Methods for peptide identification by spectral comparison

BACKGROUND: Tandem mass spectrometry followed by database search is currently the predominant technology for peptide sequencing in shotgun proteomics experiments. Most methods compare experimentally observed spectra to the theoretical spectra predicted from the sequences in protein databases. There is a growing interest, however, in comparing unknown experimental spectra to a library of previously identified spectra. This approach has the advantage of taking into account instrument-dependent factors and peptide-specific differences in fragmentation probabilities. It is also computationally more efficient for high-throughput proteomics studies. RESULTS: This paper investigates computational issues related to this spectral comparison approach. Different methods have been empirically evaluated over several large sets of spectra. First, we illustrate that the peak intensities follow a Poisson distribution. This implies that applying a square root transform will optimally stabilize the peak intensity variance. Our results show that the square root did indeed outperform other transforms, resulting in improved accuracy of spectral matching. Second, different measures of spectral similarity were compared, and the results illustrated that the correlation coefficient was most robust. Finally, we examine how to assemble multiple spectra associated with the same peptide to generate a synthetic reference spectrum. Ensemble averaging is shown to provide the best combination of accuracy and efficiency. CONCLUSION: Our results demonstrate that when combined, these methods can boost the sensitivity and specificity of spectral comparison. Therefore they are capable of enhancing and complementing existing tools for consistent and accurate peptide identification

Delayed presentation of an isolated gallbladder rupture following blunt abdominal trauma: a case report

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Isolated complete avulsion of the gallbladder (near traumatic cholecystectomy): a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>Injury of the gallbladder after blunt abdominal trauma is an unusual finding; the reported incidence is less than 2%. Three groups of injuries are described: simple contusion, laceration, and avulsion, the last of which can be partial, complete, or total traumatic cholecystectomy.</p> <p>Case presentation</p> <p>A case of isolated complete avulsion of the gallbladder (near traumatic cholecystectomy) from its hepatic bed in a 46-year-old Caucasian man without any other sign of injury is presented. The avulsion was due to blunt abdominal trauma after a car accident. The rarity of this injury and the stable condition of our patient at the initial presentation warrant a description. The diagnosis was made incidentally after a computed tomography scan, and our patient was treated successfully with ligation of the cystic duct and artery, removal of the gallbladder, coagulation of the bleeding points, and placement of a drain.</p> <p>Conclusions</p> <p>Early diagnosis of such injuries is quite difficult because abdominal signs are poor, non-specific, or even absent. Therefore, a computed tomography scan should be performed when the mechanism of injury is indicated.</p

Cold Hardiness and Supercooling Capacity in the Overwintering Larvae of the Codling Moth, Cydia pomonella

The codling moth, Cydia pomonella L. (Lepidoptera: Tortricidae), a worldwide apple pest, is classified as a freeze-intolerant organism and one of the most cold-tolerant pests. The objectives of this study were to examine the supercooling point of overwintering and non-diapausing larvae of C. pomonella as an index of its cold hardiness, and to assess larval mortality following 24 h exposure to extreme low temperatures ranging from -5 to -25°C. The mean (±SE) supercooling point for feeding larvae (third through fifth instars) was -12.4 ± 1.1°C. The mean supercooling point for cocooned, non-diapausing larvae (i.e., non-feeding stages) decreased as the days that the arvae were cocooned increased and changed between -15.1 ± 1.2°C for one to two day cocooned arvae and -19.2 ± 1.8°C for less than five day cocooned larvae. The mean (±SE) supercooling point for other non-feeding stages containing pupae and overwintering larvae were -19.9 ± 1.0°C and -20.2 ± 0.2°C, respectively. Mean supercooling points of C. pomonella larvae were significantly lower during the winter months than the summer months, and sex had no effect on the supercooling point of C. pomonella larvae. The mortality of larvae increased significantly after individuals were exposed to temperatures below the mean supercooling point of the population. The supercooling point was a good predictor of cold hardiness

Apolipoprotein E4 Frequencies in a Japanese Population with Alzheimer's Disease and Dementia with Lewy Bodies

BACKGROUND: The apolipoprotein E (APOE) ε4 allele has been reported to be a risk factor for Alzheimer's disease (AD) and dementia with Lewy bodies (DLB). Previous neuropathological studies have demonstrated similar frequencies of the APOE ε4 allele in AD and DLB. However, the few ante-mortem studies on APOE allele frequencies in DLB have shown lower frequencies than post-mortem studies. One reason for this may be inaccuracy of diagnosis. We examined APOE genotypes in subjects with AD, DLB, and a control group using the latest diagnostic criteria and MRI, SPECT, and MIBG myocardial scintigraphy. METHODS: The subjects of this study consisted of 145 patients with probable AD, 50 subjects with probable DLB, and a control group. AD subjects were divided into two groups based on age of onset: early onset AD (EOAD) and late onset AD (LOAD). All subjects had characteristic features on MRI, SPECT, and/or myocardial scintigraphy. RESULTS: The rate of APOE4 carrier status was 18.3% and the frequency of the ε4 allele was 9.7% in controls. The rate of APOE4 carrier status and the frequency of the ε4 allele were 47% and 27% for LOAD, 50% and 31% for EOAD, and 42% and 31% for DLB, respectively. CONCLUSION: The APOE4 genotypes in this study are consistent with previous neuropathological studies suggesting accurate diagnosis of AD and DLB. APOE4 genotypes were similar in AD and DLB, giving further evidence that the ε4 allele is a risk factor for both disorders

Search for neutral MSSM Higgs bosons decaying to a pair of tau leptons in pp collisions

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