compomics-utilities: an open-source Java library for computational proteomics

<p>Abstract</p> <p>Background</p> <p>The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool.</p> <p>Results</p> <p>In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development.</p> <p>Conclusions</p> <p>As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.</p

Exploring the potential of public proteomics data

In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data

Cost Analysis of Single-Level Lumbar Fusions

Study Design: Cost analysis of a retrospectively identified cohort of patients who had undergone primary single-level lumbar fusion at a single institution's orthopedic or neurosurgery department. Objective: The purpose of this article is to analyze the determinants of direct costs for single-level lumbar fusions and identify potential areas for cost reduction. Methods: Adult patients who underwent primary single-level lumbar fusion from fiscal years 2008 to 2012 were identified via administrative and departmental databases and were eligible for inclusion. Patients were excluded if they underwent multiple surgeries, had previous surgery at the same anatomic region, underwent corpectomy, kyphectomy, disc replacement, surgery for tumor or infection, or had incomplete cost data. Demographic data, surgical data, and direct cost data in the categories of supplies, services, room and care, and pharmacy, was collected for each patient. Results: The cohort included 532 patients. Direct costs ranged from $8286 to$73 727 (median = $21 781; mean =$22 890 +/- $6323). Surgical approach was an important determinant of cost. The mean direct cost was highest for the circumferential approach and lowest for posterior instrumented spinal fusions without an interbody cage. The difference in mean direct cost between transforaminal lumbar interbody fusions, anterior lumbar interbody fusions, and lateral transpsoas fusions was not statistically significant. Surgical supplies accounted for 44% of direct costs. Spinal implants were the primary component of supply costs (84.9%). Services accounted for 38% of direct costs and were highly dependent on operative time. Comorbidities were an important contributor to variance in the cost of care as evidenced by high variance in pharmacy costs and length of stay related to their management. Conclusion: The costs of spinal surgeries are highly variable. Important cost drivers in our analysis included surgical approach, implants, operating room time, and length of hospital stay. Areas of high cost and high variance offer potential targets for cost savings and quality improvements.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Arachnoid cysts do not contain cerebrospinal fluid: A comparative chemical analysis of arachnoid cyst fluid and cerebrospinal fluid in adults

<p>Abstract</p> <p>Background</p> <p>Arachnoid cyst (AC) fluid has not previously been compared with cerebrospinal fluid (CSF) from the same patient. ACs are commonly referred to as containing "CSF-like fluid". The objective of this study was to characterize AC fluid by clinical chemistry and to compare AC fluid to CSF drawn from the same patient. Such comparative analysis can shed further light on the mechanisms for filling and sustaining of ACs.</p> <p>Methods</p> <p>Cyst fluid from 15 adult patients with unilateral temporal AC (9 female, 6 male, age 22-77y) was compared with CSF from the same patients by clinical chemical analysis.</p> <p>Results</p> <p>AC fluid and CSF had the same osmolarity. There were no significant differences in the concentrations of sodium, potassium, chloride, calcium, magnesium or glucose. We found significant elevated concentration of phosphate in AC fluid (0.39 versus 0.35 mmol/L in CSF; <it>p </it>= 0.02), and significantly reduced concentrations of total protein (0.30 versus 0.41 g/L; <it>p </it>= 0.004), of ferritin (7.8 versus 25.5 ug/L; <it>p </it>= 0.001) and of lactate dehydrogenase (17.9 versus 35.6 U/L; <it>p </it>= 0.002) in AC fluid relative to CSF.</p> <p>Conclusions</p> <p>AC fluid is not identical to CSF. The differential composition of AC fluid relative to CSF supports secretion or active transport as the mechanism underlying cyst filling. Oncotic pressure gradients or slit-valves as mechanisms for generating fluid in temporal ACs are not supported by these results.</p

The Influence of Multilevel Spinal Deformity Surgery on the EuroQol 5 Dimensions' (EQ-5D) Questionnaire and Residential Status in the Elderly: A Prospective, Observational, Multicenter Study

STUDY DESIGN: Multicenter, international prospective study. OBJECTIVE: This study investigated the clinical outcome up to 2 years after multi-level spinal deformity surgery in the elderly by reporting the minimal clinically important difference (MCID) of EuroQol 5-dimensions (EQ-5D), EQ-VAS, and residential status. METHODS: As an ancillary study of 219 patients ≥60 years with spinal deformity undergoing primary instrumented fusion surgery of ≥5 levels, this study focuses on EQ-5D (3-L) as the primary outcome and EQ-VAS and residential status as secondary outcomes. Data on EQ-5D were compared between pre-operatively and postoperatively at 10 weeks, 12 months, and 24 months. An anchor-based approach was used to calculate the MCID. RESULTS: The EQ-5D index and EQ-VAS, respectively, improved significantly at each time point compared to pre-operatively (from .53 (SD .21) and 55.6 (SD 23.0) pre-operatively to .64 (SD .18) and 65.8 (SD 18.7) at 10 weeks, .74 (SD .18) and 72.7 (SD 18.1) at 12 months, and .73 (SD .20) and 70.4 (SD 20.4) at 24 months). 217 (99.1%) patients lived at home pre-operatively, while 186 (88.6%), 184 (98.4%), and 172 (100%) did so at 10 weeks, 12 months, and 24 months, respectively. Our calculated MCID for the EQ-5D index at 1 year was .22 (95% CI .15-.29). CONCLUSIONS: The EQ-5D index significantly increased at each time point over 24 months after ≥5 level spinal deformity surgery in elderly patients. The MCID of the EQ-5D-3 L was .22. Patients living at home pre-operatively can expect to be able to live at home 2 years postoperatively

Discrimination of outer membrane proteins with improved performance

<p>Abstract</p> <p>Background</p> <p>Outer membrane proteins (OMPs) perform diverse functional roles in Gram-negative bacteria. Identification of outer membrane proteins is an important task.</p> <p>Results</p> <p>This paper presents a method for distinguishing outer membrane proteins (OMPs) from non-OMPs (that is, globular proteins and inner membrane proteins (IMPs)). First, we calculated the average residue compositions of OMPs, globular proteins and IMPs separately using a training set. Then for each protein from the test set, its distances to the three groups were calculated based on residue composition using a weighted Euclidean distance (WED) approach. Proteins from the test set were classified into OMP versus non-OMP classes based on the least distance. The proposed method can distinguish between OMPs and non-OMPs with 91.0% accuracy and 0.639 Matthews correlation coefficient (MCC). We then improved the method by including homologous sequences into the calculation of residue composition and using a feature-selection method to select the single residue and di-peptides that were useful for OMP prediction. The final method achieves an accuracy of 96.8% with 0.859 MCC. In direct comparisons, the proposed method outperforms previously published methods.</p> <p>Conclusion</p> <p>The proposed method can identify OMPs with improved performance. It will be very helpful to the discovery of OMPs in a genome scale.</p