Predicting progression of mild cognitive impairment to dementia using neuropsychological data: a supervised learning approach using time windows

Background: Predicting progression from a stage of Mild Cognitive Impairment to dementia is a major pursuit in current research. It is broadly accepted that cognition declines with a continuum between MCI and dementia. As such, cohorts of MCI patients are usually heterogeneous, containing patients at different stages of the neurodegenerative process. This hampers the prognostic task. Nevertheless, when learning prognostic models, most studies use the entire cohort of MCI patients regardless of their disease stages. In this paper, we propose a Time Windows approach to predict conversion to dementia, learning with patients stratified using time windows, thus fine-tuning the prognosis regarding the time to conversion. Methods: In the proposed Time Windows approach, we grouped patients based on the clinical information of whether they converted (converter MCI) or remained MCI (stable MCI) within a specific time window. We tested time windows of 2, 3, 4 and 5 years. We developed a prognostic model for each time window using clinical and neuropsychological data and compared this approach with the commonly used in the literature, where all patients are used to learn the models, named as First Last approach. This enables to move from the traditional question "Will a MCI patient convert to dementia somewhere in the future" to the question "Will a MCI patient convert to dementia in a specific time window". Results: The proposed Time Windows approach outperformed the First Last approach. The results showed that we can predict conversion to dementia as early as 5 years before the event with an AUC of 0.88 in the cross-validation set and 0.76 in an independent validation set. Conclusions: Prognostic models using time windows have higher performance when predicting progression from MCI to dementia, when compared to the prognostic approach commonly used in the literature. Furthermore, the proposed Time Windows approach is more relevant from a clinical point of view, predicting conversion within a temporal interval rather than sometime in the future and allowing clinicians to timely adjust treatments and clinical appointments.FCT under the Neuroclinomics2 project [PTDC/EEI-SII/1937/2014, SFRH/BD/95846/2013]; INESC-ID plurianual [UID/CEC/50021/2013]; LASIGE Research Unit [UID/CEC/00408/2013

Theoretical luminescence spectra in p-type superlattices based on InGaAsN

In this work, we present a theoretical photoluminescence (PL) for p-doped GaAs/InGaAsN nanostructures arrays. We apply a self-consistent method in the framework of the effective mass theory. Solving a full 8 x 8 Kane's Hamiltonian, generalized to treat different materials in conjunction with the Poisson equation, we calculate the optical properties of these systems. The trends in the calculated PL spectra, due to many-body effects within the quasi-two-dimensional hole gas, are analyzed as a function of the acceptor doping concentration and the well width. Effects of temperature in the PL spectra are also investigated. This is the first attempt to show theoretical luminescence spectra for GaAs/InGaAsN nanostructures and can be used as a guide for the design of nanostructured devices such as optoelectronic devices, solar cells, and others.CNPq [564.739/2010-3/NanoSemiCon, 302.550/2011-9/PQ, 470.998/2010-5/Univ, 472.312/2009-0/PQ, 303578/2007-6/PQ, 577.219/2008-1/JP]CNPqCAPESCAPESFACEPEFACEPE [0553-1.05/10/APQ]FAPESPFAPESPMaterials Science, Engineering and Commercialization Program of Texas State UniversityMaterials Science, Engineering and Commercialization Program of Texas State Universit

On finding minimal absent words

<p>Abstract</p> <p>Background</p> <p>The problem of finding the shortest absent words in DNA data has been recently addressed, and algorithms for its solution have been described. It has been noted that longer absent words might also be of interest, but the existing algorithms only provide generic absent words by trivially extending the shortest ones.</p> <p>Results</p> <p>We show how absent words relate to the repetitions and structure of the data, and define a new and larger class of absent words, called minimal absent words, that still captures the essential properties of the shortest absent words introduced in recent works. The words of this new class are minimal in the sense that if their leftmost or rightmost character is removed, then the resulting word is no longer an absent word. We describe an algorithm for generating minimal absent words that, in practice, runs in approximately linear time. An implementation of this algorithm is publicly available at <url>ftp://www.ieeta.pt/~ap/maws</url>.</p> <p>Conclusion</p> <p>Because the set of minimal absent words that we propose is much larger than the set of the shortest absent words, it is potentially more useful for applications that require a richer variety of absent words. Nevertheless, the number of minimal absent words is still manageable since it grows at most linearly with the string size, unlike generic absent words that grow exponentially. Both the algorithm and the concepts upon which it depends shed additional light on the structure of absent words and complement the existing studies on the topic.</p

Minimal Absent Words in Prokaryotic and Eukaryotic Genomes

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). We investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. We find that the compositional biases observed for the shortest absent words in vertebrates are not uniform throughout different sets of minimal absent words. We further investigate the hypothesis of the inheritance of minimal absent words through common ancestry from the similarity in dinucleotide relative abundances of different sets of minimal absent words, and find that this inheritance may be exclusive to vertebrates

Use of a polyphasic approach including MALDI-TOF MS for identification of Aspergillus section Flavi strains isolated from food commodities in Brazil

Brazil is one the largest producers and exporters of food commodities in the world. The evaluation of fungi capable of spoilage and the production mycotoxins in these commodities is an important issue that can be of help in bioeconomic development. The present work aimed to identify fungi of the genus Aspergillus section Flavi isolated from different food commodities in Brazil. Thirty-five fungal isolates belonging to the section Flavi were identified and characterised. Different classic phenotypic and genotypic methodologies were used, as well as a novel approach based on proteomic profiles produced by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Type or reference strains for each taxonomic group were included in this study. Three isolates that presented discordant identification patterns were further analysed using the internal transcribed spacer (ITS) region and calmodulin gene sequences. The data obtained from the phenotypic and spectral analyses divide the isolates into three groups, corresponding to taxa closely related to Aspergillus flavus, Aspergillus parasiticus, and Aspergillus tamarii. Final polyphasic fungal identification was achieved by joining data from molecular analyses, classical morphology, and biochemical and proteomic profiles generated by MALDI-TOF MS.Acknowledgments are due to FAPEMIG - Fundacao de Amparo a Pesquisa do Estado de Minas Gerais (Brazil) for financial support. F. C. da Silva extends thanks to CAPES - Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (Brazil) for the PhD grant. C. Santos and N. Lima thank CAPES for the financial support as international visiting professors in the Post-Graduate Programme in Agricultural Microbiology, Federal University of Lavras, Lavras (MG), Brazil

Exaggerated Exercise Blood Pressure as a Marker of Baroreflex Dysfunction in Normotensive Metabolic Syndrome Patients

IntroductionExaggerated blood pressure response to exercise (EEBP = SBP ≥ 190 mmHg for women and ≥210 mmHg for men) during cardiopulmonary exercise test (CPET) is a predictor of cardiovascular risk. Sympathetic hyperactivation and decreased baroreflex sensitivity (BRS) seem to be involved in the progression of metabolic syndrome (MetS) to cardiovascular disease.ObjectiveTo test the hypotheses: (1) MetS patients within normal clinical blood pressure (BP) may present EEBP response to maximal exercise and (2) increased muscle sympathetic nerve activity (MSNA) and reduced BRS are associated with this impairment.MethodsWe selected MetS (ATP III) patients with normal BP (MetS_NT, n = 27, 59.3% males, 46.1 ± 7.2 years) and a control group without MetS (C, n = 19, 48.4 ± 7.4 years). We evaluated BRS for increases (BRS+) and decreases (BRS−) in spontaneous BP and HR fluctuations, MSNA (microneurography), BP from ambulatory blood pressure monitoring (ABPM), and auscultatory BP during CPET.ResultsNormotensive MetS (MetS_NT) had higher body mass index and impairment in all MetS risk factors when compared to the C group. MetS_NT had higher peak systolic BP (SBP) (195 ± 17 vs. 177 ± 24 mmHg, P = 0.007) and diastolic BP (91 ± 11 vs. 79 ± 10 mmHg, P = 0.001) during CPET than C. Additionally, we found that MetS patients with normal BP had lower spontaneous BRS− (9.6 ± 3.3 vs. 12.2 ± 4.9 ms/mmHg, P = 0.044) and higher levels of MSNA (29 ± 6 vs. 18 ± 4 bursts/min, P &lt; 0.001) compared to C. Interestingly, 10 out of 27 MetS_NT (37%) showed EEBP (MetS_NT+), whereas 2 out of 19 C (10.5%) presented (P = 0.044). The subgroup of MetS_NT with EEBP (MetS_NT+, n = 10) had similar MSNA (P = 0.437), but lower BRS+ (P = 0.039) and BRS− (P = 0.039) compared with the subgroup without EEBP (MetS_NT−, n = 17). Either office BP or BP from ABPM was similar between subgroups MetS_NT+ and MetS_NT−, regardless of EEBP response. In the MetS_NT+ subgroup, there was an association of peak SBP with BRS− (R = −0.70; P = 0.02), triglycerides with peak SBP during CPET (R = 0.66; P = 0.039), and of triglycerides with BRS− (R = 0.71; P = 0.022).ConclusionNormotensive MetS patients already presented higher peak systolic and diastolic BP during maximal exercise, in addition to sympathetic hyperactivation and decreased baroreflex sensitivity. The EEBP in MetS_NT with apparent well-controlled BP may indicate a potential depressed neural baroreflex function, predisposing these patients to increased cardiovascular risk

A new generation of Parsec-Colibri stellar isochrones including the TP-AGB phase

We introduce a new generation of PARSEC-COLIBRI stellar isochrones that includes a detailed treatment of the thermally pulsing asymptotic giant branch (TP-AGB) phase, covering a wide range of initial metallicities (0.0001. &lt; Z(i) &lt; 0.06). Compared to previous releases, the main novelties and improvements are use of new TP-AGB tracks and related atmosphere models and spectra for M and C-type stars; inclusion of the surface H+He +CNO abundances in the isochrone tables, accounting for the effects of diffusion, dredge-up episodes and hot-bottom burning; inclusion of complete thermal pulse cycles, with a complete description of the in-cycle changes in the stellar parameters; new pulsation models to describe the long-period variability in the fundamental and firstovertone modes; and new dust models that follow the growth of the grains during the AGB evolution, in combination with radiative transfer calculations for the reprocessing of the photospheric emission. Overall, these improvements are expected to lead to a more consistent and detailed description of properties of TP-AGB stars expected in resolved stellar populations, especially in regard to their mean photometric properties from optical to mid-infrared wavelengths. We illustrate the expected numbers of TP-AGB stars of different types in stellar populations covering a wide range of ages and initial metallicities, providing further details on the "C-star island" that appears at intermediate values of age and metallicity, and about the AGB-boosting effect that occurs at ages close to 1.6-Gyr for populations of all metallicities. The isochrones are available through a new dedicated web server