NITPICK: peak identification for mass spectrometry data

<p>Abstract</p> <p>Background</p> <p>The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments.</p> <p>Results</p> <p>This contribution proposes a sparse template regression approach to peak picking called NITPICK. NITPICK is a Non-greedy, Iterative Template-based peak PICKer that deconvolves complex overlapping isotope distributions in multicomponent mass spectra. NITPICK is based on <it>fractional averagine</it>, a novel extension to Senko's well-known averagine model, and on a modified version of sparse, non-negative least angle regression, for which a suitable, statistically motivated early stopping criterion has been derived. The strength of NITPICK is the deconvolution of overlapping mixture mass spectra.</p> <p>Conclusion</p> <p>Extensive comparative evaluation has been carried out and results are provided for simulated and real-world data sets. NITPICK outperforms pepex, to date the only alternate, publicly available, non-greedy feature extraction routine. NITPICK is available as software package for the R programming language and can be downloaded from <url>http://hci.iwr.uni-heidelberg.de/mip/proteomics/</url>.</p

Clinical and functional outcomes of the saddle prosthesis

BACKGROUND:The implantation of a saddle prosthesis after resection of a pelvic tumor has been proposed as a simple method of reconstruction that provides good stability and reduces the surgical time, thus limits the onset of intraoperative complications. There are no studies in the literature of patients evaluated using gait analysis after being implanted with a saddle prosthesis. The present study is a retrospective case review aimed at illustrating long-term clinical and functional findings in tumor patients reconstructed with a saddle prosthesis. MATERIALS AND METHODS:A series of 15 patients who received pelvic reconstruction with a saddle prosthesis were retrospectively reviewed in terms of clinical, radiographic, and functional evaluations. Two patients were additionally assessed by gait analysis. RESULTS:Long-term functional follow-up was achieved in only 6 patients, and ranged from 97 to 167 months. Function was found to be rather impaired, as a mean of only 57 % of normal activity was restored. Gait analysis demonstrated that the implant had poor biomechanics, as characterized by very limited hip motion. CONCLUSIONS: Though the saddle prosthesis was proposed as advance in tumor-related pelvic surgery, the present study indicates that it yields unsatisfactory clinical and functional results due to both clinical complications and the poor biomechanics of the device. The use of a saddle prosthesis in tumor surgery did not provide satisfactory results in long-term follow-up. It is no longer implanted at our institute, and is currently considered a "salvage technique.

Wet Granular Materials

Most studies on granular physics have focused on dry granular media, with no liquids between the grains. However, in geology and many real world applications (e.g., food processing, pharmaceuticals, ceramics, civil engineering, constructions, and many industrial applications), liquid is present between the grains. This produces inter-grain cohesion and drastically modifies the mechanical properties of the granular media (e.g., the surface angle can be larger than 90 degrees). Here we present a review of the mechanical properties of wet granular media, with particular emphasis on the effect of cohesion. We also list several open problems that might motivate future studies in this exciting but mostly unexplored field.Comment: review article, accepted for publication in Advances in Physics; tex-style change

Postural assessment of patients with non-conventional knee endoprosthesis

Objective:To investigate the correlation between the sagittal and frontal alignment and possible postural asymmetries found in patients submitted to total knee stent placement for osteosarcoma.Methods:Twenty two individuals were divided into two groups according to tumor location: femur group (13 patients) and tibia group (nine patients), who were evaluated through postural analysis software (SAPO).Results:No statistically significant difference was found between groups, supporting previous result showing that both groups present the same postural asymmetries.Conclusion:We conclude that both groups have the same postural imbalances, especially the knee of the affected limb that presents hyperextension and center of gravity shifted anteriorly and laterally to the non-affected limb, indicating changes in weight bearing and influencing the gait pattern and balance. Level of Evidence II, Prospective Comparative Study.Universidade Federal de São Paulo (UNIFESP) Instituto de Oncologia PediátricaUNIFESP, Instituto de Oncologia PediátricaSciEL

Advances in mass spectrometry-based post-column bioaffinity profiling of mixtures

In the screening of complex mixtures, for example combinatorial libraries, natural extracts, and metabolic incubations, different approaches are used for integrated bioaffinity screening. Four major strategies can be used for screening of bioactive mixtures for protein targets—pre-column and post-column off-line, at-line, and on-line strategies. The focus of this review is on recent developments in post-column on-line screening, and the role of mass spectrometry (MS) in these systems. On-line screening systems integrate separation sciences, mass spectrometry, and biochemical methodology, enabling screening for active compounds in complex mixtures. There are three main variants of on-line MS based bioassays: the mass spectrometer is used for ligand identification only; the mass spectrometer is used for both ligand identification and bioassay readout; or MS detection is conducted in parallel with at-line microfractionation with off-line bioaffinity analysis. On the basis of the different fields of application of on-line screening, the principles are explained and their usefulness in the different fields of drug research is critically evaluated. Furthermore, off-line screening is discussed briefly with the on-line and at-line approaches

Clinical characteristics and prognosis of osteosarcoma in young children: a retrospective series of 15 cases

<p>Abstract</p> <p>Background</p> <p>Osteosarcoma is the most common primary bone malignancy in childhood and adolescence. However, it is very rare in children under 5 years of age. Although studies in young children are limited in number, they all underline the high rate of amputation in this population, with conflicting results being recently reported regarding their prognosis.</p> <p>Methods</p> <p>To enhance knowledge on the clinical characteristics and prognosis of osteosarcoma in young children, we reviewed the medical records and histology of all children diagnosed with osteosarcoma before the age of five years and treated in SFCE (Société Française des Cancers et leucémies de l'Enfant) centers between 1980 and 2007.</p> <p>Results</p> <p>Fifteen patients from 7 centers were studied. Long bones were involved in 14 cases. Metastases were present at diagnosis in 40% of cases. The histologic type was osteoblastic in 74% of cases. Two patients had a relevant history. One child developed a second malignancy 13 years after osteosarcoma diagnosis.</p> <p>Thirteen children received preoperative chemotherapy including high-dose methotrexate, but only 36% had a good histologic response. Chemotherapy was well tolerated, apart from a case of severe late convulsive encephalopathy in a one-year-old infant. Limb salvage surgery was performed in six cases, with frequent mechanical and infectious complications and variable functional outcomes.</p> <p>Complete remission was obtained in 12 children, six of whom relapsed. With a median follow-up of 5 years, six patients were alive in remission, seven died of their disease (45%), in a broad range of 2 months to 8 years after diagnosis, two were lost to follow-up.</p> <p>Conclusions</p> <p>Osteosarcoma seems to be more aggressive in children under five years of age, and surgical management remains a challange.</p

Marking their own homework: The pragmatic and moral legitimacy of industry self-regulation

When is industry self-regulation (ISR) a legitimate form of governance? In principle, ISR can serve the interests of participating companies, regulators and other stakeholders. However, in practice, empirical evidence shows that ISR schemes often under-perform, leading to criticism that such schemes are tantamount to firms marking their own homework. In response, this paper explains how current management theory on ISR has failed to separate the pragmatic legitimacy of ISR based on self-interested calculations, from moral legitimacy based on normative approval. The paper traces three families of management theory on ISR and uses these to map the pragmatic and moral legitimacy of ISR schemes. It identifies tensions between the pragmatic and moral legitimacy of ISR schemes, which the current ISR literature does not address, and draws implications for the future theory and practice of ISR