Byonic: advanced peptide and protein identification software

Byonic is the name of a software package for peptide and protein identification by tandem mass spectrometry. This software, which has only recently become commercially available, facilitates a much wider range of search possibilities than previous search software such as SEQUEST and Mascot. Byonic allows the user to define an essentially unlimited number of variable modification types. Byonic also allows the user to set a separate limit on the number of occurrences of each modification type, so that a search may consider only one or two chance modifications such as oxidations and deamidations per peptide, yet allow three or four biological modifications such as phosphorylations, which tend to cluster together. Hence, Byonic can search for tens or even hundreds of modification types simultaneously without a prohibitively large combinatorial explosion. Byonic's Wildcard Search allows the user to search for unanticipated or even unknown modifications alongside known modifications. Finally, Byonic's Glycopeptide Search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites.

[Coincidence of traumatic tracheal rupture accompanied by ARDS. Illustrated by the example of a 17-year-old patient with multiple injuries]

Treatment and diagnosis of a traumatic tracheal rupture is a challenge. Due to the rarity of such injuries and the subtle and delayed clinical presentation it is difficult to diagnose. We present for the first time the successful management of a 17-year-old multiply injured patient with coincidental tracheal rupture and ARDS (acute respiratory distress syndrome) after a fall. Besides the case report and pathogenesis the essential diagnostic and therapeutic measures are mentioned and discussed. The circumstances surrounding the accident have to be balanced with the severity of the trauma to also exclude rare injuries with certainty. Finally level 1 trauma centers specialized in ARDS provide the best clinical setting for successful treatment of these life-threatening injuries.

Physical activity of moderately impaired elderly stroke patients during rehabilitation

In older adults, physical activity (PA) is promoted for public health preventive effort. It is also a major target in the rehabilitation process. Existing assessment tools in the clinical routine do not include any aspects of PA or participation and are often prone to floor or ceiling effects. The aim of this study was to document the process of rehabilitation by activity monitoring without floor or ceiling effects. Ninety-two stroke patients of a geriatric rehabilitation unit (mean age 82 years, ±6.21 years, 61% women) were included in an observational study to assess physical capacity (balance, chair rise, gait speed) and PA at admission and two weeks thereafter. PA was measured through an ambulatory activity monitor based on accelerometers and gyroscopes and showed no floor or ceiling effects. Floor effects were however documented for measures of physical capacity (admission 5-11%; follow-up 2-9%) and ceiling effects were registered for the balance test (admission 17.4%; follow-up 22.8%). Improvements were documented for measures of physical capacity as well as for PA (all p < 0.001). We conclude that the assessment of PA by activity monitoring is a valuable measure to document objectively the process of rehabilitation without floor or ceiling effects.

Direct infusion electrospray ionization-ion mobility high resolution mass spectrometry (DIESI-IM-HRMS) for rapid characterization of potential bioprocess streams

Direct infusion electrospray ionization - ion mobility - high resolution mass spectrometry (DIESI-IM-HRMS) has been utilized as a rapid technique for the characterization of total molecular composition in "whole-sample" biomass hydrolysates and extracts. IM-HRMS data reveal a broad molecular weight distribution of sample components (up to 1100 m/z) and provide trendline isolation of feedstock components from those introduced "in process." Chemical formulas were obtained from HRMS exact mass measurements (with typical mass error less than 5 ppm) and were consistent with structural carbohydrates and other lignocellulosic degradation products. Analyte assignments are supported via IM-MS collision-cross-section measurements and trendline analysis (e.g., all carbohydrate oligomers identified in a corn stover hydrolysate were found to fall within 6% of an average trendline). These data represent the first report of collision cross sections for several negatively charged carbohydrates and other acidic species occurring natively in biomass hydrolysates.

[Recommendation of an assessment protocol to describe geriatric inpatient rehabilitation of lower limb mobility based on ICF: an interdisciplinary consensus process]

Because of the growing demand of geriatric rehabilitation, objective and clear indication decisions are needed with respect to limited financial resources. The aim of an interdisciplinary consensus group was to critically evaluate the most commonly used tests of functional performance of the lower limbs and to recommend useful tests to document progress of inpatient rehabilitation. Assessment of standing, walking, walking with a dual-task, sit-to-stand transfer, lying-to-sit-to-stand transfer, and stair climbing were recommended to document functional performance of the lower limbs and to describe rehabilitation targets. Future research is needed, because reasonably validated assessment tools do not exist for all of these domains. In addition to a standardized assessment of physical capacity, physical activity and participation with regard to the International Classification of Functioning, Disability, and Health (ICF) context have to be assessed. Body fixed sensors seem to be a promising assessment tool to objectively document progress in rehabilitation.

Large-area 2D periodic crystalline silicon nanodome arrays on nanoimprinted glass exhibiting photonic band structure effects

Two-dimensional silicon nanodome arrays are prepared on large areas up to 50 cm² exhibiting photonic band structure effects in the near-infrared and visible wavelength region by downscaling a recently developed fabrication method based on nanoimprint-patterned glass, high-rate electron-beam evaporation of silicon, self-organized solid phase crystallization and wet-chemical etching. The silicon nanodomes, arranged in square lattice geometry with 300 nm lattice constant, are optically characterized by angular resolved reflection measurements, allowing the partial determination of the photonic band structure. This experimentally determined band structure agrees well with the outcome of three-dimensional optical finite-element simulations. A 16% photonic bandgap is predicted for an optimized geometry of the silicon nanodome arrays. By variation of the duration of the selective etching step, the geometry as well as the optical properties of the periodic silicon nanodome arrays can be controlled systematically.

Abstract 258: Incidence and Predictors of Cardiac Arrest in Cerebrovascular Diseases

Background and purpose: Large scale studies of cardiac arrest in hospitalized patients with cerebrovascular accident (CVA) are lacking. We sought to describe the incidence, demographics and hospital characteristics of cardiac arrest in CVA. Additionally, we aimed to indentify predictors of cardiac arrest in patients with CVA.

Methods: We analyzed the data from the Nationwide Inpatient Sample (NIS) of Healthcare Cost and Utilization Project for years 2005-2009. NIS is a discharge level 20% stratified sample of all non-federal hospitals in the US. We used International Classification of Diseases-9 (ICD-9) codes to select cases of CVA. Comparisons were made by using χ2 and student-t tests. Multivariate logistic regression was used to identify independent predictors of cardiac arrest.

Results: We included 672,161 cases of CVA [ischemic stroke: 58.2%, transient ischemic attack (TIA):28.2%, intracerebral hemorrhage (ICH): 9.7%, and subarachnoid hemorrhage (SAH): 3.9%] in our analysis. Of these, 3,154 (0.467%) also had cardiac arrest. Compared to ischemic stroke (0.413%), incidence of cardiac arrest was higher in ICH (1.221%) and SAH (2.523%) and was lower in TIA (0.038%). Patients with cardiac arrest were younger (mean age±SD: 67.8±16.4 vs. 70.5±15.7 years, p<0.001) and were less likely of female gender (51.8% vs. 55.7%, p<0.001). There was a significant difference in the incidence of cardiac arrest between various ethnic groups (Caucasian: 0.415% vs. African-American: 0.563% vs. Hispanic: 0.633% vs. Asian/Pacific Islander: 0.722%, p<0.001). Compared to the rest, patients in lowest income quartile had higher incidence of cardiac arrest (0.526% vs. 0.437%, p<0.001). Significant differences based on the hospital characteristics were as follows: 1. Bedsize: small (0.349%) vs. medium (0.443%) vs. large (0.498%), p<0.001; 2. Location: rural (0.354%) vs. urban (0.485%), p<0.001; 3. Academic status: teaching (0.553%) vs. non-teaching (0.403%), p<0.001; and 4. Region: northeast (0.399%) vs. midwest (0.403%) vs. south (0.489%) vs. west (0.553%), p<0.001. In multivariate analysis, factors associated with cardiac arrest are shown in the table.

Conclusion: This is one of the largest studies to describe the predictors of cardiac arrest in CVA. The patients with ICH and SAH are at significantly higher risk of cardiac arrest. The association of hospital characteristics and the incidence of cardiac arrest warrants further exploration into the contributing factors. The patients with higher risk profile as per the predictor model should warrant closer monitoring.

Peritoneal enterobiasis causing endometriosis-like symptoms

PURPOSE

Enterobiasis is the most common parasitic disease of the temperate zones and infects the human intestinal tract. In rare cases extraintestinal infections with Enterobius vermicularis may occur and can affect the female genital tract and peritoneal cavity. In most cases the infection is asymptomatic, but there are also cases described in which peritoneal enterobiasis can cause abdominal pain.

METHODS

A case report and review of the pertinent literature.

RESULTS

A 32-year-old patient was admitted with cyclical lower abdominal pain. With suspected endometriosis a diagnostic autofluorescence laparoscopy (DAFE) was performed. At surgery extensive peritoneal deposits were seen. Macroscopically these deposits were not typical for endometriosis. The histological examination showed granuloma caused by E. vermicularis eggs. The patient was treated with mebendazole. After completion of treatment the patient was asymptomatic. At the second-look laparoscopy no more peritoneal changes were detected.

CONCLUSION

Enterobius vermicularis may cause symptoms similar to endometriosis. In cases with reasonable suspicion it should therefore be considered in the differential diagnosis.

Combined anatomical and functional imaging using coronary CT angiography and myocardial perfusion SPECT in symptomatic adults with abnormal origin of a coronary artery

There has been a lack of standardized workup guidelines for patients with congenital abnormal origin of a coronary artery from the opposite sinus (ACAOS). We aimed to evaluate the use of cardiac hybrid imaging using multi-detector row CT (MDCT) for coronary CT angiography (Coronary CTA) and stress-rest myocardial perfusion SPECT (MPS) for comprehensive diagnosis of symptomatic adult patients with ACAOS. Seventeen symptomatic patients (12 men; 54 ± 13 years) presenting with ACAOS underwent coronary CTA and MPS. Imaging data were analyzed by conventional means, and with additional use of 3D image fusion to allocate stress induced perfusion defects (PD) to their supplying coronary arteries. An anomalous RCA arose from the left anterior sinus in eight patients, an abnormal origin from the right sinus was detected in nine patients (5 left coronary arteries, LCA and 4 LCx). Five of the 17 patients (29%) demonstrated a reversible PD in MPS. There was no correlation between the anatomical variants of ACAOS and the presence of myocardial ischemia. Image fusion enabled the allocation of reversible PD to the anomalous vessel in three patients (two cases in the RCA and the other in the LCA territory); PD in two patients were allocated to the territory of artery giving rise to the anomalies, rather than the anomalies themselves. In a small cohort of adult symptomatic patients with ACAOS anomaly there was no relation found between the specific anatomical variant and the appearance of stress induced myocardial ischemia using cardiac hybrid imaging.

Multiband spectroscopy of ultracold fermions: observation of reduced tunneling in attractive Bose-Fermi mixtures

We perform a detailed experimental study of the band excitations and tunneling properties of ultracold fermions in optical lattices. Employing a novel multiband spectroscopy for fermionic atoms, we can measure the full band structure and tunneling energy with high accuracy. In an attractive Bose-Fermi mixture we observe a significant reduction of the fermionic tunneling energy, which depends on the relative atom numbers. We attribute this to an interaction-induced increase of the lattice depth due to the self-trapping of the atoms.

[Securing the future through research - light on the horizon?]

Research is more important than ever for urology as a clinical specialty. The enormous advances being achieved in molecular medicine should not develop outside the realm of urology. In fact, implementing them in urology serves to guarantee the further existence of our specialty with its current clinical scope. If drug therapy for cancer is to remain an enduring part of urology or if kidney transplantation is to continue to be an integral part of urology and not belong to transplant surgery, then the expertise in these clinical entities and understanding of their pathogenetic relationships must be found in urology. As a result, research must be an essential part of our specialty on the one hand and the results of research must be applied to the whole extent of urology on the other hand.

Influence of anabolic combinations of an androgen plus an estrogen on biochemical pathways in bovine uterine endometrium and ovary

The application of anabolic steroids in food producing animals is forbidden in the EU since 1988, but the abuse of such drugs is a potential problem. The existing test systems are based on known compounds and can be eluded by newly emerging substances. The examination of physiological effects of anabolic hormones on different tissues to indirectly detect misuse might overcome this problem. Two studies were conducted with post-pubertal 24-months old Nguni heifers and pre-pubertal female 2-4 weeks old Holstein Friesian calves, respectively. The animals of the accordant treatment groups were administered combinations of estrogenic and androgenic compounds. The measurement of the gene expression pattern was undertaken with RT-qPCR. Target genes of different functional groups (receptors, angiogenesis, steroid synthesis, proliferation, apoptosis, nutrient metabolism and others) have been quantified. Several biochemical pathways were shown to be influenced by anabolic treatment. Both studies identified significant regulations in steroid and growth factor receptors (AR, ERβ, LHR, FSHR, Flt-1, PR, IGF-1R, Alk-6), angiogenic and tissue remodeling factors (VEGFs, FGFs, BMPs, ANGPT-2, MMPs, TIMP-2, CTSB), steroid synthesis (S5A1, HSD17, CYP19A1), proliferation (TNFα, IGF-1, IGFBPs, p53, c-fos; CEBPD, c-kit), apoptosis (CASP3, FasL, p53) and others (C7, INHA, STAR). Several genes were regulated to opposite directions in post-pubertal compared to pre-pubertal animals. PCA for Nguni heifers demonstrated a distinct separation between the control and the treatment group. In conclusion, anabolics modify hormone sensitivity and steroid synthesis, and they induce proliferative effects in the whole reproductive tract (uterus and ovary) as well as anti-angiogenic effects in the ovary. However, the extent will depend on the developmental stage of the animals.

Preview: a program for surveying shotgun proteomics tandem mass spectrometry data

Database search programs for peptide identification by tandem mass spectrometry ask their users to set various parameters, including precursor and fragment mass tolerances, digestion specificity, and allowed types of modifications. Even proteomics experts with detailed knowledge of their samples may find it difficult to make these choices without significant investigation, and poor choices can lead to missed identifications and misleading results. Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. Moreover, Preview optionally recalibrates mass over charge measurements, leading to further improvement in identification results. In a study of Bruton's tyrosine kinase, we find that the use of Preview improved the number of confidently identified mass spectra and phosphorylation sites by about 50%.

Uprighting and distalisation of first permanent maxillary molars in patients with undermining resorption: a case report

This case report describes a treatment method for distalisation and uprighting of first permanent maxillary molars with the aim of preventing complications in the presence of undermining resorption of the second deciduous molar. We present a fixed appliance, which is a compliance-independent and effective alternative to the methods used thus far such as removable plates with distal screws or separating ligatures.

Availability and use of hip protectors in residents of nursing homes

SUMMARY

Potential predictors of availability and use of hip protectors were studied in residents of 48 nursing homes. The likelihood of being offered a hip protector was reduced in men, in residents with very low or very high care needs, in residents with migration background, and in recipients of welfare aid.

INTRODUCTION

The purpose of this study is to analyze potential predictors of availability and use of hip protectors in residents of nursing homes.

METHODS

In 48 German nursing homes, individual information on availability and use of hip protectors was collected from all institutionalized residents (3,924 residents; 78.2% women). Information on nursing home characteristics was obtained by telephone interview. The effect of individual variables and of nursing home characteristics on hip protector availability and use was estimated using multilevel logistic regression analyses.

RESULTS

The prevalence of hip protectors being made available was 10.0% in women and 6.2% in men. Sixty-four percent of those with a hip protector used it during the 4 weeks prior to the examination. The likelihood of being offered a hip protector was reduced in men (odds ratio (OR), 0.59; 95% confidence interval (CI), 0.43; 0.83), in residents with very low or very high care needs (OR, 0.32; 95% CI, 0.18; 0.56 and OR, 0.55; 95% CI, 0.38; 0.79, respectively), in residents with a migration background (OR, 0.30; 95% CI, 0.09; 0.99), and in recipients of welfare aid (OR, 0.60; 95% CI, 0.44; 0.81). Nursing home characteristics such as the size of the nursing home or staff participation rate in training measures had no effect on hip protector availability and use.

CONCLUSION

Predictors of hip protector availability were sex, the degree of care need, migration status, and welfare aid. The lower availability of hip protectors in residents with welfare aid and migration status may be an indicator for health inequality in the German health system.

[Mental practice has influence on limitation of motion and muscle atrophy following immobilisation of the radiocarpal joint - a prospective randomised experimental study]

PURPOSE

Distal radial fracture is the most common bony injury in man. Still there are unsatisfying treatment results, such as limited joint movement, muscle atrophy and pain, resulting from immobilisation while the fracture is healing. During this period, also joint movement seems to be "forgotten". This study experimentally examined if the method of mental practice, meaning the systematic repetition of a consciously imagined movement or action without simultaneous practical execution, can positively influence these findings.

MATERIALS AND METHODS

21 right-handed males had application of a circular forearm plaster for immobilisation of their left radiocarpal joint, simulating a distal radial fracture for three weeks. Following randomisation, half of the study participants learned mental practice for "virtual movement" of their radiocarpal joint and had to perform it, the others were not treated at all. At beginning and end of the experiment, joint movement was measured, and an MRI examination of the forearm muscles was performed. The brain (cortex) areas, responsible for radiocarpal joint movement, were examined concerning their activity with functional MRI at the beginning and also at the end of the three weeks. The experiment was also performed on three "real" patients suffering from a distal radial fracture demanding plaster immobilisation, all of them were mentally treated.

RESULTS

Mental practice significantly ameliorated dorsal extension and ulnar abduction after plaster removal in comparison to those not having been mentally trained. Muscle atrophy of forearm muscles, measured via MRI, was significantly less in those having mental training. The cortex areas responsible for radiocarpal joint movements (supplementary motor area, precentral gyrus, putamen, nucleus caudatus, prefrontal cortex, thalamus and cerebellum) showed significant signal changes at the end of the three weeks in those having been mentally trained. There were significant correlations between MRI and functional MRI findings. The findings in the three "real" patients were similiar.

CONCLUSIONS

The results of this experimental study show that mental practice can have a positive influence on the outcome of distal radial fractures demanding immobilisation. A study with a larger number of "real patients" should follow.

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides also added at specific sites. The existence of insertional editing makes gene identification difficult and localization of editing sites has relied upon characterization of individual cDNAs. We have now determined the complete mitochondrial transcriptome of Physarum using Illumina deep sequencing of purified mitochondrial RNA. We report the first instances of A and G insertions and sites of partial and extragenic editing in Physarum mitochondrial RNAs, as well as an additional 772 C, U and dinucleotide insertions. The notable lack of antisense RNAs in our non-size selected, directional library argues strongly against an RNA-guided editing mechanism. Also of interest are our findings that sites of C to U changes are unedited at a significantly higher frequency than insertional editing sites and that substitutional editing of neighboring sites appears to be coupled. Finally, in addition to the characterization of RNAs from 17 predicted genes, our data identified nine new mitochondrial genes, four of which encode proteins that do not resemble other proteins in the database. Curiously, one of the latter mRNAs contains no editing sites.

NSAID use and risk of Parkinson disease: a population-based case-control study

BACKGROUND

Previous epidemiologic studies have produced inconsistent findings regarding the association between the use of non-steroidal anti-inflammatory drugs (NSAIDs) and the risk of Parkinson disease (PD).

METHODS

We conducted a case-control analysis using the General Practice Research Database. Cases (≥40 years) had a new diagnosis of PD between 1994 and 2009. We matched four controls to each PD case on age, sex, general practice, and index date. Use of NSAIDs, aspirin, and acetaminophen was stratified by exposure timing and duration for both cases and controls. We calculated odds ratios (OR) using conditional logistic regression. For additional analyses, the index date was brought backward 1, 2, and 3 years, respectively.

RESULTS

We identified 4026 cases with an incident idiopathic PD diagnosis and 15,969 matched controls. Compared with patients without any previous prescription for NSAIDs, those with prior use had no increased risk of a PD diagnosis (OR 1.07, 95% CI 0.99-1.16). Long-term use (≥15 prescriptions) was associated with a slightly lower PD risk (adjusted OR 0.94, 95% CI 0.83-1.07). The relative PD risks of the use of aspirin or acetaminophen were not materially higher (PD risk of long-term use: adjusted ORs 1.16, 95% CI 1.03-1.30 and 1.15, 95% CI 1.02-1.30, respectively) compared with those for non-users. The risk estimate diminished toward the null in subsequent analyses with shifted index dates.

CONCLUSION

In this large observational study with data from the UK primary care, the long-term use of NSAIDs, aspirin, or acetaminophen was not associated with a substantially altered risk of developing PD.

Improvement of balance after audio-biofeedback. A 6-week intervention study in patients with progressive supranuclear palsy

Progressive supranuclear palsy (PSP) is a neurodegenerative disease with no sufficient treatment options to date. The most devastating symptom is the loss of balance with consecutive falls. Based on the observation that postural control improved in patients with vestibular dysfunction after audio-biofeedback training, we tested the effects of this training in PSP patients. Eight PSP patients were included into an uncontrolled 6-week intervention trial. The focus of the training was the improvement of posture and dynamic balance by using audio-biofeedback. The device was well accepted. No adverse events occurred. A significant improvement in the Berg Balance Scale was observed (T2 vs. T1, p=0.016), which remained significant at the 4-week follow-up (T3 vs. T1, p=0.008). Significant improvement of the Parkinson's disease questionnaire was demonstrated. No significant changes were found in the Timed Up-and-Go Test, the Five Chair Rise Test, and in specific clinical scales. To our knowledge, the present study is the first to demonstrate that audio-biofeedback training with PSP patients is associated with improvements of balance and psychosocial aspects.

Workplace bullying and psychotropic drug use: the mediating role of physical and mental health status

OBJECTIVES

The association between workplace bullying and psychotropic drug use is not well established. This study was aimed at exploring the association between workplace bullying, and its characteristics, and psychotropic drug use and studying the mediating role of physical and mental health.

METHODS

The study population consisted of a random sample of 3132 men and 4562 women of the working population in the south-east of France. Workplace bullying, evaluated using the validated instrument elaborated by Leymann, and psychotropic drug use, as well as covariates, were measured using a self-administered questionnaire. Covariates included age, marital status, presence of children, education, occupation, working hours, night work, physico-chemical exposures at work, self-reported health, and depressive symptoms. Statistical analysis was performed using logistic regression analysis and was carried out separately for men and women.

RESULTS

Workplace bullying was strongly associated with psychotropic drug use. Past exposure to bullying increased the risk for this use. The more frequent and the longer the exposure to bullying, the stronger the association with psychotropic drug use. Observing bullying on someone else at the workplace was associated with psychotropic drug use. Adjustment for covariates did not modify the results. Additional adjustment for self-reported health and depressive symptoms reduced the magnitude of the associations, especially for men.

CONCLUSIONS

The association between bullying and psychotropic drug use was found to be significant and strong and was partially mediated by physical and mental health.

Excess mortality after pelvic fractures in institutionalized older people

Mortality after pelvic fracture was calculated in residents of nursing homes. Compared with a matched comparison nonfracture group, excess mortality was found during the first 2 months after pelvic fracture.

INTRODUCTION

Low energy pelvic fractures are mainly observed in people of advanced older age. The incidence of these fractures has increased considerably during the last decades. Information about excess mortality after pelvic fractures in older people is not available.

METHODS

To calculate excess mortality, a retrospective cohort study was conducted. Data from residents institutionalized in Bavarian nursing homes between 2001 and 2006 were used. For each patient with a pelvic fracture (n=1,154), five residents without pelvic fracture (n=5,770) were matched by sex, age, date of admission to the nursing home, and level of care (measure for the need of care). Hazard regression models were applied.

RESULTS

An excess mortality was found during the first months after pelvic fracture. In women, the increased mortality risk was limited to the first (hazard rate ratio (HR) 1.83, 95% confidence interval (CI) 1.42-2.37) and second (HR 1.52, 95% CI 1.13-2.04) months after the injury. In men, excess mortality was more pronounced (HR 2.95, 95% CI 1.57-5.54 for the first month) and appeared to last longer than in women. The majority of deaths due to pelvic fractures in the first 2 months after injury occurred following discharge from the hospital to the nursing home.

CONCLUSION

Pelvic fractures are associated with an increased mortality. These results should encourage the development of preventive measures to reduce this excess mortality.