Miracle-dz/UniFAR-FTUs huggingface dataset:
Calibration and standardization of the emission light path of confocal microscopes

Recently, there has been a large expansion in the usage of optical microscopes for obtaining quantitative information from biological samples in order to determine fundamental biological information such as molecular kinetics and interaction, and heterogeneity within cell populations. Consequently, we built a highly stable, uniform, isotropically emitting and convenient‐to‐use light source, and designed image analysis procedures for calibrating the emission light path of optical microscopes. We used the source and procedures to analyse the quantitative imaging properties of a widely used model of laser scanning confocal microscope. Results showed that the overall performance was as high as could be expected given the inherent limitations of the optical components and photomultiplier tubes. We observed that the photon detection efficiency did not vary with photomultiplier tube gain and that the highest dynamic range was achieved with relatively low gain and 12‐bit digitization. Practical applications of the light source for checking the transmission of optical components in the emission light path are presented.
Effects of wavelets on quality of features in motor-imagery EEG signal classification

This paper examines the quality of feature set obtained from Wavelet based Energy-entropy with variation of scale and wavelet type. Here motor imagery of left-right hand movement classification problem has been studied. Elliptic bandpass filters are used to discard unwanted signals and also to extract alpha & beta rhythms. We have implemented wavelet-based energy-entropy with three level of decomposition in combination with ten wavelet types (Daubechies). We want to identify the best pair of level of decomposition and wavelet type for EEG based motor imagery classifications. We have verified our study with three classifiers- Naïve Bayes, Multi layered Perceptron and Support Vector Machine. The classifiers performance for best wavelet decomposition level is analyzed using evaluation metrics such as accuracy, F-measure and area under ROC.
Predictive accuracy of the Framingham coronary risk score in British men:prospective cohort study

Abstract Objective To establish the predictive accuracy of the Framingham risk score for coronary heart disease in a representative British population. Design Prospective cohort study. Setting 24 towns in the United Kingdom. Participants 6643 British men aged 40-59 years and free from cardiovascular disease at entry into the British regional heart study. Main outcome measures Comparison of observed 10 year coronary heart disease mortality and event rates with predicted rates for each individual, using the relevant Framingham risk equation. Results Of 6643 men, 2.8% (95% confidence interval 2.4% to 3.2%) died from coronary heart disease compared with 4.1% predicted (relative overestimation 47%, P < 0.0001). A fatal or non-fatal coronary heart disease event occurred in 10.2% (9.5% to 10.9%) of the men compared with 16.0% predicted (relative overestimation 57%, P < 0.0001). These relative degrees of overestimation were similar at all levels of coronary heart disease risk, so that overestimation of absolute risk was greatest for those at highest risk. A simple adjustment provided an improved level of accuracy. In a “high risk score” approach, most cases occur in the low risk group. In this case, 84% of the deaths from coronary heart disease and non-fatal events occurred in the 93% of men classified at low risk (< 30% in 10 years) by the Framingham score. Conclusion Guidelines for the primary prevention of coronary heart disease advocate offering preventive measures to individuals at high risk. Currently recommended risk scoring methods derived from the Framingham study significantly overestimate the absolute coronary risk assigned to individuals in the United Kingdom.
Imbalance of Endogenous Hydrogen Sulfide and Homocysteine in Chronic Obstructive Pulmonary Disease Combined with Cardiovascular Disease

Background: Considerable studies showed associations between chronic obstructive pulmonary disease (COPD) and cardiovascular disease (CVD), we evaluated the role of endogenous hydrogen sulfide (H2S)/homocysteine (Hcy) in patients with COPD combined with CVD. Methods: Fifty one stable patients with COPD were enrolled (25 COPD, 26 COPD + CVD). Lung function, sputum, peripheral blood samples, serum H2S, Hcy, high-sensitivity C-reactive protein (hs-CRP) and tumor necrosis factor-α (TNF-α) levels were measured. Dyspnea, symptoms and quality of life were quantified by modified Medical Research Council dyspnea scale (mMRC), COPD assessment test (CAT) and St. George’s Respiratory Questionnaire (SGRQ). Results: Compared with COPD group, waist circumference and body mass index (BMI) were higher in COPD + CVD group, mMRC, CAT and activity scores were also higher, high density lipoprotein cholesterol (HDL-C) was lower, total cells, neutrophils (%) in sputum and serum hs-CRP level were higher, whereas macrophages (% ) in sputum was lower. H2S and Hcy levels from COPD + CVD group were higher than those from COPD group, but H2S/Hcy ratio was lower. With increasing COPD severity, H2S level was decreased, however, Hcy level was increased. H2S level was positively correlated with FEV1/FVC, FEV1% predicted, lymphocytes (%) and macrophages (%) in sputum, but negatively correlated with smoking pack-years and neutrophils (%) in sputum. Hcy level was positively correlated with BMI and total cells in sputum. The ratio of H2S/Hcy was also positively correlated with FEV1/FVC, but negatively correlated with total cells in sputum. Conclusion: The imbalance of H2S/Hcy may be involved in the pathogenesis of COPD combined with CVD and provide novel targets for therapy.
Disorder and order in unfolded and disordered peptides and proteins: A view derived from tripeptide conformational analysis. I. Tripeptides with long and predominantly hydrophobic side chains

We performed a conformational analysis of the central residues of three tripeptides glycyl‐L‐isoleucyl‐glycine (GIG), glycyl‐L‐tyrosyl‐glycine (GYG) and glycyl‐L‐arginyl‐glycine (GRG) in aqueous solution, based on a global analysis of amide I′ band profiles and NMR J‐coupling constants. The results are compared with recently reported distributions of GVG, GFG and GEG. For GIG and GYG, we found that even though the polyproline II (pPII) fraction is below 0.5, it is still the most populated conformation, whereas GVG and GFG show both a larger β‐strand fraction. For GRG, we observed a clear dominance of pPII over β‐strand, reminiscent of observations for GEG and GKG. This finding indicates that terminal charges on otherwise hydrophobic residue side chains stabilize pPII over β‐strand conformations. For all peptides investigated we found that a variety of compact and turn‐like conformations constitute nearly 20 percent of their conformational distributions. Attempts to analyze our data with a simple two‐state pPII⇔︁β model therefore do not yield any satisfactory reproduction of experimental results. A comparison of the obtained GxG ensembles with conformational distributions of GxG segments in truncated coil libraries (helices and sheets omitted) revealed a much larger fraction of type II βi+2 and type III β like conformations for the latter. Thus, a comparison of conformational distributions of unfolded peptide segments in solution and in coil libraries reveal interesting information on how the interplay between intrinsic propensities of amino acid residues and non‐local interactions in polypeptide chains determine the conformations of loop segments in proteins. Proteins 2013; © 2012 Wiley Periodicals, Inc.
Breastfeeding, the Immune Response, and Long-term Health

Abstract Breastfeeding provides unsurpassed natural nutrition to the newborn and infant. Human breast milk also contains numerous protective factors against infectious disease and may influence immune system development, as noted in previous studies of infant response to vaccination and thymus gland development. If immune system development is significantly improved with the introduction of components of breast milk, then prematurely discontinued breastfeeding may facilitate pathogenesis of many chronic diseases later in life (eg, autoimmune disorders). The authors summarize the reported effects of breastfeeding on the development of the suckling infant's immune system and discuss possible consequences to immunologic health when breastfeeding is discontinued prematurely.
Experimental evaluation of Echinops echinatus as an effective hepatoprotective

Aerial parts of Echinops echinatus (Family: Asteraceae) were subjected to in vivo hepatoprotective study in order to validate its traditional use in hepatobiliary disorders, by native people of Cholistan Desert, Pakistan. Hepatoprotective effects of pre-treatment with aerial parts (ethanolic extract) of E. echinatus (EE), (500 and 750 mg/kg/day, p.o., for 7 days) against CCl4 (0.75 ml/kg., s/c.) intoxicated rabbits were evaluated by serum biochemical parameters and liver histopathological observations. Silymarin (100 mg/kg/day, p.o., for 7 days) was used as a standard hepatoprotective drug. CCl4 intoxicated group had raised levels of SGOT, SGPT and ALP significantly but TB level was not raised as compared to normal control group. EE Extract (500 mg/kg) produced more significant results as compared to extract (750 mg/kg). However, (both doses of 500 and 750 mg/kg) showed hepatoprotection as obvious by significant reinstatement of levels of SGOT, SGPT, ALP and even TB as compared to CCl4 and Silymarin control groups. Histopathological examination of the liver tissue further corroborated these results. Therefore, the outcome of the present study supports the traditional beliefs on hepatoprotective effects of E. echinatus (aerial parts). Key words: Echinops echinatus, hepatoprotection, Carbon tetrachloride, serum biochemical parameters, histopathology of liver.
Motion based 3D Target Tracking with Interacting Multiple Linear Dynamic Models

In this paper, an algorithm is proposed for vision-based object identification and tracking by autonomous vehicles. In order to estimate the speed of the tracking object, this algorithm fuses information captured by on-board sensors such as camera and inertial sensors. To formulate the tracking algorithm it is necessary to use a proper model which describes the dynamics of the tracking object. However due to complex nature of the moving object, it is necessary to have different dynamic models. Here, several simple and basic linear dynamic models are combined to approximate unpredictable, complex dynamics of the moving target. With these basic linear dynamic models, a detailed description of the three dimensional (3D) target tracking scheme using an interacting multiple model (IMM) along with an Extended Kalman Filtering is presented. Thefinal state of the target is estimated as a weighted combination of the outputs from each different dynamic model. Performance of the proposed interacting multiple dynamic model tracking algorithm is demonstrated through experimental results.
Essay on mind

Mind as a Biological Problem. Self-Knowledge and the Self. Biological Threads in the Philosophic Fabric. The Evolution of Mind and Behavior. Heredity, the I.Q. , and Attendant Confusions. A Psychological Theory. Perception and Cognitive Development. The Structure of Thought. Scientific Law in Human Thought. A World of Thought.
On the delicate balance between RE and Testing: Experiences from a large company

Requirements Engineering and Testing are considered inseparable and together enable successful projects. One could make a statement that serious negligence of any of the two will bring catastrophic consequences for the project, delays, failures and unhappy customers. Thus, alignment and cooperation between the two are not only recommended but highly required for contemporary complex software and system development. In this paper, we share some experiences from a large company that significantly downplayed requirements engineering activities while shifting the focus to testing and QA activities. Despite that, the company's products are well received by its customers and the company remains profitable and significantly growing. We share our experiences and discuss how this unbalance may actually be a recipe for success and what contextual factors enable using this approach.
High Prevalence of HIV Infection Associated With Incarceration Among Community-Based Injecting Drug Users in Tehran, Iran

Objectives: To determine the prevalence and correlates of HIV-1 infection among community-based injecting drug users (IDUs) in Tehran, Iran. Methods: In October 2004, 213 IDUs were recruited from a drop-in center and its neighboring parks and streets in Tehran. Participants were interviewed using a structured questionnaire regarding their sociodemographics and HIV risk characteristics, and specimens of oral mucosal transudate were collected and tested for HIV-1 antibodies. Data were analyzed using &khgr;2 and multiple logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI). Results: The prevalence of HIV-1 infection was 23.2% (48 of 207) among male injecting drug users. In the multivariable analysis, a history of shared drug injection inside prison (OR, 2.45; 95% CI, 1.01-5.97) and that of multiple incarcerations (OR, 3.13; 95% CI, 1.08-9.09) were associated with significantly higher prevalence of HIV-1 infection. Conclusions: The prevalence of HIV-1 infection has reached an alarming level among IDUs in Tehran, with incarceration-related exposures revealed to be the main correlates of HIV-1 infection. Urgent and comprehensive harm reduction programs for drug users in prison and those in the community in Tehran are of prime importance to prevent further transmission of HIV infection.
Problems with the use of web search engines to find results in foreign languages

Purpose – This paper's aim is to test the ability of the major search engines Google, Yahoo, MSN and Ask to distinguish between German‐ and English‐language documents.Design/methodology/approach – A total of 50 queries using words common in both German and English were submitted to the search engines. The advanced search option of language restriction was used, once in German and once in English, and the first 20 results per engine in each language were investigated.Findings – While none of the search engines faced problems providing results in the language of the interface that was used, both Google and MSN faced difficulties when the results were restricted to a foreign language.Research limitations/implications – Search engines were only tested in German and English. There is only anecdotal evidence that the problems are the same with other languages.Practical implications – Searchers should not use the language restriction in Google and MSN when searching for foreign‐language documents. Instead, searc.
Distributed computing column 50: distributing trusted third parties, innovation prize, and SIROCCO review

Trusted Third Parties (TTPs) are widely employed in various scenarios for providing fairness guarantees (e.g., in fair exchange or e-commerce protocols, including secure two-party computation), for distributing secrets (e.g., in authentication or secret-sharing protocols, as well as group signatures), and for creating trust (e.g., as certificate authorities). Such wide use of TTPs, as well as the trust requirement that is put on them make them a prime target for distributed systems and cryptography research. There are some well-known and proven solutions to the problem of distributing the trust put on TTPs: byzantine agreement or secure multi-party computation techniques can be employed to distribute the job of any TTP to multiple parties, tolerating up to half or one-third of those parties being malicious. Such techniques are not widely-employed in practice possibly due to their quadratic complexity or inter-operation requirements. This brings up the question of distributing TTPs in a much more efficient way, possibly via using autonomous agents, who do not directly communicate with each other. In this paper, we present various known techniques for distributing the trust put on TTPs. Then, we concentrate on using multiple autonomous parties, who do not communicate with each other at all, to realize a single TTP. We discuss the role of synchrony in such attempts, and conclude with some open questions.
Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition

Fat deposition is highly correlated with the growth, meat quality, reproductive performance and immunity of pigs. Fatty acid synthesis takes place mainly in the adipose tissue of pigs; therefore, in this study, a high-throughput massively parallel sequencing approach was used to generate adipose tissue transcriptomes from two groups of Songliao black pigs that had opposite backfat thickness phenotypes. The total number of paired-end reads produced for each sample was in the range of 39.29–49.36 millions. Approximately 188 genes were differentially expressed in adipose tissue and were enriched for metabolic processes, such as fatty acid biosynthesis, lipid synthesis, metabolism of fatty acids, etinol, caffeine and arachidonic acid and immunity. Additionally, many genetic variations were detected between the two groups through pooled whole-genome resequencing. Integration of transcriptome and whole-genome resequencing data revealed important genomic variations among the differentially expressed genes for fat deposition, for example, the lipogenic genes. Further studies are required to investigate the roles of candidate genes in fat deposition to improve pig breeding programs.
Performance modeling and prediction for linear algebra algorithms

This dissertation incorporates two research projects: performance modeling and prediction for dense linear algebra algorithms, and high-performance computing on clouds. The first project is focused on dense matrix computations, which are often used as computational kernels for numerous scientific applications. To solve a particular mathematical operation, linear algebra libraries provide a variety of algorithms. The algorithm of choice depends, obviously, on its performance. Performance of such algorithms is affected by a set of parameters, which characterize the features of the computing platform, the algorithm implementation, the size of the operands, and the data storage format. Because of this complexity, predicting algorithmic performance is a challenging task, to the point that developers are often forced to rely on extensive trial-and-error technique. We approach this problem from a different perspective. Instead of performing exhaustive tests, we introduce two techniques for modeling performance: one is based on measurements and requires a limited number of sampling tests, while the other needs neither the execution of the algorithms nor parts of them. Both techniques employ a bottom-up approach: we first model the performance of the BLAS kernels. Then, using these results we create models for higher-level algorithms, e.g. the LU factorization, that are built on top of the BLAS kernels. As a result, by using the hierarchical and modular structure of linear algebra libraries, we develop two techniques for hierarchical performance modeling; both techniques yielding accurate predictions. The second project is concerned with high-performance computing on commercial cloud environments. We empirically study the computational efficiency of computeintensive scientific applications in such an environment, where resources are shared under high contention. Although high performance is occasionally obtained, contention for the CPU and cache space degrades the expected performance and introduces significant variance. Using the matrix-matrix multiplication kernel of BLAS and the LINPACK benchmark, we show that the underutilization of resources substantially improves the expected performance. For instance, for a number of cluster configurations, the solution is reached considerably faster when the available resources are underutilized. Finally, since the performance measurements of scientific applications show high fluctuation, we propose alternatives, such as expected performance, expected execution time, and cost per GFlop, to the standard definitions of efficiency.
Counting without sampling: Asymptotics of the log‐partition function for certain statistical physics models

In this article we propose new methods for computing the asymptotic value for the logarithm of the partition function (free energy) for certain statistical physics models on certain type of finite graphs, as the size of the underlying graph goes to infinity. The two models considered are the hard‐core (independent set) model when the activity parameter λ is small, and also the Potts (q‐coloring) model. We only consider the graphs with large girth. In particular, we prove that asymptotically the logarithm of the number of independent sets of any r‐regular graph with large girth when rescaled is approximately constant if r ≤ 5. For example, we show that every 4‐regular n‐node graph with large girth has approximately (1.494…)n‐many independent sets, for large n. Further, we prove that for every r‐regular graph with r ≥ 2, with n nodes and large girth, the number of proper q ≥ r + 1 colorings is approximately ${[q{(1 - {1 \over q})}^{r \over 2} ]^n}$ n, for large n. We also show that these results hold for random regular graphs with high probability (w.h.p.) as well.
Activation of SAPK/JNK by camptothecin sensitizes androgen-independent prostate cancer cells to Fas-induced apoptosis

We have previously shown that the androgen-independent prostate cancer cells DU145, despite expressing Fas and FasL, were resistant to anti-Fas-induced apoptosis, and that this resistance could be overcome by pretreating the cells with sublethal doses of camptothecin. Here, we provide evidence that SAPK/JNK activity is required for camptothecin sensitization to anti-Fas-induced apoptosis. Camptothecin, but not Fas ligation, was shown to activate SAPK/JNK in a time-dependent manner, and to induce c-Jun expression. The effects were more prominent in cells treated with both camptothecin and anti-Fas. The expression levels of MKP-1, a phosphatase which regulates SAPK/JNK and which has been implicated in prostate cancer resistance to apoptosis, remained unchanged. Inhibition of caspases had no effect on the SAPK/JNK activation, suggesting that this activation is an upstream event in the Fas-signalling pathway, and is independent of caspase activity. Antisense oligonucleotides targeted to JNK1 and JNK2 reversed the effect of camptothecin. These results suggest that stress kinase activation can significantly influence the fate of androgen-independent prostate cancer cells following Fas receptor ligation. © 2000 Cancer Research Campaign