbia University, New York, NY, USA.

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.
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http://dx.doi.org/10.1097/SAP.0b013e3181978715DOI Listing
December 2009

Implications of high level pseudogene transcription in Mycobacterium leprae.

BMC Genomics 2009 Aug 25;10:397. Epub 2009 Aug 25.

HRSA, BPHC, Division of National Hansen's Disease Programs, Laboratory Research Branch, Molecular Biology Research Department, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.

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.
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http://dx.doi.org/10.1186/1471-2164-10-397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753549PMC
August 2009
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