Miracle-dz/UniFAR-FTUs huggingface dataset:
iMap 4: An Open Source Toolbox for the Statistical Fixation Mapping of Eye Movement data with Linear Mixed Modeling.

A major challenge in modern eye movement research is to statistically map where observers are looking at, as well as isolating statistical significant differences between groups and conditions. Compared to signals of contemporary neuroscience measures, such as M/EEG and fMRI, eye movement data are sparse with much larger variations across trials and participants. As a result, the implementation of a conventional Hierarchical Linear Model approach on two-dimensional fixation distributions often returns unstable estimations and underpowered results, leaving this statistical problem unresolved. Here, we tackled this issue by using the statistical framework implemented in diverse state-of-the-art neuroimaging data processing toolboxes: Statistical Parametric Mapping (SPM), Fieldtrip and LIMO EEG. We first estimated the mean individual fixation maps per condition by using trimmean to account for the sparseness and the high variations of fixation data. We then applied a univariate, pixel-wise linear mixed model (LMM) on the smoothed fixation data with each subject as a random effect, which offers the flexibility to code for multiple between- and within- subject comparisons. After this step, our approach allows to perform all the possible linear contrasts for the fixed effects (main effects, interactions, etc.). Importantly, we also introduced a novel spatial cluster test based on bootstrapping to assess the statistical significance of the linear contrasts. Finally, we validated this approach by using both experimental and computer simulation data with a Monte Carlo approach. iMap 4 is a freely available MATLAB open source toolbox for the statistical fixation mapping of eye movement data, with a user-friendly interface providing straightforward, easy to interpret statistical graphical outputs and matching the standards in robust statistical neuroimaging methods. iMap 4 represents a major step in the processing of eye movement fixation data, paving the way to a routine use of robust data-driven analyses in this important field of vision sciences. Meeting abstract presented at VSS 2015.
A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis

Angiogenesis is an important adaptation mechanism of the blood vessels to the changing requirements of the body during development, aging, and wound healing. Angiogenesis allows existing blood vessels to form new connections or to reabsorb existing ones. Blood vessels are composed of a layer of endothelial cells (ECs) covered by one or more layers of mural cells (smooth muscle cells or pericytes). We constructed a computational Boolean model of the molecular regulatory network involved in the control of angiogenesis. Our model includes the ANG/TIE, HIF, AMPK/mTOR, VEGF, IGF, FGF, PLCγ/Calcium, PI3K/AKT, NO, NOTCH, and WNT signaling pathways, as well as the mechanosensory components of the cytoskeleton. The dynamical behavior of our model recovers the patterns of molecular activation observed in Phalanx, Tip, and Stalk ECs. Furthermore, our model is able to describe the modulation of EC behavior due to extracellular micro-environments, as well as the effect due to loss- and gain-of-function mutations. These properties make our model a suitable platform for the understanding of the molecular mechanisms underlying some pathologies. For example, it is possible to follow the changes in the activation patterns caused by mutations that promote Tip EC behavior and inhibit Phalanx EC behavior, that lead to the conditions associated with retinal vascular disorders and tumor vascularization. Moreover, the model describes how mutations that promote Phalanx EC behavior are associated with the development of arteriovenous and venous malformations. These results suggest that the network model that we propose has the potential to be used in the study of how the modulation of the EC extracellular micro-environment may improve the outcome of vascular disease treatments.
The Association of Measured Breast Tissue Characteristics with Mammographic Density and Other Risk Factors for Breast Cancer

Background: We have examined the relationships between the measured properties of breast tissue and mammographic density and other risk factors for breast cancer, using breast tissue obtained at forensic autopsy and not selected for the presence of abnormalities. Methods: We used randomly selected tissue blocks taken from breast tissue slices obtained by s.c. mastectomy at the time of forensic autopsy to measure histologic features using quantitative microscopy. The proportions of the biopsy occupied by cells (estimated by nuclear area), glandular structures, and collagen were determined. These measurements were examined in relation to the percent density in the faxitron image of the tissue slice from which the biopsy was taken and other risk factors for breast cancer. Results: The percent mammographic density was associated with the proportion of the area of the biopsy occupied by nuclei, both epithelial and nonepithelial, and by collagen and the area of glandular structures. Several other risk factors for breast cancer, notably body weight, parity, and number of births, and menopausal status, that are associated with variations in mammographic density, were also associated with differences in one or more of these tissue features. Conclusion: All risk factors for breast cancer must ultimately exert their influence by an effect on the breast, and these findings suggest that, for some risk factors, this influence includes an effect on the number of cells and the quantity of collagen.
Detection of altered protein conformations in living cells.

The maturation, conformational stability, and the rate of in vivo degradation are specific for each protein and depend on both the intrinsic features of the protein and those of the surrounding cellular environment. While synthesis and degradation can be measured in living cells, stability and maturation of proteins are more difficult to quantify. We developed the split-ubiquitin method into a tool for detecting and analyzing changes in protein conformation. The biophysical parameter that forms the basis of these measurements is the time-averaged distance between the N terminus and C terminus of a protein. Starting from three proteins of known structure, we demonstrate the feasibility of this approach, and employ it to elucidate the effect of a previously described mutation in the protein Sec62p on its conformation in living cells.
Volumetric Segmentation Using Weibull E-SD Fields

This paper presents a coarse-grain approach for segmentation of objects with gray levels appearing in volume data. The input data is on a 3D structured grid of vertices v(i. j. k), each associated with a scalar value. In this paper, we consider a voxel as a /spl kappa/ /spl times/ /spl kappa/ /spl times/ /spl kappa/ cube and each voxel is assigned two values: expectancy and standard deviation (E-SD). We use the Weibull noise index to estimate the noise in a voxel and to obtain more precise E-SD values for each voxel. We plot the frequency of voxels which have the same E-SD, then 3D segmentation based on the Weibull E-SD field is presented. Our test bed includes synthetic data as well as real volume data from a confocal laser scanning microscope (CLSM). Analysis of these data all show distinct and defining regions in their E-SD fields. Under the guide of the E-SD field, we can efficiently segment the objects embedded in real and simulated 3D data.
Design of a Hybrid Intelligent System for Transitional Bladder Cell Carcinoma Diagnosis

Transitional Bladder cell carcinoma is one of the most common cancers of the urinary tract, accounting for approximately 90% of Bladder cancers. In this research a new computer-based system "Design of a Hybrid Intelligent System for Transitional Bladder Cell Carcinoma Diagnosis" (DHSTCCD) has been proposed and implemented. The proposed system is composed of two main phases, the first phase is the "cell analysis phase" which consists of three main stages including segmentation stage using "Genetic Optimization Based Fuzzy Image Segmentation Algorithm" (GOFISA), morphometric and photometric feature extraction stage and "Neuro-Fuzzy Classifier Model" (NFCM) stage that has been developed and implemented to classify a set of
Hypoxia Potentiates LPS-Mediated Cytotoxicity of BV2 Microglial Cells In Vitro by Synergistic Effects on Glial Cytokine and Nitric Oxide System

Abstract Background Microglial activation due to a variety of stimuli induces secretion of neurotoxic substances including inflammatory cytokines and nitric oxide (NO). Clinical studies indicate a cross-link between inflammatory and hypoxia-regulated pathways suggesting that bacterial infections markedly sensitize the immature brain to hypoxic injury. Methods The impact of inflammation and hypoxia on interleukin (IL)-1β, IL-6, tumor necrosis factor α (TNF-α), and NO secretion and microglia-induced cytotoxicity was investigated exposing BV2 cells to lipopolysaccharides (LPS) and hypoxia (1% O2). Cytotoxicity, NO, and cytokine release was quantified by MTS and Griess assays and by enzyme-linked immunosorbent assays, respectively. Results LPS exposure of BV2 cells induced a significant, persistent production of NO, IL-1β, IL-6, and TNF-α. Even after LPS removal, ongoing NO and cytokine secretion was observed. Hypoxia mediated exclusively a significant, short-term IL-1β increase, but enhanced LPS-induced cytokine and NO secretion significantly. In addition, LPS-induced supernatants exhibited a stronger cytotoxic effect in glial and neuronal cells than LPS exposition (p < 0.001). Hypoxia potentiated LPS-induced cytotoxicity. Conclusion Present data prove that LPS-induced soluble factors rather than LPS exposure mediate microglial toxicity under conditions of hypoxia in vitro. Apart from potential protective effects of the hypoxia-inducible transcription factor (HIF)-1α system, activation of proinflammatory pathways may markedly sensitize microglial cells to promote hypoxia-induced injuries of the developing brain.
Very high concentrations of n-3 fatty acids in peri-and postmenopausal Inuit women from Greenland

Objectives. The objectives of this study were to examine the profile of relative concentrations in plasma phospholipids of n-3 fatty acids among periand postmenopausal Inuit women living in Greenland and to verify their relationships with ischemic heart disease risk factors and more particularly, with concentrations of plasma triacylglycerols. Study Design. This study was part of a survey conducted in 2000, which aimed to assess the prevalence of osteoporosis and the associated risk factors among peri-and postmenopausal Greenland Inuit women. Methods. The study population consisted of 153 women aged 49–69 years (mean ± SD: 55.3 ± 4.4 y) randomly selected. Data were obtained through an interview (questionnaire on lifestyle habits, medical history etc) and a clinical session (physiologic and anthropologic measurements). Plasma samples were used to measure the fatty acid composition of plasma phospholipids. Results. The mean body mass index of women was 27.9 ± 6.1. Seventy-five percent were smokers and 9% were currently on hormone replacement therapy. Relative concentrations of total n-3 fatty acids were very high (13.8%, 95% CI: 13.1-14.6), with docosahexanoic and eicosapentanoic acids accounting for 4.7% and 7.2%, respectively. The ratio of n-3:n-6 fatty acids was 0.67. n-3 fatty acids were inversely correlated to triacylglycerols. Conclusion. These data show that peri-and post-menopausal Greenland Inuit women have very high plasma concentrations of n-3 fatty acids that protect them from ischemic heart disease.
A unified approach to network anomaly detection

This paper presents a unified approach for the detection of network anomalies. Current state of the art methods are often able to detect one class of anomalies at the cost of others. Our approach is based on using a Linear Dynamical System (LDS) to model network traffic. An LDS is equivalent to Hidden Markov Model (HMM) for continuous-valued data and can be computed using incremental methods to manage high-throughput (volume) and velocity that characterizes Big Data. Detailed experiments on synthetic and real network traces shows a significant improvement in detection capability over competing approaches. In the process we also address the issue of robustness of network anomaly detection systems in a principled fashion.
Reactions of the corn borer Ch. agamemnon Bles. towards some physical factors.

[1. The third instar larvae of the corn borer Chilo agamemnon Bles. were sensitive to small temperature differences of 1-2°C above 35°C in an alternative chamber, where a strong avoiding reaction to the warmer side was observed. The prefered zone of temperature was between 25-25°C and the linear velocity of the larvae increased proportionally with the temperature increase between 15 and 35°C. 2. The larvae always prefered high humidities and the average reaction intensity progressively increased with increase in the difference between the two alternative humidities in the arena. 3. The larvae were photonegative. The lateral ocelli served as photoreceptors by means of which the larvae sum up the light from various directions and moved in a path influenced by the more intense light and deviating towards the low intensity beam (tropotaxis). The larval reactions towards dark objects was skototactic. 4. Orthokinesis, klinokinesis and klinotaxis were the main mechanisms regulating the larval behaviour towards temperature, humidity and light. 5. The reactions towards two or three combined variable factors at the same time show that both temperature and relative humidity probably affect the behaviour of the larvae more than light. 6. 'The larval behaviour and its correlation to the normal environment was also discussed. , 1. The third instar larvae of the corn borer Chilo agamemnon Bles. were sensitive to small temperature differences of 1-2°C above 35°C in an alternative chamber, where a strong avoiding reaction to the warmer side was observed. The prefered zone of temperature was between 25-25°C and the linear velocity of the larvae increased proportionally with the temperature increase between 15 and 35°C. 2. The larvae always prefered high humidities and the average reaction intensity progressively increased with increase in the difference between the two alternative humidities in the arena. 3. The larvae were photonegative. The lateral ocelli served as photoreceptors by means of which the larvae sum up the light from various directions and moved in a path influenced by the more intense light and deviating towards the low intensity beam (tropotaxis). The larval reactions towards dark objects was skototactic. 4. Orthokinesis, klinokinesis and klinotaxis were the main mechanisms regulating the larval behaviour towards temperature, humidity and light. 5. The reactions towards two or three combined variable factors at the same time show that both temperature and relative humidity probably affect the behaviour of the larvae more than light. 6. 'The larval behaviour and its correlation to the normal environment was also discussed. ]
Robust and high‐resolution simulations of nonlinear electrokinetic processes in variable cross‐section channels

We present a model and an associated numerical scheme to simulate complex electrokinetic processes in channels with nonuniform cross‐sectional area. We develop a quasi‐1D model based on local cross‐sectional area averaging of the equations describing unsteady, multispecies, electromigration‐diffusion transport. Our approach uses techniques of lubrication theory to approximate electrokinetic flows in channels with arbitrary variations in cross‐section; and we include chemical equilibrium calculations for weak electrolytes, Taylor–Aris type dispersion due of nonuniform bulk flow, and the effects of ionic strength on species mobility and on acid–base equilibrium constants. To solve the quasi‐1D governing equations, we provide a dissipative finite volume scheme that adds numerical dissipation at selective locations to ensure both unconditional stability and high accuracy. We couple the numerical scheme with a novel adaptive grid refinement algorithm that further improves the accuracy of simulations by minimizing numerical dissipation. We benchmark our numerical scheme with existing numerical schemes by simulating nonlinear electrokinetic problems, including ITP and electromigration dispersion in CZE. Simulation results show that our approach yields fast, stable, and high‐resolution solutions using an order of magnitude less grid points compared to the existing dissipative schemes. To highlight our model's capabilities, we demonstrate simulations that predict increase in detection sensitivity of ITP in converging cross‐sectional area channels. We also show that our simulations of ITP in variable cross‐sectional area channels have very good quantitative agreement with published experimental data.
Searle's Chinese box: the Chinese room argument and artificial intelligence (volumes I and II)

The apparently intelligent doings of computers occasion philosophical debate about artificial intelligence (AI). Evidence of AI (such doings) is not bad; arguments against AI are: such is the case for. One argument against AI--currently, perhaps, the most influential--is considered in detail: John Searle's Chinese room argument (CRA). This argument and its attendant thought experiment (CRE) are shown to be unavailing against claims (of AI proper) that computers can and even do think. CRA is formally invalid and informally fallacious. CRE's putative experimental result is not robust (similar "experiments" give conflicting results) and fails to generalize from understanding to other mental attributes as claimed. Further, CRE depends for its credibility, in the first place, on a dubious tender of the epistemic privilege of overriding all "external" behavioral evidence to first person disavowals of mental properties like understanding. Advertised as effective against AI, Searle's argument is an ignoratio elenchi, feigning to refute AI by disputing a similar (but logically independent) claim of "strong AI" or Turing machine functionalism (FUN) metaphysically identifying minds with programs. AI, however, is warranted independently of FUN: even if CRA disproved FUN this would still fail to refute or seriously disconfirm claims of AI. Searle's contention that everyday predications of mental terms of computers are discountable as equivocal (figurative) "as-if" predications--impugning independent seeming-evidence of AI if tenable--is unwarranted. Lacking intuitive basis, such accusations of ambiguity require theoretical support. The would-be theoretical differentiation of intrinsic intentionality (ours) from as-if intentionality (theirs) Searle propounds to buttress allegations of ambiguity against mental attributions to computers, however, depends either on dubious doctrines of objective intrinsicality according to which meanings are physically in the head or on even more dubious (as if dualistic) notions of subjective intrinsicality according to which meanings are phenomenologically "in" consciousness. Neither would such would-be differentiae as these unproblematically rule out seeming instances of AI if granted. The dubiousness of as if dualistic identification of thought with consciousness also undermines the epistemic privileging of the "first person point of view" crucial to Searle's thought experiment.
Impact of new chemotherapeutic and targeted agents on survival in stage IV non-small cell lung cancer.

e18015 Background: Significant advances in the systemic management of metastatic non-small cell lung cancer (NSCLC) have occurred over the past decade, with options now including multiple lines of chemotherapy, EGFR inhibitors, and anti-angiogenic agents. Improvements in overall survival have been demonstrated in randomized controlled trials comparing these newer agents to best supportive care (BSC) or standard therapy. This study examined uptake of these therapies in general practice and their impact on survival. METHODS This retrospective cohort study compared demographic, treatment and survival data among 987 patients diagnosed with stage IV NSCLC at two institutions in 1998, 2003, and 2008. Cohorts were selected based on intervals when doublet chemotherapy, second line chemotherapy, and targeted agents were incorporated into the standard treatment regimen. RESULTS The proportion of patients receiving systemic therapy increased over time (20% in 1998, 42% in 2008). Treated patients diagnosed in 2008 were more likely to receive ≥2 lines of systemic therapy (60% vs. 7% in 1998). Overall survival improved significantly across cohorts (P <0.001), with 2 year survival rates of 0.3% in 1998, 4% in 2003, and 15% in 2008. After controlling for other variables, risk of death was diminished by 55% in patients receiving 1 line of systemic therapy and 72% in those receiving ≥2 lines, compared with BSC alone. Elderly patients (age ≥70 years) were also more likely to receive systemic therapy over time, with improved overall survival (P <0.001). CONCLUSIONS Over the past decade, there has been increased use of systemic therapy in stage IV NSCLC patients, including the elderly. This has been associated with significantly improved overall survival.
Non‐muscle myosins in tumor progression, cancer cell invasion, and metastasis

The actin cytoskeleton, which regulates cell polarity, adhesion, and migration, can influence cancer progression, including initial acquisition of malignant properties by normal cells, invasion of adjacent tissues, and metastasis to distant sites. Actin‐dependent molecular motors, myosins, play key roles in regulating tumor progression and metastasis. In this review, we examine how non‐muscle myosins regulate neoplastic transformation and cancer cell migration and invasion. Members of the myosin superfamily can act as either enhancers or suppressors of tumor progression. This review summarizes the current state of knowledge on how mutations or epigenetic changes in myosin genes and changes in myosin expression may affect tumor progression and patient outcomes and discusses the proposed mechanisms linking myosin inactivation or upregulation to malignant phenotype, cancer cell migration, and metastasis. © 2014 Wiley Periodicals, Inc.
Gravitational energy in a small region for the modified Einstein and Landau–Lifshitz pseudotensors

The purpose of the classical Einstein and Landau–Lifshitz and other pseudotensors is to determine the gravitational energy. Neither of them can guarantee a positive energy in holonomic frames. In the small sphere approximation, it has been required that the quasilocal expression for the gravitational energy–momentum density should be proportional to the Bel–Robinson tensor Bαβμν. However, we propose a new tensor Vαβμν that is the sum of certain tensors Sαβμν and Kαβμν; it has certain properties so that it gives the same gravitational ‘energy–momentum’ density content as Bαβμν does. In comparison, the main difference is that Bαβμν fulfils the dominant energy condition while Vαβμν does not. Moreover, we show that a modified Einstein pseudotensor turns out to be a generalization of one of the Chen–Nester quasilocal expressions, while the modified Landau–Lifshitz pseudotensor becomes the Papapetrou pseudotensor; these two modified pseudotensors have positive gravitational energy in a small region.