Classification of proteins using sequential and structural features

Classification of proteins is an important process in many areas of bioinformatics research. In this thesis, we devised three different strategies to classify proteins with high accuracy that may have implications for function and attribute annotation. First, protein families were classified into different functional subtypes using a classification-via-clustering approach by using relative complexity measure with reduced amino acid alphabets (RAAA). The devised procedure does not require multiple alignment of sequences and produce high classification accuracies. Second, different fixed-length motif and RAAA combinations were used as features to represent proteins from different thermostability classes. A T-test based dimensionality reduction scheme was applied to reduce the number of features and those features were used to develop support vector machine classifiers. The devised procedure produced better results with less number of features than purely using native protein alphabet. Third, a non-homologous protein structure dataset containing hyperthermophilic, thermophilic, and mesophilic proteins was assembled de novo. Comprehensive statistical analyses of the dataset were carried out to highlight novel features correlated with increased thermostability and machine learning approaches were used to discriminate the proteins. For the first time, our results strongly indicate that combined sequential and structural features are better predictors of protein thermostability than purely sequential or structural features. Furthermore, the discrimination capability of machine learning models strongly depends on RAAAs

Apofizealne avulzijske ozljede prednje donje šiljaste izbočine: rehabilitacija sine qua non – prikaz slučaja

Apophyseal injuries of the anterior superior iliac spine and pubic bone are common, whereas injuries to the anterior inferior iliac spine are only rarely encountered. When it occurs in children, it may be difficult to diagnose and is easily mistaken for slipped capital femoral epiphysis. To make timely and correct diagnosis, the physician must have thorough understanding of the basic anatomical relationships and awareness of the existence of this injury. In this case report treatment and follow-up period in a 12-year-old patient with apophyseal avulsion of anterior inferior iliac spine is described and the differential diagnosis is discussed.Apofizealne ozljede prednje gornje šiljaste izbočine bočne kosti i stidne kosti su česte, dok su ozljede prednje donje šiljaste izbočine bočne kosti rijetke. Kada se dogodi u djece ponekad je teško postaviti dijagnozu i lako se zamijeni s poskliznućem epifize glave femura. Da bi se postavila točna i pravovremena dijagnoza liječnik mora temeljito razumijeti osnovne anatomske odnose i biti svjestan mogućnosti pojave ove ozljede. U ovom prikazu slučaja iznosi se liječenje i praćenje tijekom dvije godine 12-godišnjeg bolesnika s apofizealnom avulzijom prednje donje šiljaste izbočine bočne kosti, a raspravljeno je o diferencijalnoj dijagnozi

Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets

Background: Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize multiple alignment of sequences and are based on an evolutionary model. However, multiple alignment is not an automated procedure and requires human intervention to maintain alignment integrity and to produce phylogenies consistent with the functional splits in underlying sequences. To address this problem, we propose to use the alignment-free Relative Complexity Measure (RCM) combined with reduced amino acid alphabets to cluster protein families into functional subtypes purely on sequence criteria. Comparison with an alignment-based approach was also carried out to test the quality of the clustering. Results: We demonstrate the robustness of RCM with reduced alphabets in clustering of protein sequences into families in a simulated dataset and seven well-characterized protein datasets. On protein datasets, crotonases, mandelate racemases, nucleotidyl cyclases and glycoside hydrolase family 2 were clustered into subfamilies with 100% accuracy whereas acyl transferase domains, haloacid dehalogenases, and vicinal oxygen chelates could be assigned to subfamilies with 97.2%, 96.9% and 92.2% accuracies, respectively. Conclusions: The overall combination of methods in this paper is useful for clustering protein families into subtypes based on solely protein sequence information. The method is also flexible and computationally fast because it does not require multiple alignment of sequences

Quantitative spectroscopy of Deneb

Quantitative spectroscopy of luminous BA-type supergiants offers a high potential for modern astrophysics. The degree to which we can rely on quantitative studies of this class of stars as a whole depends on the quality of the analyses for benchmark objects. We constrain the basic atmospheric parameters and fundamental stellar parameters as well as chemical abundances of the prototype A-type supergiant Deneb to unprecedented accuracy (Teff = 8525 +/- 75 K, log(g) = 1.10 +/- 0.05 dex, M_spec = 19 +/- 3 M_sun, L = 1.96 +/- 0.32 *10^5 L_sun, R = 203 +/- 17 R_sun, enrichment with CN-processed matter) by applying a sophisticated hybrid NLTE spectrum synthesis technique which has recently been developed and tested. The study is based on a high-resolution and high-S/N spectrum obtained with the Echelle spectrograph FOCES on the Calar Alto 2.2m telescope. Practically all inconsistencies reported in earlier studies are resolved. Multiple metal ionization equilibria and numerous hydrogen lines from the Balmer, Paschen, Brackett and Pfund series are brought into match simultaneously for the stellar parameter determination. Stellar wind properties are derived from H_alpha line-profile fitting using line-blanketed hydrodynamic non-LTE models. A self-consistent view of Deneb is thus obtained, allowing us to discuss its evolutionary state in detail by comparison with the most recent generation of evolution models for massive stars. (abridged)Comment: 17 pages, 12 figures. Accepted for publication in A&

Quantitative Spectroscopy of BA-type Supergiants

Luminous BA-SGs allow topics ranging from NLTE physics and the evolution of massive stars to the chemical evolution of galaxies and cosmology to be addressed. A hybrid NLTE technique for the quantitative spectroscopy of BA-SGs is discussed. Thorough tests and first applications of the spectrum synthesis method are presented for four bright Galactic objects. Stellar parameters are derived from spectroscopic indicators. The internal accuracy of the method allows the 1sigma-uncertainties to be reduced to <1-2% in Teff and to 0.05-0.10dex in log g. Elemental abundances are determined for over 20 chemical species, with many of the astrophysically most interesting in NLTE. The NLTE computations reduce random errors and remove systematic trends in the analysis. Inappropriate LTE analyses tend to systematically underestimate iron group abundances and overestimate the light and alpha-process element abundances by up to factors of 2-3 on the mean. Contrary to common assumptions, significant NLTE abundance corrections of ~0.3dex can be found even for the weakest lines. NLTE abundance uncertainties amount to typically 0.05-0.10dex (random) and \~0.10dex (systematic 1sigma-errors). Near-solar abundances are derived for the heavier elements, and patterns indicative of mixing with nuclear-processed matter for the light elements. These imply a blue-loop scenario for Eta Leo, while the other three objects appear to have evolved directly from the main sequence. In the most ambitious computations several ten-thousand spectral lines are accounted for, permitting the accurate reproduction of the entire observed spectra from the visual to NIR. This prerequisite for the quantitative interpretation of medium-resolution spectra opens up BA-SGs as versatile tools for extragalactic stellar astronomy beyond the Local Group. (abridged)Comment: 36 pages, 18 figures, accepted for publication in A&

Design, Performance, and Calibration of the CMS Hadron-Outer Calorimeter

The CMS hadron calorimeter is a sampling calorimeter with brass absorber and plastic scintillator tiles with wavelength shifting fibres for carrying the light to the readout device. The barrel hadron calorimeter is complemented with an outer calorimeter to ensure high energy shower containment in the calorimeter. Fabrication, testing and calibration of the outer hadron calorimeter are carried out keeping in mind its importance in the energy measurement of jets in view of linearity and resolution. It will provide a net improvement in missing \et measurements at LHC energies. The outer hadron calorimeter will also be used for the muon trigger in coincidence with other muon chambers in CMS

CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe

Rehabilitacijski protokol kod stres frakture talusa niskog stupnja

Bone stress injuries are common overuse injuries seen in active people. The pathogenesis is multifactorial and usually involves repetitive submaximal stresses. No comprehensive studies describing rehabilitation protocol of low grade bone stress injury of the talus have been published. The aim of this case series was to describe a conservative treatment protocol for low grade bone stress injury of the talus.The rehabilitation and pain features in 15 patients with low grade bone stress injury of the talus, as confirmed by magnetic resonance imaging (MRI), were reviewed retrospectively. Of 15 patients (8 female and 7 male; age range 16-50 years; median age 29.1 years; mean duration of symptoms 2.5 (range, 1 to 12) weeks, MRI studies showed low grade bone marrow edema of the talus in six cases, whereas in other nine cases (5/15 calcaneus, 3/15 navicular and 1/15 cuboideum) adjacent osseous structures were affected as well. In four cases, the entire talus was involved and in eleven cases, only a portion of the bone was affected. The mean visual analogue scale for pain before treatment was 53.5 mm. The median duration of walking boot usage was 16.2 (7 to 70) days. Patients became symptom free in a mean of 23.2 (12-40) days. Ten patients returned to daily life and sportive activities without difficulty. Early diagnosis and appropriate conservative treatment of low grade bone stress injury of the talus allow favorable outcome in most cases.Stres ozljede kosti su uobičajene ozljede prenaprezanja u aktivnih osoba. Njihova patogeneza je multifaktorijalna i obično uključuju ponavljajući submaksimalni stres. Do sada nisu objavljene sveobuhvatne studije koje bi opisale rehabilitacijski protokol stres ozljeda talusa niskog stupnja. Cilj ove serije slučajeva je bio opisati konzervativni terapijski protokol za stres ozljede talusa niskog stupnja. Osobine rehabilitacije i boli u 15 pacijenata sa stres ozljedom talusa niskog stupnja, potvrđeno magnetskom rezonancijom (MR), su retrospektivno pregledani. Od 15 pacijenata (8 žena i 7 muškaraca; raspon dobi 16-50 godina; medijan dobi 29,1 godina; srednje trajanje simptoma 2,5 tjedana (raspon 1 do 12 tjedana), MR je pokazala edem koštane srži niskog stupnja talusa u šest slučajeva, dok je u preostalih devet slučajeva (5 petnih kostiju, 3 navikularne kosti I 1 kuboidne kosti) obližnje koštane strukture su bile također zahvaćene. U četiri slučaja bio je zahvaćen cijeli talus a u jedanaest slučajeva samo dio kosti. Srednja vrijednost jačine boli na vizualnoj analognoj ljestvici (VAS) je prije liječenja bila 53,5 mm. Srednje trajanje primjene imobilizacije (čizma) je bilo 16,2 dana (raspon 7 do 70). Pacijenti su postali bez simptoma za prosječno 23,2 dana (raspon 12-40). Deset pacijenata se vratilo aktivnostima svakodnevnog života i sportskim aktivnostima bez da imaju bilo kakve poteškoće. Rana dijagnoza i odgovarajuće konzervativno liječenje stres ozljede talusa niskog stupnja omogućuje povoljan ishod u većini slučajeva

Apofizealne avulzijske ozljede prednje donje šiljaste izbočine: rehabilitacija sine qua non – prikaz slučaja

Apophyseal injuries of the anterior superior iliac spine and pubic bone are common, whereas injuries to the anterior inferior iliac spine are only rarely encountered. When it occurs in children, it may be difficult to diagnose and is easily mistaken for slipped capital femoral epiphysis. To make timely and correct diagnosis, the physician must have thorough understanding of the basic anatomical relationships and awareness of the existence of this injury. In this case report treatment and follow-up period in a 12-year-old patient with apophyseal avulsion of anterior inferior iliac spine is described and the differential diagnosis is discussed.Apofizealne ozljede prednje gornje šiljaste izbočine bočne kosti i stidne kosti su česte, dok su ozljede prednje donje šiljaste izbočine bočne kosti rijetke. Kada se dogodi u djece ponekad je teško postaviti dijagnozu i lako se zamijeni s poskliznućem epifize glave femura. Da bi se postavila točna i pravovremena dijagnoza liječnik mora temeljito razumijeti osnovne anatomske odnose i biti svjestan mogućnosti pojave ove ozljede. U ovom prikazu slučaja iznosi se liječenje i praćenje tijekom dvije godine 12-godišnjeg bolesnika s apofizealnom avulzijom prednje donje šiljaste izbočine bočne kosti, a raspravljeno je o diferencijalnoj dijagnozi