PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios

<p>Abstract</p> <p>Background</p> <p>Recent development of novel technologies paved the way for quantitative proteomics. One of the most important among them is iTRAQ, employing isobaric tags for relative or absolute quantitation. Despite large progress in technology development, still many challenges remain for derivation and interpretation of quantitative results. One of these challenges is the consistent assignment of peptides to proteins.</p> <p>Results</p> <p>We have developed Peptide Profiling Guided Identification of Proteins (PPINGUIN), a statistical analysis workflow for iTRAQ data addressing the problem of ambiguous peptide quantitations. Motivated by the assumption that peptides uniquely derived from the same protein are correlated, our method employs clustering as a very early step in data processing prior to protein inference. Our method increases experimental reproducibility and decreases variability of quantitations of peptides assigned to the same protein. Giving further support to our method, application to a type 2 diabetes dataset identifies a list of protein candidates that is in very good agreement with previously performed transcriptomics meta analysis. Making use of quantitative properties of signal patterns identified, PPINGUIN can reveal new isoform candidates.</p> <p>Conclusions</p> <p>Regarding the increasing importance of quantitative proteomics we think that this method will be useful in practical applications like model fitting or functional enrichment analysis. We recommend to use this method if quantitation is a major objective of research.</p

Predictors for rTMS response in chronic tinnitus

Background: Repetitive transcranial magnetic stimulation (rTMS) has been studied as a treatment option for chronic tinnitus for almost 10 years now. Although most of these studies have demonstrated beneficial effects, treatment results show high interindividual variability and yet, little is known about predictors for treatment response. Methods: Data from 538 patients with chronic tinnitus were analyzed. Patients received either low-frequency rTMS over the left temporal cortex (n = 345, 1 Hz, 110% motor threshold, 2000 stimuli/day) or combined temporal and frontal stimulation (n = 193, 110% motor threshold, 2000 stimuli at 20 Hz over left dorsolateral prefrontal cortex plus 2000 stimuli at 1 Hz over temporal cortex). Numerous demographic, clinical, and audiological variables as well as different tinnitus characteristics were analyzed as potential predictors for treatment outcome, which was defined as change in the tinnitus questionnaire (TQ) score. Results: Both stimulation protocols resulted in a significant decrease of TQ scores. Effect sizes were small, however. In the group receiving combined treatment, patients with comorbid temporomandibular complaints benefited more from rTMS than patients without those complaints. In addition, patients with higher TQ scores at baseline had more pronounced TQ reductions than patients with low TQ baseline scores. Also, patients who had already improved from screening to baseline benefited less than patients without initial improvement. Conclusions: The results from this large sample demonstrate that rTMS shows only small but clinically significant effects in the treatment of chronic tinnitus. There are no good demographic or clinical predictors for treatment outcome

Speech Comprehension Difficulties in Chronic Tinnitus and Its Relation to Hyperacusis

Objective: Many tinnitus patients complain about difficulties regarding speech comprehension. In spite of the high clinical relevance little is known about underlying mechanisms and predisposing factors. Here, we performed an exploratory investigation in a large sample of tinnitus patients to (1) estimate the prevalence of speech comprehension difficulties among tinnitus patients, to (2) compare subjective reports of speech comprehension difficulties with behavioral measurements in a standardized speech comprehension test and to (3) explore underlying mechanisms by analyzing the relationship between speech comprehension difficulties and peripheral hearing function (pure tone audiogram), as well as with co-morbid hyperacusis as a central auditory processing disorder. Subjects and Methods: Speech comprehension was assessed in 361 tinnitus patients presenting between 07/2012 and 08/2014 at the Interdisciplinary Tinnitus Clinic at the University of Regensburg. The assessment included standard audiological assessments (pure tone audiometry, tinnitus pitch, and loudness matching), the Goettingen sentence test (in quiet) for speech audiometric evaluation, two questions about hyperacusis, and two questions about speech comprehension in quiet and noisy environments ("How would you rate your ability to understand speech?"; "How would you rate your ability to follow a conversation when multiple people are speaking simultaneously?"). Results: Subjectively-reported speech comprehension deficits are frequent among tinnitus patients, especially in noisy environments (cocktail party situation). 74.2% of all investigated patients showed disturbed speech comprehension (indicated by values above 21.5 dB SPL in the Goettingen sentence test). Subjective speech comprehension complaints (both for general and in noisy environment) were correlated with hearing level and with audiologically-assessed speech comprehension ability. In contrast, co-morbid hyperacusis was only correlated with speech comprehension difficulties in noisy environments, but not with speech comprehension difficulties in general. Conclusion: Speech comprehension deficits are frequent among tinnitus patients. Whereas speech comprehension deficits in quiet environments are primarily due to peripheral hearing loss, speech comprehension deficits in noisy environments are related to both peripheral hearing loss and dysfunctional central auditory processing. Disturbed speech comprehension in noisy environments might be modulated by a central inhibitory deficit. In addition, attentional and cognitive aspects may play a role

Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset

Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics

Paired Associative Stimulation of the Auditory System: A Proof-Of-Principle Study

Background Paired associative stimulation (PAS) consisting of repeated application of transcranial magnetic stimulation (TMS) pulses and contingent exteroceptive stimuli has been shown to induce neuroplastic effects in the motor and somatosensory system. The objective was to investigate whether the auditory system can be modulated by PAS. Methods Acoustic stimuli (4 kHz) were paired with TMS of the auditory cortex with intervals of either 45 ms (PAS(45 ms)) or 10 ms (PAS(10 ms)). Two-hundred paired stimuli were applied at 0.1 Hz and effects were compared with low frequency repetitive TMS (rTMS) at 0.1 Hz (200 stimuli) and 1 Hz (1000 stimuli) in eleven healthy students. Auditory cortex excitability was measured before and after the interventions by long latency auditory evoked potentials (AEPs) for the tone (4 kHz) used in the pairing, and a control tone (1 kHz) in a within subjects design. Results Amplitudes of the N1-P2 complex were reduced for the 4 kHz tone after both PAS(45 ms) and PAS(10 ms), but not after the 0.1 Hz and 1 Hz rTMS protocols with more pronounced effects for PAS(45 ms). Similar, but less pronounced effects were observed for the 1 kHz control tone. Conclusion These findings indicate that paired associative stimulation may induce tonotopically specific and also tone unspecific human auditory cortex plasticity

Breaking ECC2K-130

Elliptic-curve cryptography is becoming the standard public-key primitive not only for mobile devices but also for high-security applications. Advantages are the higher cryptographic strength per bit in comparison with RSA and the higher speed in implementations. To improve understanding of the exact strength of the elliptic-curve discrete-logarithm problem, Certicom has published a series of challenges. This paper describes breaking the ECC2K-130 challenge using a parallelized version of Pollard\u27s rho method. This is a major computation bringing together the contributions of several clusters of conventional computers, PlayStation~3 clusters, computers with powerful graphics cards and FPGAs. We also give /preseestimates for an ASIC design. In particular we present * our choice and analysis of the iteration function for the rho method; * our choice of finite field arithmetic and representation; * detailed descriptions of the implementations on a multitude of platforms: CPUs, Cells, GPUs, FPGAs, and ASICs; * details about running the attack

A DNA Spiegelmer to staphylococcal enterotoxin B

Bacterial staphylococcal enterotoxin B is involved in several severe disease patterns and it was therefore used as a target for the generation of biologically stable mirror-image oligonucleotide ligands, so called Spiegelmers. The toxin is a 28 kDa protein consisting of 239 amino acids. Since the full-length protein is not accessible to chemical peptide synthesis, a stable domain of 25 amino acids was identified as a suitable selection target. DNA in vitro selection experiments were carried out against the equivalent mirror-image d-peptide domain resulting in high affinity d-DNA aptamers. As expected, the corresponding enantiomeric l-DNA Spiegelmer showed comparable binding characteristics to the l-peptide domain. Moreover, the Spiegelmer bound the whole protein target with only slightly reduced affinity. Dissociation constants of both peptide–oligonucleotide complexes were measured in the range of 200 nM, whereas the Spiegelmer binding to the full-length protein was determined at ∼420 nM. These data demonstrate the possibility to identify Spiegelmers against large protein targets by a domain approach

Occurence of a round window membrane rupture in patients with sudden sensorineural hearing loss

BACKGROUND: Aim of the present study was to evaluate the occurence of a round window membrane rupture and the effects of hearing restoration after exploratory tympanotomy and sealing of the round window (niche) in patients with unilateral sudden deafness. METHODS: Retrospective analysis of patients' charts in a tertiary referral center. Charts of 69 patients with sudden deafness followed by exploratory tympanotomy were retrospectively analyzed. Pure-tone audiometry data before and after tympanotomy were compared to determine the outcome of hearing recovery. The postoperative hearing test values were documented 3 weeks after tympanotomy. All surgical reports were reviewed with regard to the surgical technique performed and the intraoperative findings. RESULTS: 18.8% of the patients revealed a visible perilymphatic fistula in the round window niche. 89.8% of the patients reported no typical history for a round window membrane rupture. All patients were treated with an exploratory tympanotomy under local anesthesia and an intravenous corticosteroid treatment regimen. The majority of the surgeons used a fat plomb to cover the round window. Postoperative hearing was significantly improved compared to the preoperative hearing test data. No patient showed a worsened hearing curve after the treatment. CONCLUSION: Most patients suffering from unilateral sudden deafness had no visible perilymphatic fistula. In our study population, the majority of patients reported no typical history of a pressure elevation in the inner ear. Exploratory tympanotomy is a safe procedure that may support hearing recovery in patients with sudden deafness in addition to the established treatment regimen including high-dose steroids