Envelope: interactive software for modeling and fitting complex isotope distributions

<p>Abstract</p> <p>Background</p> <p>An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope labeling patterns. These patterns can be quite complex, in particular with <it>in vivo </it>metabolic labeling experiments producing fractional atomic labeling or fractional residue labeling of peptides or other macromolecules. In general, it can be difficult to distinguish the contributions of species with different labeling patterns to an experimental spectrum and difficult to calculate a theoretical isotope distribution to fit such data. There is a need for interactive and user-friendly software that can calculate and fit the entire isotope distribution of a complex mixture while comparing these calculations with experimental data and extracting the contributions from the differently labeled species.</p> <p>Results</p> <p>Envelope has been developed to be user-friendly while still being as flexible and powerful as possible. Envelope can simultaneously calculate the isotope distributions for any number of different labeling patterns for a given peptide or oligonucleotide, while automatically summing these into a single overall isotope distribution. Envelope can handle fractional or complete atom or residue-based labeling, and the contribution from each different user-defined labeling pattern is clearly illustrated in the interactive display and is individually adjustable. At present, Envelope supports labeling with ²H, ¹³C, and ¹⁵N, and supports adjustments for baseline correction, an instrument accuracy offset in the m/z domain, and peak width. Furthermore, Envelope can display experimental data superimposed on calculated isotope distributions, and calculate a least-squares goodness of fit between the two. All of this information is displayed on the screen in a single graphical user interface. Envelope supports high-quality output of experimental and calculated distributions in PNG or PDF format. Beyond simply comparing calculated distributions to experimental data, Envelope is useful for planning or designing metabolic labeling experiments, by visualizing hypothetical isotope distributions in order to evaluate the feasibility of a labeling strategy. Envelope is also useful as a teaching tool, with its real-time display capabilities providing a straightforward way to illustrate the key variable factors that contribute to an observed isotope distribution.</p> <p>Conclusion</p> <p>Envelope is a powerful tool for the interactive calculation and visualization of complex isotope distributions for comparison to experimental data. It is available under the GNU General Public License from <url>http://williamson.scripps.edu/envelope/</url>.</p

Acromioclavicular joint reconstruction with coracoacromial ligament transfer using the docking technique

<p>Abstract</p> <p>Background</p> <p>Symptomatic Acromioclavicular (AC) dislocations have historically been surgically treated with Coracoclavicular (CC) ligament reconstruction with transfer of the Coracoacromial (CA) ligament. Tensioning the CA ligament is the key to success.</p> <p>Methods</p> <p>Seventeen patients with chronic, symptomatic Type III AC joint or acute Type IV and V injuries were treated surgically. The distal clavicle was resected and stabilized with CC ligament reconstruction using the CA ligament. The CA ligament was passed into the medullary canal and tensioned, using a modified 'docking' technique. Average follow-up was 29 months (range 12–57).</p> <p>Results</p> <p>Postoperative ASES and pain significantly improved in all patients (p = 0.001). Radiographically, 16 (94%) maintained reduction, and only 1 (6%) had a recurrent dislocation when he returned to karate 3 months postoperatively. His ultimate clinical outcome was excellent.</p> <p>Conclusion</p> <p>The docking procedure allows for tensioning of the transferred CA ligament and healing of the ligament in an intramedullary bone tunnel. Excellent clinical results were achieved, decreasing the risk of recurrent distal clavicle instability.</p

Cognitive activity for the treatment of older adults with mild Alzheimer's Disease (AD) - PACE AD: study protocol for a randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Participation in cognitive stimulation therapy (CST) may reduce the rate of cognitive decline in people with Alzheimer's disease (AD), however it is unclear if the training of carers to deliver activities is sufficient to improve the clinical outcome of patients. The Promoting Healthy Ageing with Cognitive Exercise for Alzheimer's Disease (PACE-AD) study has been designed to determine if change in cognitive function over a six month period can be achieved with participation in cognitive stimulating activities when the intervention is delivered to carers only as opposed to carers and patients.</p> <p>Methods/Design</p> <p>The study will aim to recruit 128 community-dwelling men and women with probable AD according to NINCDS-ADRDS criteria. Participants will be randomly allocated to one of two cognitive activity treatment groups: (1) Participants with mild AD and their companions together (2) Companions of participants with mild AD alone. The intervention will consist of a twelve-week program of cognitive stimulation. Seven weeks of the program will involve 90-minute group sessions delivered once per week while the remaining weeks of the program will involve structured home based activities with telephone support. The primary outcome measure of the study is the change from baseline in the total score on the Alzheimer Disease Assessment Scale-Cognitive (ADAS-COG). Secondary outcomes of interest include changes in health related quality of life, mood, memory, language, executive functions, independent living abilities and psychiatric symptoms for participants with mild AD. Changes in companion quality of life, mood, and general health will also be monitored. Primary endpoints will be collected 13 and 26 weeks after the baseline assessment.</p> <p>Discussion</p> <p>The proposed project will provide evidence as to whether CST for people with AD and their companions is more beneficial than when used for companions alone. Outcomes sought include a reduction of further cognitive decline and improved quality of life amongst older adults with mild AD. We anticipate that the results of this study will have implications for the development of cost-effective evidence-based best practice to treat people with mild AD.</p> <p>Trial registration</p> <p><a href="http://www.anzctr.org.au/ACTRN12610000653066.aspx">ACTRN12610000653066</a></p

Surgery for scapula process fractures: Good outcome in 26 patients

Background Generally, scapula process fractures (coracoid and acromion) have been treated nonoperatively with favorable outcome, with the exception of widely displaced fractures. Very little has been published, however, regarding the operative management of such fractures and the literature that is available involves very few patients. Our hypothesis was that operative treatment of displaced acromion and coracoid fractures is a safe and effective treatment that yields favorable surgical results

Acromioclavicular joint dislocation: a comparative biomechanical study of the palmaris-longus tendon graft reconstruction with other augmentative methods in cadaveric models

<p>Abstract</p> <p>Background</p> <p>Acromioclavicular injuries are common in sports medicine. Surgical intervention is generally advocated for chronic instability of Rockwood grade III and more severe injuries. Various methods of coracoclavicular ligament reconstruction and augmentation have been described. The objective of this study is to compare the biomechanical properties of a novel palmaris-longus tendon reconstruction with those of the native AC+CC ligaments, the modified Weaver-Dunn reconstruction, the ACJ capsuloligamentous complex repair, screw and clavicle hook plate augmentation.</p> <p>Hypothesis</p> <p>There is no difference, biomechanically, amongst the various reconstruction and augmentative methods.</p> <p>Study Design</p> <p>Controlled laboratory cadaveric study.</p> <p>Methods</p> <p>54 cadaveric native (acromioclavicular and coracoclavicular) ligaments were tested using the Instron machine. Superior loading was performed in the 6 groups: 1) in the intact states, 2) after modified Weaver-Dunn reconstruction (WD), 3) after modified Weaver-Dunn reconstruction with acromioclavicular joint capsuloligamentous repair (WD.ACJ), 4) after modified Weaver-Dunn reconstruction with clavicular hook plate augmentation (WD.CP) or 5) after modified Weaver-Dunn reconstruction with coracoclavicular screw augmentation (WD.BS) and 6) after modified Weaver-Dunn reconstruction with mersilene tape-palmaris-longus tendon graft reconstruction (WD. PLmt). Posterior-anterior (horizontal) loading was similarly performed in all groups, except groups 4 and 5. The respective failure loads, stiffnesses, displacements at failure and modes of failure were recorded. Data analysis was carried out using a one-way ANOVA, with Student's unpaired t-test for unpaired data (S-PLUS statistical package 2005).</p> <p>Results</p> <p>Native ligaments were the strongest and stiffest when compared to other modes of reconstruction and augmentation except coracoclavicular screw, in both posterior-anterior and superior directions (p < 0.005).</p> <p>WD.ACJ provided additional posterior-anterior (P = 0. 039) but not superior (p = 0.250) stability when compared to WD alone.</p> <p>WD+PLmt, in loads and stiffness at failure superiorly, was similar to WD+CP (p = 0.066). WD+PLmt, in loads and stiffness at failure postero-anteriorly, was similar to WD+ACJ (p = 0.084).</p> <p>Superiorly, WD+CP had similar strength as WD+BS (p = 0.057), but it was less stiff (p < 0.005).</p> <p>Conclusions and Clinical Relevance</p> <p>Modified Weaver-Dunn procedure must always be supplemented with acromioclavicular capsuloligamentous repair to increase posterior-anterior stability. Palmaris-Longus tendon graft provides both additional superior and posterior-anterior stability when used for acromioclavicular capsuloligamentous reconstruction. It is a good alternative to clavicle hook plate in acromioclavicular dislocation.</p

Advances in structure elucidation of small molecules using mass spectrometry

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules

Measures of frailty in population-based studies: An overview

Although research productivity in the field of frailty has risen exponentially in recent years, there remains a lack of consensus regarding the measurement of this syndrome. This overview offers three services: first, we provide a comprehensive catalogue of current frailty measures; second, we evaluate their reliability and validity; third, we report on their popularity of use

Microbial shifts in the aging mouse gut

YesBackground: The changes that occur in the microbiome of aging individuals are unclear, especially in light of the imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, but these results may be confounded by other variables that often change with age such as diet and place of residence. To test these associations in a more controlled model system, we examined the relationship between age, frailty, and the gut microbiome of female C57BL/6 J mice. Results: The frailty index, which is based on the evaluation of 31 clinical signs of deterioration in mice, showed a near-perfect correlation with age. We observed a statistically significant relationship between age and the taxonomic composition of the corresponding microbiome. Consistent with previous human studies, the Rikenellaceae family, which includes the Alistipes genus, was the most significantly overrepresented taxon within middle-aged and older mice. The functional profile of the mouse gut microbiome also varied with host age and frailty. Bacterial-encoded functions that were underrepresented in older mice included cobalamin (B12) and biotin (B7) biosynthesis, and bacterial SOS genes associated with DNA repair. Conversely, creatine degradation, associated with muscle wasting, was overrepresented within the gut microbiomes of the older mice, as were bacterial-encoded β-glucuronidases, which can influence drug-induced epithelial cell toxicity. Older mice also showed an overabundance of monosaccharide utilization genes relative to di-, oligo-, and polysaccharide utilization genes, which may have a substantial impact on gut homeostasis. Conclusion: We have identified taxonomic and functional patterns that correlate with age and frailty in the mouse microbiome. Differences in functions related to host nutrition and drug pharmacology vary in an age-dependent manner, suggesting that the availability and timing of essential functions may differ significantly with age and frailty. Future work with larger cohorts of mice will aim to separate the effects of age and frailty, and other factors.This work was supported by the Canadian Institutes of Health Research (CIHR) through an Emerging Team Grant to RGB, CIHR Operating Grants to Langille et al. Microbiome 2014, 2:50 Page 10 of 12 http://www.microbiomejournal.com/content/2/1/50 SEH (MOP 126018) and RAR (MOP 93718), and a CIHR Fellowship to MGIL. Infrastructure was supported by the Canada Foundation for Innovation through a grant to RGB. RGB also acknowledges the support of the Canada Research Chairs program