Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying melanin spatial distribution using pump-probe microscopy and a 2-D morphological autocorrelation transformation for melanoma diagnosis

Abstract. Pump-probe microscopy is an emerging molecular imaging technique that probes the excited state dynamics properties of pigmented samples. This method has been particularly intriguing for melanoma because, unlike other methods available, it can provide nondestructive, quantitative chemical information regarding different types of melanins, with high spatial resolution. In this Letter, we present a method based on mathematical morphology to quantify melanin structure (eumelanin, pheomelanin, and total melanin content, uniquely available with pump-probe microscopy) to aid in melanoma diagnosis. The approach applies a two-dimensional autocorrelation function and utilizes statistical parameters of the corresponding autocorrelation images, specifically, the second moments and entropy, to parameterize image structure. Along with bulk melanin chemical information, we show that this method can differentiate invasive melanomas from noninvasive and benign lesions with high sensitivity and specificity (92.3% and 97.5%, respectively, with N=53). The mathematical method and the statistical analysis are described in detail and results from cutaneous and ocular conjunctival melanocytic lesions are presented.
A general method for assessing brain–computer interface performance and its limitations

Objective. When researchers evaluate brain–computer interface (BCI) systems, we want quantitative answers to questions such as: How good is the system’s performance? How good does it need to be? and: Is it capable of reaching the desired level in future? In response to the current lack of objective, quantitative, study-independent approaches, we introduce methods that help to address such questions. We identified three challenges: (I) the need for efficient measurement techniques that adapt rapidly and reliably to capture a wide range of performance levels; (II) the need to express results in a way that allows comparison between similar but non-identical tasks; (III) the need to measure the extent to which certain components of a BCI system (e.g. the signal processing pipeline) not only support BCI performance, but also potentially restrict the maximum level it can reach. Approach. For challenge (I), we developed an automatic staircase method that adjusted task difficulty adaptively along a single abstract axis. For challenge (II), we used the rate of information gain between two Bernoulli distributions: one reflecting the observed success rate, the other reflecting chance performance estimated by a matched random-walk method. This measure includes Wolpaw’s information transfer rate as a special case, but addresses the latter’s limitations including its restriction to item-selection tasks. To validate our approach and address challenge (III), we compared four healthy subjects’ performance using an EEG-based BCI, a ‘Direct Controller’ (a high-performance hardware input device), and a ‘Pseudo-BCI Controller’ (the same input device, but with control signals processed by the BCI signal processing pipeline). Main results. Our results confirm the repeatability and validity of our measures, and indicate that our BCI signal processing pipeline reduced attainable performance by about 33% (21 bits min−1). Significance. Our approach provides a flexible basis for evaluating BCI performance and its limitations, across a wide range of tasks and task difficulties.
Sequence Analysis of APOA5 Among the Kuwaiti Population Identifies Association of rs2072560, rs2266788, and rs662799 With TG and VLDL Levels

Common variants of Apolipoprotein A5 (APOA5) have been associated with lipid levels yet very few studies have reported full sequence data from various ethnic groups. The purpose of this study was to analyse the full APOA5 gene sequence to identify variants in 100 healthy Kuwaitis of Arab ethnicities and assess their association with variation in lipid levels in a cohort of 733 samples. Sanger method was used in the direct sequencing of the full 3.7 Kb APOA5 and multiple sequence alignment was used to identify variants. The complete APOA5 sequence in Kuwaiti Arabs has been deposited in GenBank (KJ401315). A total of 20 reported single nucleotide polymorphisms (SNPs) were identified. Two novel SNPs were also identified: a synonymous 2197G>A polymorphism at genomic position 116661525 and a 3′ UTR 3222 C>T polymorphism at genomic position 116660500 based on human genome assembly GRCh37/hg:19. Five SNPs along with the two novel SNPs were selected for validation in the cohort. Association of those SNPs with lipid levels was tested and minor alleles of three SNPs (rs2072560, rs2266788, and rs662799) were found significantly associated with TG and VLDL levels. This is the first study to report the full APOA5 sequence and SNPs in an Arab ethnic group. Analysis of the variants identified and comparison to other populations suggests a distinctive genetic component in Arabs. The positive association observed for rs2072560 and rs2266788 with TG and VLDL levels confirms their role in lipid metabolism.
Finite Element based Bayesian Particle Filtering for the estimation of crack damage evolution on metallic panels

A lot of studies are nowadays devoted to structural health monitoring, especially inside the aeronautical environment. In particular, focusing the attention on metallic structures, fatigue cracks represent both a design and maintenance issue. The disposal of real time diagnostic technique for the assessment of structural health has led the attention also toward the prognostic assessment of the residual useful life, trying to develop robust prognostic health management systems to assist the operators in scheduling maintenance actions. The work reported inside this paper is about the development of a Bayesian particle filter to be used to refine the posterior probability density functions of both the damage condition and the residual useful life, given a prior knowledge on damage evolution is available from NASGRO material characterization. The prognostic algorithm has been applied to two cases. The former consists in an off-line application, receiving diagnostic inputs retrieved with manual structure scanning for fault identification. The latter is used on-line to filter the input coming from a real-time automatic diagnostic system. A massive usage of FEM simulations is used in order to enhance the algorithm performances.
Iron oxide nanoparticles and induced autophagy in human monocytes

Superparamagnetic iron oxide nanoparticles have been widely used in biomedical applications, but understanding of their interactions with the biological immune system is relatively limited. This work is focused on dextran-coated iron oxide nanoparticles and their induced autophagy in human monocytes. We found that these nanoparticles can be taken up by human monocytes, followed by localization within vesicles or free in cytoplasm. Autophagosome formation was observed with increased expression of LC3II protein, the specific marker of autophagy. The autophagy substrate p62 was degraded in a dose-dependent manner, and autophagy was blocked by autophagy (or lysosome) inhibitors alone or along with iron oxide nanoparticles, indicating that autophagosome accumulation was mainly due to autophagy induction, rather than blockade of autophagy flux. Interestingly, iron oxide nanoparticles increased the viability of human monocytes, but the mechanism was not clear. We further found that inhibition of autophagy mostly attenuated the survival of cells, with acceleration of the inflammation induced by these nanoparticles. Taken together, autophagic activation in human monocytes may play a protective role against the cytotoxicity of iron oxide nanoparticles.
Meta-Analysis Evaluation of the Potential Excess of Statistically Significant Findings in Published Genetic Association Studies : Application to Alzheimer ’ s Disease

The authors evaluated whether there is an excess of statistically significant results in studies of genetic associations with Alzheimer’s disease reflecting either between-study heterogeneity or bias. Among published articles on genetic associations entered into the comprehensive AlzGene database (www.alzgene.org) through January 31, 2007, 1,348 studies included in 175 meta-analyses with 3 or more studies each were analyzed. The number of observed studies (O) with statistically significant results (P 1⁄4 0.05 threshold) was compared with the expected number (E ) under different assumptions for the magnitude of the effect size. In the main analysis, the plausible effect size of each association was the summary effect presented in the respective meta-analysis. Overall, 19 meta-analyses (all with eventually nonsignificant summary effects) had a documented excess ofO over E: Typically single studies had significant effects pointing in opposite directions and early summary effects were dissipated over time. Across the whole domain, O was 235 (17.4%), while E was 164.8 (12.2%) (P < 10 ). The excess showed a predilection for meta-analyses with nonsignificant summary effects and between-study heterogeneity. The excess was seen for all levels of statistical significance and also for studies with borderline P values (P 1⁄4 0.05–0.10). The excess of significant findings may represent significance-chasing biases in a setting of massive testing.
Parenting Influences on Depression: A Moderated Mediated Model

Little is known about the developmental processes through which parenting factors may influence clinical depression among youth. This study investigated whether parenting influences the onset of clinical depression through the mediating mechanism of negative attributional style, particularly under conditions of high stress, in a community sample of children and adolescents (N = 289). Results supported a moderated mediation model in which low levels of observed parent positive regard and sensitivity to distress during a youth stressor task were indirectly associated with an increased likelihood of experiencing an episode of depression over an18 month period, through the mediating influence of youth negative attributional style, but only for youth who also experienced a high number of peer stressors. These findings elucidate mechanisms through which parenting may contribute to risk for depression during the transition into and across adolescence.
UNDERSTANDING THE PROBLEMS OF ENTERPRISE SYSTEM IMPLEMENTATIONS - Beyond Critical Success Factors

Many companies continue to implement Enterprise Systems (ES) in order to take advantage of the integrating potential of having a single common system across the organization that can replace a multitude of independent legacy systems. While increasingly popular, research continues to show that such systems are difficult to implement successfully. A number of studies have identified the critical success factors for such implementations. However, in practice, it is often difficult to ensure that these critical factors are in place and are maintained in place across the lifespan of the implementation project. In this paper we identify the socio-political and cultural issues that explain why this is difficult and suggest some meta-level processes (induction, informality and improvisation) that can help to offset the problems with maintaining the critical success factors.1
Optimal ECG Sampling Rate for Non-Linear Heart Rate Variability

principle difficulty with the analysis of the heart rate variability (HRV) is that heart rate dynamics are non-linear and non-stationary. Detrended fluctuation analysis (DFA) and correlation dimension (CD) are non-linear HRV measures to quantify fractal-like autocorrelation properties and to characterize the complex behaviour of nonlinear time series. Optimal ECG sampling rate is an important issue for accurate quantification of HRV. High ECG sampling rate results in very high processing time and low sampling rate produces signal quality degradation results in clinically misinterpreted HRV. In this work the impact of ECG sampling frequency on non-linear HRV have been quantified in terms of short-range & long-range DFA and CD on short-term (N=200), medium- term (N=500) and long-term (N=1000) data. Non-linear HRV parameters are found to be sensitive to ECG sampling frequency and effect of sampling frequency will be a function of data length. KeywordsHRV, Sampling frequency, DFA, CD, Signal processing.
Intestinal mucosal alterations in rats with carbon tetrachloride‐induced cirrhosis: Changes in glycosylation and luminal bacteria

Spontaneous bacterial peritonitis is a major cause of mortality after liver cirrhosis. Altered permeability of the mucosa and deficiencies in host immune defenses through bacterial translocation from the intestine due to intestinal bacterial overgrowth have been implicated in the development of this complication. Molecular mechanisms underlying the process are not well known. In order to understand mechanisms involved in translocation of bacteria, this study explored the role of oxidative stress in mediating changes in intestinal mucosal glycosylation and luminal bacterial content during cirrhosis. CCl4‐induced cirrhosis in rats led to prolonged oxidative stress in the intestine, accompanied by increased sugar content of both intestinal brush border and surfactant layers. This was accompanied by changes in bacterial flora in the gut, which showed increased hydrophobicity and adherence to the mucosa. Inhibition of xanthine oxidase using sodium tungstate or antioxidant supplementation using vitamin E reversed the oxidative stress, changes in brush border membrane sugar content, and bacterial adherence. In conclusion, oxidative stress in the intestine during cirrhosis alters mucosal glycosylation, accompanied by an increased hydrophobicity of luminal bacteria, enabling increased bacterial adherence onto epithelial cells. This might facilitate translocation across the mucosa, resulting in complications such as spontaneous bacterial peritonitis. (HEPATOLOGY 2006;43:837–846.)
Self-Calibration for the LOFAR Radio Astronomical Array

LOFAR is a low-frequency radio astronomical array currently under development in The Netherlands. It is designed to produce synthesis images of the most distant celestial objects yet observed. Due to high redshift levels, observations must be at unusually low frequencies (30-240 MHz), over large apertures (100 km), using thousands of antennas. At these frequencies, Earth's ionosphere acts as a random refractive sheet which over the large aperture induces source direction dependent gain and phase errors that must be estimated and calibrated out. Current radio astronomy "self-calibration" algorithms do not address direction dependence and will not work in the LOFAR environment. This paper presents a formal study of the parameter estimation problem for LOFAR calibration. A data model is proposed, and a Cramer-Rao lower bound (CRB) analysis is developed with a new general formulation to easily incorporate a variety of constraining signal models. It is shown that although the unconstrained direction dependent calibration problem is ambiguous, physically justifiable constraints can be applied in LOFAR to yield viable solutions. Use of a "compact core" of closely spaced array elements as part of the larger array is shown to significantly improve full array direction dependent calibration performance. Candidate algorithms are proposed and compared to the CRB.
Anytime Anyspace AND/OR Best-First Search for Bounding Marginal MAP

Marginal MAP is a key task in Bayesian inference and decision-making. It is known to be very difficult in general, particularly because the evaluation of each MAP assignment requires solving an internal summation problem. In this paper, we propose a best-first search algorithm that provides anytime upper bounds for marginal MAP in graphical models. It folds the computation of external maximization and internal summation into an AND/OR tree search framework, and solves them simultaneously using a unified best-first search algorithm. The algorithm avoids some unnecessary computation of summation sub-problems associated with MAP assignments, and thus yields significant time savings. Furthermore, our algorithm is able to operate within limited memory. Empirical evaluation on three challenging benchmarks demonstrates that our unified best-first search algorithm using pre-compiled variational heuristics often provides tighter anytime upper bounds compared to those state-of-the-art baselines.
Omni-Directional Regeneration (ODR) of Gap Sensor Signal for Journal Bearing System Diagnosis

We have developed a technique that enhances the detectability of sensors used to acquire data from a journal bearing rotor system. Usually, at an axial position for the rotating shaft on a journal bearing system, two sensors are fixed in radial direction at a right angle. The conventional diagnosis researches use only the acquired signals. However, two fixed sensors may not give sufficient information for diagnosis of the system since anomalies can happen in arbitrary direction. To improve the robustness of the diagnosis, coordinate transformed gap sensor signal is generated in arbitrary direction without installing extra sensors or adjusting sensor positions. With the original signals, the generated signals are used in the process of diagnosis. The powerful but simple method is described in the paper, and is verified by data sets from the experiment.
Effect of modified zirconium oxide nano-fillers addition on some properties of heat cure acrylic denture base material

Background: Polymer nano composite attracted great attention especially because of their unexpected hybrid properties that are synergistically derived from the two components. The aim of this study was to evaluate the effect of addition of modified nano-zirconium oxide on some properties of heat cured acrylic denture base material. Materials and methods: Zirconium oxide nano fillers modified by a silane coupling agent Tri (methoxysilyl) propyl methacrylate before dispersed and sonicated in monomer (MMA)in different percentage 2%,3%and 5%by weight. Three hundreds and twenty specimens were prepared for these studies were divided into five main groups according to the test used. The tests were abrasive wear, water sorption and solubility, porosity, tensile and fatigue strength test. For each test four sub groups (one control and three for different weight percentage of nano-ZrO2). Scanning electron microscope techniques used to analyze the fracture surface of fatigue test and estimate the dispersion and distribution of the nano-ZrO2 particles. Results: Highly significant increase in abrasive wear resistance with 3wt% and 5wt% of nano fillers with all groups of denture cleansers. highly significant decrease in water sorption and solubility. Significant decrease in porosity in 3wt% and 5wt%. Highly significant increase in both tensile and fatigue strength in all groups but slightly decreased in 5wt% as compared with 3wt% but still high significant as compared with control group. Conclusion: incorporating the modified nano-ZrO2 into acrylic resin results in improvement in abrasive wear resistance, tensile and fatigue strength in addition decrease in water sorption, solubility and porosity of heat cure denture base resin.
Energy Minimization for Wireless Communication With Rotary-Wing UAV

This paper studies unmanned aerial vehicle (UAV)-enabled wireless communication, where a rotary-wing UAV is dispatched to communicate with multiple ground nodes (GNs). We aim to minimize the total UAV energy consumption, including both propulsion energy and communication related energy, while satisfying the communication throughput requirement of each GN. To this end, we first derive a closed-form propulsion power consumption model for rotary-wing UAVs, and then formulate the energy minimization problem by jointly optimizing the UAV trajectory and communication time allocation among GNs, as well as the total mission completion time. The problem is difficult to be optimally solved, as it is non-convex and involves infinitely many variables over time. To tackle this problem, we first consider the simple fly-hover-communicate design, where the UAV successively visits a set of hovering locations and communicates with one corresponding GN while hovering at each location. For this design, we propose an efficient algorithm to optimize the hovering locations and durations, as well as the flying trajectory connecting these hovering locations, by leveraging the travelling salesman problem with neighborhood and convex optimization techniques. Next, we consider the general case, where the UAV also communicates while flying. We propose a new path discretization method to transform the original problem into a discretized equivalent with a finite number of optimization variables, for which we obtain a high-quality suboptimal solution by applying the successive convex approximation technique. The numerical results show that the proposed designs significantly outperform the benchmark schemes.
Fission yeast myosin I facilitates PI(4,5)P2-mediated anchoring of cytoplasmic dynein to the cortex

Significance Molecular motors perform a variety of functions such as muscle movement and nuclear positioning during cell division. One such motor protein, cytoplasmic dynein, is responsible for oscillations of the nucleus during meiosis of the unicellular eukaryote, fission yeast. In this study, we used genetics, live-cell fluorescence microscopy, and image processing to identify the key players that keep dynein at the cortex while it performs the function of back-and-forth nuclear movement by producing force on the microtubule. We discovered that the membrane phospholipid PI(4,5)P2 and, surprisingly, the myosin I motor Myo1 are both indispensable for nuclear oscillations in fission yeast. This study thus demonstrates one of the few instances of interplay between different classes of motor proteins in the cell. Several key processes in the cell, such as vesicle transport and spindle positioning, are mediated by the motor protein cytoplasmic dynein, which produces force on the microtubule. For the functions that require movement of the centrosome and the associated nuclear material, dynein needs to have a stable attachment at the cell cortex. In fission yeast, Mcp5 is the anchor protein of dynein and is required for the oscillations of the horsetail nucleus during meiotic prophase. Although the role of Mcp5 in anchoring dynein to the cortex has been identified, it is unknown how Mcp5 associates with the membrane as well as the importance of the underlying attachment to the nuclear oscillations. Here, we set out to quantify Mcp5 organization and identify the binding partner of Mcp5 at the membrane. We used confocal and total internal reflection fluorescence microscopy to count the number of Mcp5 foci and the number of Mcp5 molecules in an individual focus. Further, we quantified the localization pattern of Mcp5 in fission yeast zygotes and show by perturbation of phosphatidylinositol 4-phosphate 5-kinase that Mcp5 binds to phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Remarkably, we discovered that the myosin I protein in fission yeast, Myo1, which is required for organization of sterol-rich domains in the cell membrane, facilitates the localization of Mcp5 and that of cytoplasmic dynein on the membrane. Finally, we demonstrate that Myo1-facilitated association of Mcp5 and dynein to the membrane determines the dynamics of nuclear oscillations and, in essence, dynein activity.