Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation of Alzheimer Disease Neuropathologic Changes With Cognitive Status: A Review of the Literature

Abstract Clinicopathologic correlation studies are critically important for the field of Alzheimer disease (AD) research. Studies on human subjects with autopsy confirmation entail numerous potential biases that affect both their general applicability and the validity of the correlations. Many sources of data variability can weaken the apparent correlation between cognitive status and AD neuropathologic changes. Indeed, most persons in advanced old age have significant non-AD brain lesions that may alter cognition independently of AD. Worldwide research efforts have evaluated thousands of human subjects to assess the causes of cognitive impairment in the elderly, and these studies have been interpreted in different ways. We review the literature focusing on the correlation of AD neuropathologic changes (i.e. &bgr;-amyloid plaques and neurofibrillary tangles) with cognitive impairment. We discuss the various patterns of brain changes that have been observed in elderly individuals to provide a perspective forunderstanding AD clinicopathologic correlation and conclude that evidence from many independent research centers strongly supports the existence of a specific disease, as defined by the presence of A&bgr; plaques and neurofibrillary tangles. Although A&bgr; plaques may play a key role in AD pathogenesis, the severity of cognitive impairment correlates best with the burden of neocortical neurofibrillary tangles.
Design and optimization of 3D digital microfluidic biochips for the polymerase chain reaction

A digital microfluidic biochip (DMFB) is an attractive technology platform for revolutionizing immunoassays, clinical diagnostics, drug discovery, DNA sequencing, and other laboratory procedures in biochemistry. In most of these applications, real-time polymerase chain reaction (PCR) is an indispensable step for amplifying specific DNA segments. In recent years, three-dimensional (3D) DMFBs that integrate photodetectors (i.e., cyberphysical DMFBs) have been developed. They offer the benefits of smaller size, higher sensitivity and quicker time-to-results. However, current DMFB design methods target optimization in only two dimensions, hence they ignore the 3D two-layer structure of a DMFB. Moreover, these techniques ignore practical constraints related to the interference between on-chip device pairs, the performance-critical PCR thermal loop, and the physical size of devices. In this paper, we describe an optimization solution for a 3D DMFB, and present a three-stage algorithm to realize a compact 3D PCR chip layout, which includes: (i) PCR thermal-loop optimization; (ii) 3D global placement based on Strong-Push-Weak-Pull (SPWP) model; (iii) constraint-aware legalization. Simulation results for four laboratory protocols demonstrate that the proposed approach is effective for the design and optimization of a 3D chip for real-time PCR.
Synergistic Effects of Alpha-Toxin and Perfringolysin O in Clostridium perfringens-Mediated Gas Gangrene

ABSTRACT To examine the synergistic effects of alpha-toxin and perfringolysin O in clostridial myonecrosis, homologous recombination was used to construct an alpha-toxin deficient derivative of a perfringolysin O mutant of Clostridium perfringens. The subsequent strain was complemented with separate plasmids that carried the alpha-toxin structural gene (plc), the perfringolysin O gene (pfoA), or both toxin genes, and the resultant isogenic strains were examined in a mouse myonecrosis model. Synergistic effects were clearly observed in these experiments. Infection with the control strain, which did not produce either toxin, resulted in very minimal gross pathological changes, whereas the isogenic strain that was reconstituted for both toxins produced a pathology that was clearly more severe than when alpha-toxin alone was reconstituted. These changes were most apparent in the rapid spread of the disease, the gross pathology of the footpad and in the rate at which the mice had to be euthanatized for ethical reasons. Elimination of both alpha-toxin and perfringolysin O production removed most of the histopathological features typical of clostridial myonecrosis. These effects were restored when the mutant was complemented with the alpha-toxin structural gene, but reconstituting only perfringolysin O activity produced vastly different results, with regions of coagulative necrosis, apparently enhanced by vascular disruption, being observed. Reconstitution of both alpha-toxin and perfringolysin O activity produced histopathology most similar to that observed with the alpha-toxin reconstituted strain. The spreading of myonecrosis was very rapid in these tissues, and coagulative necrosis appeared to be restricted to the lumen of the blood vessels. The results of these virulence experiments clearly support the hypothesis that alpha-toxin and perfringolysin O have a synergistic effect in the pathology of gas gangrene.
Scalable Variational Bayesian Matrix Factorization with Side Information

Bayesian matrix factorization (BMF) is a popular method for collaborative prediction, because of its robustness to overfitting as well as of being free from cross-validation for fine tuning of regularization parameters. In practice, however, due to its cubic time complexity with respect to the rank of factor matrices, existing variational inference algorithms for BMF are not well suited to web-scale datasets where billions of ratings provided by millions of users are available. The time complexity even increases when the side information, such as user binary implicit feedback or item content information, is incorporated into variational Bayesian matrix factorization (VBMF). For instance, a state of the arts in VBMF with side information, is to place Gaussian priors on user and item factor matrices, where mean of each prior is regressed on the corresponding side information. Since this approach introduces additional cubic time complexity with respect to the size of feature vectors, the use of rich side information in a form of highdimensional feature vector is prohibited. In this paper, we present a scalable inference for VBMF with side information, the complexity of which is linear in the rank K of factor matrices. Moreover, the algorithm can be easily parallelized on multi-core systems. Experiments on large-scale datasets demonstrate the useful behavior of our algorithm such as scalability, fast learning, and prediction accuracy. Appearing in Proceedings of the 17 International Conference on Artificial Intelligence and Statistics (AISTATS) 2014, Reykjavik, Iceland. JMLR: W&CP volume 33. Copyright 2014 by the authors.
Approaches to describe ventilatory threshold in professional sports

Ventilatory threshold is one of the ways to measure cardiovasculatory fitness of the body. Therefore, in the present study it was decided to demonstrate which physiological parameters most accurately express the second ventilatory threshold (VAT2) depending on the cardiovasculatory fitness of different groups of athletes and untrained men. The study involved the following athletes: race walkers (n=14), weightlifters (n=16), powerlifters (n=16), runners (n=14), professional soccer players (n=13), amateur soccer players (n=16), martial arts (n=12), and untrained men (n=15). Subjects’ VAT2 and maximal load (ML) were recorded and at these levels were determined the value of achievable maximal power (P), oxygen uptake (VO2), heart rate (HR), the ratio for oxygen uptake and heart rate (VO2/HR) and the rate-pressure produkt (RPP). It was shown that subjects were of similar age but different body mass (BM) and BMI. There were also differences between athlete groups at VAT2 and ML in relation to: P, VO2, VO2/HR (p<0.001) and RPP only at VAT2 (p<0.023). Reached HR values at VAT2 as well as at ML have not differed between the groups. There were also intergroup differences at VAT2 in terms of relative values: %VO2max (p<0.002), %Pmax(p<0.016), %VO2max/%HRmax (p<0.03). Relatively expressed %HRmax and %RPPmax reached at VAT2 did not differ between the two groups. Runners, professional soccer players and race walkers achieved the most favorable indicators of physical performance. It has been demonstrated that VAT2 besides P i %Pmax was best described by VO2, %VO2max and by VO2/HR and %VO2max/%HRmax, as well as by RPP. On the other hand HR and %HRmax, as well as %RPPmax are not useful in this regard. Furthermore it should be recognized that athletes in whose structure of the training occurred running of varying intensity achieved the highest physical fitness.
A description of the finite dierencing used by the B-grid dynamical core

This paper describes the dynamical part of a global, hydrostatic grid point model developed from models described in Mesinger et al. (1988) and Wyman (1996). The model described here solves the same set of dynamical equations but has a modified vertical and horizontal grid. The vertical grid is a hybrid sigma-pressure coordinate system, sigma coordinate surfaces in the lower model levels may gradually transform to pressure coordinate surfaces in the upper model levels. The horizontal grid has been switched to the Arakawa B-grid (Arakawa and Lamb 1977). This has several advantages over the previously used E-grid configuration, especially in the global domain, where the convergence of diagonal fluxes near the pole of the E-grid has been eliminated in the B-grid. An additional benefit is the simplification of model output, a single field on the B-grid is essentially on its own rectangular A-grid. The basic time differencing schemes used has not changed from either of the preceding models. The step-mountain (eta) coordinate is no longer a supported option, although much of the code remains in place, very little effort has been made to ensure that it works correctly. This paper will describe the finite difference schemes used to solve the dynamical equations on the global B-grid. This will include descriptions of the time differencing, horizontal mixing, lateral boundary conditions, and polar filtering.
Teacher’s Qualification and Dyslexia Identification in Primary Schools in Oyo State, Nigeria

ABSTRACT The study examined the relationship between teachers’ qualifications and dyslexia identification in primary schools in Oyo State, Nigeria. Data were collected through the use of a well-structured questionnaire – the Teacher Dyslexia Awareness Checklist – administered to 147 primary school teachers in the state. Data were analysed using descriptive statistics, Principal Component Analysis (PCA), ANOVA and correlation coefficient. Demographic characteristics of teachers reveal that more female than males are engaged in the teaching profession with majority holding a National Certificate of Education (NCE) with more than 20 years teaching experience. The PCA shows that the level of knowledge of dyslexia among the teachers is low, as only 31% were knowledgeable about dyslexia. Results further show that the relationship between teachers’ qualifications and teaching experiences is weak implying that teachers’ qualifications and teaching experience are independent of each other. Thus, teachers’ knowledge about dyslexia is not in relation to their qualification or teaching experiences. It is recommended that teachers undergo periodic in-service training on the manifestation and management practices for learning disabilities at least once a term and formal testing to assist them in identifying different types of psychological issues affecting pupils, as early identification of learning disabilities (such as dyslexia) is the best way to curtail their lifelong effects.
Tenofovir Disoproxil Fumarate for Prevention of HIV Infection in Women: A Phase 2, Double-Blind, Randomized, Placebo-Controlled Trial

Objectives: The objective of this trial was to investigate the safety and preliminary effectiveness of a daily dose of 300 mg of tenofovir disoproxil fumarate (TDF) versus placebo in preventing HIV infection in women. Design: This was a phase 2, randomized, double-blind, placebo-controlled trial. Setting: The study was conducted between June 2004 and March 2006 in Tema, Ghana; Douala, Cameroon; and Ibadan, Nigeria. Participants: We enrolled 936 HIV-negative women at high risk of HIV infection into this study. Intervention: Participants were randomized 1:1 to once daily use of 300 mg of TDF or placebo. Outcome measures: The primary safety endpoints were grade 2 or higher serum creatinine elevations (>2.0 mg/dl) for renal function, grade 3 or 4 aspartate aminotransferase or alanine aminotransferase elevations (>170 U/l) for hepatic function, and grade 3 or 4 phosphorus abnormalities (<1.5 mg/dl). The effectiveness endpoint was infection with HIV-1 or HIV-2. Results: Study participants contributed 428 person-years of laboratory testing to the primary safety analysis. No significant differences emerged between treatment groups in clinical or laboratory safety outcomes. Study participants contributed 476 person-years of HIV testing to the primary effectiveness analysis, during which time eight seroconversions occurred. Two were diagnosed in participants randomized to TDF (0.86 per 100 person-years) and six in participants receiving placebo (2.48 per 100 person-years), yielding a rate ratio of 0.35 (95% confidence interval = 0.03–1.93), which did not achieve statistical significance. Owing to premature closures of the Cameroon and Nigeria study sites, the planned person-years of follow-up and study power could not be achieved. Conclusion: Daily oral use of TDF in HIV-uninfected women was not associated with increased clinical or laboratory adverse events. Effectiveness could not be conclusively evaluated because of the small number of HIV infections observed during the study.
KT-ORAM : An Efficient ORAM Built on kary Tree of PIR Nodes

This paper proposes KT-ORAM, a new hybrid ORAM-PIR construction, to protect a client’s access pattern to outsourced data. KT-ORAM organizes the server storage as a k-ary tree with each node acting as a fully-functional PIR storage, and adopts a novel delayed eviction technique to optimize the eviction process. KT-ORAM is proved to protect the data access pattern privacy at a failure probability negligible in N (N is the number of exported data blocks), when system parameter k = logN . Under the same configuration, KT-ORAM has an asymptotical communication cost of O( logN log logN · B) when the recursion level on meta data is of O(1) depth, which can be achieved if block size B = N ε (0 < ε < 1), or O( log 2 N log logN · B) when the number of recursion levels is O(logN). The costs of KT-ORAM are compared with those of several state-of-the-art ORAMs. The results show that, KT-ORAM achieves the best communication, storage and client-side computational efficiency simultaneously, at the price of requiring O( log 2 N log logN · B) computational cost at the storage server for each data query.
Ultra-High-Resolution Computed Tomography of the Lung: Image Quality of a Prototype Scanner

Purpose The image noise and image quality of a prototype ultra-high-resolution computed tomography (U-HRCT) scanner was evaluated and compared with those of conventional high-resolution CT (C-HRCT) scanners. Materials and Methods This study was approved by the institutional review board. A U-HRCT scanner prototype with 0.25 mm x 4 rows and operating at 120 mAs was used. The C-HRCT images were obtained using a 0.5 mm x 16 or 0.5 mm x 64 detector-row CT scanner operating at 150 mAs. Images from both scanners were reconstructed at 0.1-mm intervals; the slice thickness was 0.25 mm for the U-HRCT scanner and 0.5 mm for the C-HRCT scanners. For both scanners, the display field of view was 80 mm. The image noise of each scanner was evaluated using a phantom. U-HRCT and C-HRCT images of 53 images selected from 37 lung nodules were then observed and graded using a 5-point score by 10 board-certified thoracic radiologists. The images were presented to the observers randomly and in a blinded manner. Results The image noise for U-HRCT (100.87 ± 0.51 Hounsfield units [HU]) was greater than that for C-HRCT (40.41 ± 0.52 HU; P < .0001). The image quality of U-HRCT was graded as superior to that of C-HRCT (P < .0001) for all of the following parameters that were examined: margins of subsolid and solid nodules, edges of solid components and pulmonary vessels in subsolid nodules, air bronchograms, pleural indentations, margins of pulmonary vessels, edges of bronchi, and interlobar fissures. Conclusion Despite a larger image noise, the prototype U-HRCT scanner had a significantly better image quality than the C-HRCT scanners.
Investment Options, Assets in Place, and the Risk of Stocks

This study views the firm's future investment opportunities as operating options and examines the effect of growth opportunities on the firm's systematic risk using contingent claims analysis. The study predicts that the greater the portion of a stock's market value accounted for by the firm's growth opportunities, the higher the systematic risk. Overall, our empirical results strongly support this hypothesis. Furthermore, including firm size in empirical analysis does not significantly change the relationship between the stock beta and growth variables. Thus, we conclude that the effect of growth on stock risk is independent of firm size.
Strategic Impacts of Technology Switch-Over: Who Benefits from Electronic Commerce?

The introduction of new digital production and distribution technologies may alter the firms' strategy sets, as they are not able to commit credibly to quantity strategies anymore. Mixed oligopoly markets may emerge where some companies compete in prices, while others adjust their quantities. Using an approach first published by Reinhard Selten (1971) and developed further by Richard Cornes and Roger Hartley (2001), I calculate the Nash equilibrium of such an N-person game in a linear specification. Then I discuss the strategic effect of a technology switch-over on market performance and social welfare. A firm that introduces new technology suffers a srategic disadvantage, while consumers benefit.
Network Structure and Spatial Separation

This research aims to identify the role of network architecture in influencing individual travel behavior using travel survey data from Minneapolis-Saint Paul and Florida (Fort Lauderdale and Miami). Various measures of network structure, compiled from existing sources, are used to quantify roadway networks, and to capture the arrangement and connectivity of nodes and links in the networks and the spatial variations that exist among and within networks. The regression models show that travel behavior is correlated with network design.
Pastimes in Cancer Biology

Scientific discoveries spring not only from intellect, intuition, and persistent effort but also from unforeseen circumstances, accidental observations, and chance interpersonal encounters. Unanticipated detours from intended career paths can nurture an inclination to shift one's focus and take on risk, providing the freedom to explore uncharted avenues. Here I recount some early events that transformed the directions of my own research.
Adaptive SPWV distribution with adjustable volume 2-D separable kernel

In practical time-frequency (T-F) analysis of nonstationary signals associated with the use of the smooth pseudo Wigner-Ville distribution (SPWV), an important issue is a choice of the smoothing window. To address this problem, a fast sub-optimal technique is proposed, relating the window length to the approximate slope of the frequency modulation. The results obtained by using this automated procedure are comparable to results given by supervised decompositions and are more (locally) adapted. The developed method has been used in processing of radar returns. In order to objectively assess the performance of the transforms, several measures can be used. For signals with unknown modulation laws, cost functions are available, including measures based on entropy function. Their application to evaluation of the obtained T-F distributions is demonstrated.
A Light Adaptive 4000 Pixels Analog Silicon Retina for Edge Extraction and Motion Detection

An analog vision chip has been designed 011 the basis of retina models. Biological retinas perforni a massively parallel computation well suited to low level visual processing applications such as edge extraction, motion detection and light adaptation. An analog electrical model has been developed that is suitable for designing analog neural network circuits with low power consumption. This 4000 pixel neuromorphic circuit extracts edges or detects motion over a large dynamic range of luminosity and velocity. Experimental results are presented.
The identification of functional modules from the genomic association of genes

By combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. Here we study the properties of such networks to identify functional modules: sets of proteins that together are involved in a biological process. The complete network contains 3,033 orthologous groups of proteins in 38 genomes. It consists of one giant component, containing 1,611 orthologous groups, and of 516 small disjointed clusters that, on average, contain only 2.7 orthologous groups. These small clusters have a homogeneous functional composition and thus represent functional modules in themselves. Analysis of the giant component reveals that it is a scale-free, small-world network with a high degree of local clustering (C = 0.6). It consists of locally highly connected subclusters that are connected to each other by linker proteins. The linker proteins tend to have multiple functions, or are involved in multiple processes and have an above average probability of being essential. By splitting up the giant component at these linker proteins, we identify 265 subclusters that tend to have a homogeneous functional composition. The rare functional inhomogeneities in our subclusters reflect the mixing of different types of (molecular) functions in a single cellular process, exemplified by subclusters containing both metabolic enzymes as well as the transcription factors that regulate them. Comparative genome analysis, thus, allows identification of a level of functional interaction between that of pairwise interactions, and of the complete genome.
INTRAUTERINE GROWTH RETARDATION IN NEWBORN CHILDREN

Rationale Birthweight is one of the most sensitive – and also one of the most important – measures of the well-being of children. Weight at birth is directly influenced by the general level of health status of the mother. In developing countries, especially, maternal nutrition is one of the most important determinants of birthweight. Three aspects are of particular importance: inadequate maternal nutritional status before conception, short stature of the mother (mostly due to undernutrition and repeated infections during childhood), and poor maternal nutrition during pregnancy. In developed countries the most important contributing factor to low birthweight is maternal smoking.
CACAO Project at the LogCLEF Track

This paper presents the participation of the CACAO prototype to the Log Analysis for Digital Societies (LADS) task of LogCLEF 2009 track. CACAO (Cross-language Access to Catalogues And On-line libraries) is an EU project devoted to enabling cross-language access to the contents of a federation of digital libraries with a set of software tools for harvesting, indexing and serching over such data. In our experiment we investigated the possibility to exploit the TEL logs data as a source for inferring new translations, thus enriching already existing translation dictionaries; the proposed approach is based on the assumption that users consulting a multilingual digital collection are likely to repeat the same query in different languages. We applyed our approach to the logs from TEL and the results obtained are very promising.