918 research outputs found
MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.
BACKGROUND: The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs) needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. RESULTS: Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. CONCLUSION: Our approach not only enhances the computational performance, and thus the turn around time of MS-based experiments in proteomics, but also improves the information content with benefits of a higher proteome coverage. This improvement, for instance, increases the chance to identify important drug targets or biomarkers for drug development or molecular diagnostics
Autonomic and Renal Alterations in the Offspring of Sleep-Restricted Mothers During Late Pregnancy
OBJECTIVES: Considering that changes in the maternal environment may result in changes in progeny, the aim of this study was to investigate the influence of sleep restriction during the last week of pregnancy on renal function and autonomic responses in male descendants at an adult age. METHODS: After confirmation of pregnancy, female Wistar rats were randomly assigned to either a control or a sleep restriction group. The sleep-restricted rats were subjected to sleep restriction using the multiple platforms method for over 20 hours per day between the 14th and 20th day of pregnancy. After delivery, the litters were limited to 6 offspring that were designated as offspring from control and offspring from sleep-restricted mothers. Indirect measurements of systolic blood pressure (BPi), renal plasma flow, glomerular filtration rate, glomerular area and number of glomeruli per field were evaluated at three months of age. Direct measurements of cardiovascular function (heart rate and mean arterial pressure), cardiac sympathetic tone, cardiac parasympathetic tone, and baroreflex sensitivity were evaluated at four months of age. RESULTS: The sleep-restricted offspring presented increases in BPi, glomerular filtration rate and glomerular area compared with the control offspring. The sleep-restricted offspring also showed higher basal heart rate, increased mean arterial pressure, increased sympathetic cardiac tone, decreased parasympathetic cardiac tone and reduced baroreflex sensitivity. CONCLUSIONS: Our data suggest that reductions in sleep during the last week of pregnancy lead to alterations in cardiovascular autonomic regulation and renal morpho-functional changes in offspring, triggering increases in blood pressure
Estudo da suscetibilidade ao escurecimento por radiação gama de quartzo róseo-leitoso da provÃncia pegmatÃtica da Borborema
Este estudo considera as transformações induzidas pela radiação γ sobre os defeitos estruturais em quartzo róseo e leitoso da ProvÃncia PegmatÃtica da Borborema (ParaÃba e Rio Grande do Norte, Brasil). Amostras de coloração rósea e leitosa foram irradiadas com doses de raios γ (60Co) entre 0,5 e 96 kGy. Defeitos pontuais relacionados à s impurezas de Al, Ge, Li e grupos OH foram caracterizados por espectroscopias ultravioleta visÃvel e infravermelha e ressonância paramagnética eletrônica, antes e após a irradiação. A espectrometria de massa com plasma indutivamente acoplado foi empregada para quantificar as concentrações de Al, Li, Ge, Fe, Ti e outras impurezas em fragmentos de diferentes tonalidades. Constatou-se que os defeitos [AlO4]0, [AlO4/H]0 e [GeO4/Li]0 são formados pela dissociação dos defeitos [AlO4/Li]0 e [Li-OH], a partir de doses de 0,5 kGy. A diminuição do sinal da ressonância paramagnética eletrônica do centro [GeO4/Li]0 e a formação de centros E'1 perturbados por Ge para doses acima de 8 kGy confirmou a grande mobilidade dos Ãons Li+ pela estrutura do quartzo. O aumento da população de defeitos [AlO4]0 e o consequente escurecimento das amostras foi semelhante para ambos os tipos de quartzo. Análises preliminares por microscopia eletrônica mostraram a presença de fibras nanométricas apenas no resÃduo da digestão ácida de amostras róseas, indicando que a coloração rósea do quartzo da ProvÃncia PegmatÃtica da Borborema está provavelmente relacionada à s inclusões de dumortierita
An Improved Description of the Dielectric Breakdown in Oxides Based on a Generalized Weibull distribution
In this work, we address modal parameter fluctuations in statistical
distributions describing charge-to-breakdown and/or
time-to-breakdown during the dielectric breakdown regime of
ultra-thin oxides, which are of high interest for the advancement of electronic
technology. We reobtain a generalized Weibull distribution (-Weibull), which
properly describes data when oxide thickness fluctuations are
present, in order to improve reliability assessment of ultra-thin oxides by
time-to-breakdown extrapolation and area scaling. The incorporation
of fluctuations allows a physical interpretation of the -Weibull
distribution in connection with the Tsallis statistics. In support to our
results, we analyze data of SiO-based MOS devices obtained
experimentally and theoretically through a percolation model, demonstrating an
advantageous description of the dielectric breakdown by the -Weibull
distribution.Comment: 5 pages, 3 figure
Organic film thickness influence on the bias stress instability in Sexithiophene Field Effect Transistors
In this paper, the dynamics of bias stress phenomenon in Sexithiophene (T6)
Field Effect Transistors (FETs) has been investigated. T6 FETs have been
fabricated by vacuum depositing films with thickness from 10 nm to 130 nm on
Si/SiO2 substrates. After the T6 film structural analysis by X-Ray diffraction
and the FET electrical investigation focused on carrier mobility evaluation,
bias stress instability parameters have been estimated and discussed in the
context of existing models. By increasing the film thickness, a clear
correlation between the stress parameters and the structural properties of the
organic layer has been highlighted. Conversely, the mobility values result
almost thickness independent
Identificação molecular de Bartonella henselae em paciente com SIDA soronegativo para doença da arranhadura do gato no Rio de Janeiro, Brasil
Bartonella henselae is associated with a wide spectrum of clinical manifestations, including cat scratch disease, endocarditis and meningoencephalitis, in immunocompetent and immunocompromised patients. We report the first molecularly confirmed case of B. henselae infection in an AIDS patient in state of Rio de Janeiro, Brazil. Although DNA sequence of B. henselae has been detected by polymerase chain reaction in a lymph node biopsy, acute and convalescent sera were nonreactive.Bartonella henselae está associada a um amplo espectro de manifestações clÃnicas, incluindo a doença da arranhadura de gato, endocardite, e meningoencefalite, em pacientes imunocompetentes e imunocomprometidos. Relatamos o primeiro caso confirmado por método molecular de B. henselae em um paciente com SIDA no estado do Rio de Janeiro, Brasil. Apesar da sequência de DNA de B. henselae ser detectada pela reação em cadeia da polimerase em uma biópsia do linfonodo, soros das fases aguda e convalescente foram não reativos
The 1:1 resonance in Extrasolar Systems: Migration from planetary to satellite orbits
We present families of symmetric and asymmetric periodic orbits at the 1/1
resonance, for a planetary system consisting of a star and two small bodies, in
comparison to the star, moving in the same plane under their mutual
gravitational attraction. The stable 1/1 resonant periodic orbits belong to a
family which has a planetary branch, with the two planets moving in nearly
Keplerian orbits with non zero eccentricities and a satellite branch, where the
gravitational interaction between the two planets dominates the attraction from
the star and the two planets form a close binary which revolves around the
star. The stability regions around periodic orbits along the family are
studied. Next, we study the dynamical evolution in time of a planetary system
with two planets which is initially trapped in a stable 1/1 resonant periodic
motion, when a drag force is included in the system. We prove that if we start
with a 1/1 resonant planetary system with large eccentricities, the system
migrates, due to the drag force, {\it along the family of periodic orbits} and
is finally trapped in a satellite orbit. This, in principle, provides a
mechanism for the generation of a satellite system: we start with a planetary
system and the final stage is a system where the two small bodies form a close
binary whose center of mass revolves around the star.Comment: to appear in Cel.Mech.Dyn.Ast
On the dynamics of Extrasolar Planetary Systems under dissipation. Migration of planets
We study the dynamics of planetary systems with two planets moving in the
same plane, when frictional forces act on the two planets, in addition to the
gravitational forces. The model of the general three-body problem is used.
Different laws of friction are considered. The topology of the phase space is
essential in understanding the evolution of the system. The topology is
determined by the families of stable and unstable periodic orbits, both
symmetric and non symmetric. It is along the stable families, or close to them,
that the planets migrate when dissipative forces act. At the critical points
where the stability along the family changes, there is a bifurcation of a new
family of stable periodic orbits and the migration process changes route and
follows the new stable family up to large eccentricities or to a chaotic
region. We consider both resonant and non resonant planetary systems. The 2/1,
3/1 and 3/2 resonances are studied. The migration to larger or smaller
eccentricities depends on the particular law of friction. Also, in some cases
the semimajor axes increase and in other cases they are stabilized. For
particular laws of friction and for special values of the parameters of the
frictional forces, it is possible to have partially stationary solutions, where
the eccentricities and the semimajor axes are fixed.Comment: Accepted in Celestial Mechanics and Dynamical Astronom
Technical performance of milk producers in the state of Goiás , Brazil, in the short and long terms
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