Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical monitoring of complex dynamics of blood sedimentation and lymph flow in vessels

In this paper a few examples of the complex behavior of biological systems detected by optical techniques are described. All examples are related to cell suspensions behavior in in vitro and in vivo studies. In vitro studies performing investigation of a fine structure of blood sedimentation process and establishing nonlinear features of blood sedimentation as disease prognostic parameters are overviewed. Three optical techniques: OCT, CW laser beam transverse synchronized transillumination method and spatially-modulated laser beam transillumination method were considered. In blood sedimentation studied by OCT the regular or irregular oscillations of the RBC/plasma boundary were observed. The functional properties of erythrocytes in patients with coronary heart disease by mean of spatially-modulated laser beam transillumination method to reveal the stages of the acute coronary syndrome formation are discussed. The laser speckle and intravital TV-microscopic techniques applied to in vivo studies of lymph flow in microvessels are overviewed. The hypothesis on the alternating-translation (shuttle-stream) character of lymph flow is discussed.
Production of Extracellular Enzymes and Enterotoxins A, B, and C by Staphylococcus aureus

Eighty-seven strains of Staphylococcus aureus were examined for their ability to produce enterotoxins A, B, and C, deoxyribonuclease, lysozyme, proteinase, lipase, and α-, β-, and δ-hemolysins. Enterotoxigenic strains showed a significant tendency to be high lipase producers, but none of the other enzymes formed were correlated with the ability of the staphylococci to produce enterotoxins A, B, or C. The conversion of ent− to ent+ strains by lysogenization did not affect significantly the ability of the strains to produce any of the above extracellular enzymes. The formation of enzymes such as deoxyribonuclease and lysozyme by staphylococci is not therefore an indication, necessarily, of their potential enterotoxigenicity.
TtgV Represses Two Different Promoters by Recognizing Different Sequences

ABSTRACT Expression of the multidrug efflux pump ttgDEF and ttgGHI operons is modulated in vivo mainly by the TtgV repressor. TtgV is a multidrug recognition repressor that exhibits a DNA binding domain with a long interaction helix comprising residues 47 to 64. The pattern of expression of the two pumps is different in Pseudomonas putida: in the absence of effectors, the promoter for the ttgD gene is silent, whereas the ttgG gene is expressed at a high basal level. This correlates with the fact that TtgV exhibits a higher affinity for the ttgD operator (K D = 10 ± 1 nM) than for the ttgG (K D = 19 ± 1 nM) operator. Sequence analysis revealed that both operators are 40% identical, and mutational analysis of the ttgD and ttgG operators combined with electrophoretic mobility shift assays and in vivo expression analysis suggests that TtgV recognizes an inverted repeat with a high degree of palindromicity around the central axis. We generated a collection of alanine substitution mutants with substitutions between residues 47 and 64 of TtgV. The results of extensive combinations of promoter variants with these TtgV alanine substitution mutants revealed that TtgV modulates expression from ttgD and ttgG promoters through the recognition of both common and different sequences in the two promoters. In this regard, we found that TtgV mutants at residues 48, 50, 53, 54, 60, and 61 failed to bind ttgG but recognized the ttgD operator. TtgV residues R47, R52, L57, and T49 are critical for binding to both operators. Based on three-dimensional models, we propose that these residues contact nucleotides within the major groove of DNA.
On flow-sensitive security types

This article investigates formal properties of a family of semantically sound flow-sensitive type systems for tracking information flow in simple While programs. The family is indexed by the choice of flow lattice.By choosing the flow lattice to be the powerset of program variables, we obtain a system which, in a very strong sense, subsumes all other systems in the family (in particular, for each program, it provides a principal typing from which all others may be inferred). This distinguished system is shown to be equivalent to, though more simply described than, Amtoft and Banerjee's Hoare-style independence logic (SAS'04). In general, some lattices are more expressive than others. Despite this, we show that no type system in the family can give better results for a given choice of lattice than the type system for that lattice itself.Finally, for any program typeable in one of these systems, we show how to construct an equivalent program which is typeable in a simple flow-insensitive system. We argue that this general approach could be useful in a proof-carrying-code setting.
Clinical ascertainment of health outcomes among adults treated for childhood cancer.

IMPORTANCE Adult survivors of childhood cancer are known to be at risk for treatment-related adverse health outcomes. A large population of survivors has not been evaluated using a comprehensive systematic clinical assessment to determine the prevalence of chronic health conditions. OBJECTIVE To determine the prevalence of adverse health outcomes and the proportion associated with treatment-related exposures in a large cohort of adult survivors of childhood cancer. DESIGN, SETTING, AND PARTICIPANTS Presence of health outcomes was ascertained using systematic exposure-based medical assessments among 1713 adult (median age, 32 [range, 18-60] years) survivors of childhood cancer (median time from diagnosis, 25 [range, 10-47] years) enrolled in the St Jude Lifetime Cohort Study since October 1, 2007, and undergoing follow-up through October 31, 2012. MAIN OUTCOMES AND MEASURES Age-specific cumulative prevalence of adverse outcomes by organ system. RESULTS Using clinical criteria, the crude prevalence of adverse health outcomes was highest for pulmonary (abnormal pulmonary function, 65.2% [95% CI, 60.4%-69.8%]), auditory (hearing loss, 62.1% [95% CI, 55.8%-68.2%]), endocrine or reproductive (any endocrine condition, such as hypothalamic-pituitary axis disorders and male germ cell dysfunction, 62.0% [95% CI, 59.5%-64.6%]), cardiac (any cardiac condition, such as heart valve disorders, 56.4% [95% CI, 53.5%-59.2%]), and neurocognitive (neurocognitive impairment, 48.0% [95% CI, 44.9%-51.0%]) function, whereas abnormalities involving hepatic (liver dysfunction, 13.0% [95% CI, 10.8%-15.3%]), skeletal (osteoporosis, 9.6% [95% CI, 8.0%-11.5%]), renal (kidney dysfunction, 5.0% [95% CI, 4.0%-6.3%]), and hematopoietic (abnormal blood cell counts, 3.0% [95% CI, 2.1%-3.9%]) function were less common. Among survivors at risk for adverse outcomes following specific cancer treatment modalities, the estimated cumulative prevalence at age 50 years was 21.6% (95% CI, 19.3%-23.9%) for cardiomyopathy, 83.5% (95% CI, 80.2%-86.8%) for heart valve disorder, 81.3% (95% CI, 77.6%-85.0%) for pulmonary dysfunction, 76.8% (95% CI, 73.6%-80.0%) for pituitary dysfunction, 86.5% (95% CI, 82.3%-90.7%) for hearing loss, 31.9% (95% CI, 28.0%-35.8%) for primary ovarian failure, 31.1% (95% CI, 27.3%-34.9%) for Leydig cell failure, and 40.9% (95% CI, 32.0%-49.8%) for breast cancer. At age 45 years, the estimated cumulative prevalence of any chronic health condition was 95.5% (95% CI, 94.8%-98.6%) and 80.5% (95% CI, 73.0%-86.6%) for a serious/disabling or life-threatening chronic condition. CONCLUSIONS AND RELEVANCE Among adult survivors of childhood cancer, the prevalence of adverse health outcomes was high, and a systematic risk-based medical assessment identified a substantial number of previously undiagnosed problems that are more prevalent in an older population. These findings underscore the importance of ongoing health monitoring for adults who survive childhood cancer.
Inappropriateness of Medication Prescriptions to Elderly Patients in the Primary Care Setting: A Systematic Review

Background Inappropriate medication prescription is a common cause of preventable adverse drug events among elderly persons in the primary care setting. Objective The aim of this systematic review is to quantify the extent of inappropriate prescription to elderly persons in the primary care setting. Methods We systematically searched Ovid-Medline and Ovid-EMBASE from 1950 and 1980 respectively to March 2012. Two independent reviewers screened and selected primary studies published in English that measured (in)appropriate medication prescription among elderly persons (>65 years) in the primary care setting. We extracted data sources, instruments for assessing medication prescription appropriateness, and the rate of inappropriate medication prescriptions. We grouped the reported individual medications according to the Anatomical Therapeutic and Chemical (ATC) classification and compared the median rate of inappropriate medication prescription and its range within each therapeutic class. Results We included 19 studies, 14 of which used the Beers criteria as the instrument for assessing appropriateness of prescriptions. The median rate of inappropriate medication prescriptions (IMP) was 20.5% [IQR 18.1 to 25.6%. ]. Medications with largest median rate of inappropriate medication prescriptions were propoxyphene 4.52(0.10–23.30)%, doxazosin 3.96 (0.32 15.70)%, diphenhydramine 3.30(0.02–4.40)% and amitriptiline 3.20 (0.05–20.5)% in a decreasing order of IMP rate. Available studies described unequal sets of medications and different measurement tools to estimate the overall prevalence of inappropriate prescription. Conclusions Approximately one in five prescriptions to elderly persons in primary care is inappropropriate despite the attention that has been directed to quality of prescription. Diphenhydramine and amitriptiline are the most common inappropriately prescribed medications with high risk adverse events while propoxyphene and doxazoxin are the most commonly prescribed medications with low risk adverse events. These medications are good candidates for being targeted for improvement e.g. by computerized clinical decision support.
Retinal Vessel Diameter Measurement Using Unsupervised Linear Discriminant Analysis

An automatic vessel diameter measurement technique based on linear discriminant analysis (LDA) has been proposed. After estimating the vessel wall, the vessel cross-section profile is divided into three regions: two corresponding to the background and one to the vessel. The algorithm was tested on more than 5000 cross-sections of retinal vessels from the REVIEW dataset through comparative study with the state-of-the-art techniques. Cross-correlation analyses were performed to determine the degree to which the proposed technique was close to the ground truth. The results indicate that proposed algorithm consistently performed better than most of other techniques and was highly correlated with the manual measurement as the reference diameter. The proposed method does not require any supervision and is suitable for automatic analysis.
A Context Awareness based prediction for remedy system

In this paper, we present a method to predict the examination result for remedy, called Context Awareness Score Prediction System (CASPS). CASPS builds on an awareness environment and predicts the learning situations. The main task of the method is in the analysis of the test results and in the provision of the learning suggestion and the remedial courses. The main contributions of the CASPS system described herein are twofold: (1) The system can produce the learning curve based on the examination result, which would make it easy for the students and teachers to understand the learning results. (2) The system can provide the course contents to the students to help them review after the examination. Moreover, it provides suggestions for teaching on the not yet familiar and confused contents.
Cost-Effective EEG Signal Acquisition and Recording System

such a device are simplicity, ease of use and applicability. The uniqueness of this device is that it uses only three electrodes while most other systems use the 10-20 system of electrode placement which requires 21 electrodes. But the reduction in electrodes must not invalidate the output of the system, which is the EEG signal. For this reason, it is critical that the electrodes are placed in the scalp location where we can observe distinguishable change in the various wave patterns of the EEG signal. The main circuit is made of simple electronic elements. The circuit consists of an amplifier, filter and an opto-isolator. In this paper, EEG signal acquisition principles are discussed, applied, and some suggestions for improving signal acquisition are presented.
Large-Scale Video Summarization Using Web-Image Priors

Given the enormous growth in user-generated videos, it is becoming increasingly important to be able to navigate them efficiently. As these videos are generally of poor quality, summarization methods designed for well-produced videos do not generalize to them. To address this challenge, we propose to use web-images as a prior to facilitate summarization of user-generated videos. Our main intuition is that people tend to take pictures of objects to capture them in a maximally informative way. Such images could therefore be used as prior information to summarize videos containing a similar set of objects. In this work, we apply our novel insight to develop a summarization algorithm that uses the web-image based prior information in an unsupervised manner. Moreover, to automatically evaluate summarization algorithms on a large scale, we propose a framework that relies on multiple summaries obtained through crowdsourcing. We demonstrate the effectiveness of our evaluation framework by comparing its performance to that of multiple human evaluators. Finally, we present results for our framework tested on hundreds of user-generated videos.
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference

We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for detecting potential recombination, especially between highly divergent sequences and complex HIV-1 recombinants for which simpler methods like neighbor joining (NJ) may be less powerful. SlidingBayes guides Markov Chain Monte Carlo (MCMC) sampling performed by MrBayes in a sliding window across the alignment (Bayesian scanning). The tool can be used for nucleotide and amino acid sequences and combines all the modeling possibilities of MrBayes with the ability to plot the posterior probability support for clustering of various combinations of taxa.
Scent evolution in Chinese roses

The phenolic methyl ether 3,5-dimethoxytoluene (DMT) is a major scent compound of many modern rose varieties, and its fragrance participates in the characteristic “tea scent” that gave their name to Tea and Hybrid Tea roses. Among wild roses, phenolic methyl ether (PME) biosynthesis is restricted to Chinese rose species, but the progenitors of modern roses included both European and Chinese species (e.g., Rosa chinensis cv Old Blush), so this trait was transmitted to their hybrid progeny. The last steps of the biosynthetic pathways leading to DMT involve two methylation reactions catalyzed by the highly similar orcinol O-methyltransferases (OOMT) 1 and 2. OOMT1 and OOMT2 enzymes exhibit different substrate specificities that are consistent with their operating sequentially in DMT biosynthesis. Here, we show that these different substrate specificities are mostly due to a single amino acid polymorphism in the phenolic substrate binding site of OOMTs. An analysis of the OOMT gene family in 18 species representing the diversity of the genus Rosa indicated that only Chinese roses possess both the OOMT2 and the OOMT1 genes. In addition, we provide evidence that the Chinese-rose-specific OOMT1 genes most probably evolved from an OOMT2-like gene that has homologues in the genomes of all extant roses. We propose that the emergence of the OOMT1 gene may have been a critical step in the evolution of scent production in Chinese roses.
Riga: from FrameNet to Semantic Frames with C6.0 Rules

For the purposes of SemEval-2015 Task-18 on the semantic dependency parsing we combined the best-performing closed track approach from the SemEval-2014 competition with state-of-the-art techniques for FrameNet semantic parsing. In the closed track our system ranked third for the semantic graph accuracy and first for exact labeled match of complete semantic graphs. These results can be attributed to the high accuracy of the C6.0 rule-based sense labeler adapted from the FrameNet parser. To handle large SemEval training data the C6.0 algorithm was extended to provide multi-class classification and to use fast greedy search without significant accuracy loss compared to exhaustive search. A method for improved FrameNet parsing using semantic graphs is proposed.
Thermal power plant analysis using artificial neural network

Coal-based thermal power stations are the leaders in electricity generation in India and are highly complex nonlinear systems. The thermal performance data obtained from MAHAGENCO KORADI UNIT 5 thermal power plant shows that heat rate and boiler efficiency is changing constantly and the plant is probably losing some Megawatts of electric power, and more fuel usage thus resulting in much higher carbon footprints. It is very difficult to analyse the raw data recorded weekly during the full power operation of the plant because a thermal power plant is a very complex system with thousands of parameters. Thus there is a need for nonlinear modeling for the power plant performance analysis in order to meet the growing demands of economic and operational requirements. The intention of this paper is to give an overview of using artificial neural network (ANN) techniques in power systems. Here Back Propagation Neural Network (BPNN) and Radial Basis Neural Network (RBNN) are used for comparative purposes to model the thermodynamic process of a coal-fired power plant, based on actual plant data and this works as the internal model for prediction of the Heat Rate and Boiler Efficiency. This ANN model of the thermodynamics of a power plant is used to determine the influence of changes in different variables upon the heat rate and boiler efficiency through the use of sensitivity coefficients, which indicate the directions of change in the variable that will improve heat rate and boiler efficiency, and thus indicates the relative importance of these different variables. This information can be used to provide guidance to the plant operators and engineers as to where they should expend their efforts to improve the heat rate and boiler efficiency. Further variation in these key parameters predicted by sensitivity analysis helps in improvisation of Heat Rate and Boiler Efficiency.
Exploring Entity Relations for Named Entity Disambiguation

Named entity disambiguation is the task of linking an entity mention in a text to the correct real-world referent predefined in a knowledge base, and is a crucial subtask in many areas like information retrieval or topic detection and tracking. Named entity disambiguation is challenging because entity mentions can be ambiguous and an entity can be referenced by different surface forms. We present an approach that exploits Wikipedia relations between entities co-occurring with the ambiguous form to derive a range of novel features for classifying candidate referents. We find that our features improve disambiguation results significantly over a strong popularity baseline, and are especially suitable for recognizing entities not contained in the knowledge base. Our system achieves state-of-the-art results on the TAC-KBP 2009 dataset.
Bilateral Spike-Triggered Average Effects in Arm and Shoulder Muscles from the Monkey Pontomedullary Reticular Formation

Pontomedullary reticular formation (PMRF) neurons (309) were recorded simultaneously with electromyographic activity from arm and shoulder muscles in four monkeys performing arm-reaching tasks. Spike-triggered averages (SpikeTAs) were compiled for 292 neurons (3836 neuron–muscle pairs). Fourteen PMRF neurons located in a region ventral to the abducens nucleus produced 42 significant SpikeTA effects in arm and shoulder muscles. Of these 14 PMRF neurons, nine produced SpikeTA effects bilaterally. Overall, PMRF neurons facilitated ipsilateral flexors and contralateral extensors, while suppressing ipsilateral extensors and contralateral flexors. Spike- and stimulus-triggered averaging effects obtained from the same recording site were similar. These findings indicate that single PMRF neurons can directly influence movements of both upper limbs.
The role of E-cadherin and integrins in mesoderm differentiation and migration at the mammalian primitive streak.

We have examined the role of cell-cell and cell-extracellular matrix (ECM) interactions during mesoderm differentiation and migration at the primitive streak of the mouse embryo with the use of function-perturbing antibodies. Explants of epiblast or mesoderm tissue dissected from the primitive streak of 7.5- to 7.8-day mouse embryos were cultured on a fibronectin substratum in serum-free, chemically defined medium. After 16-24 hours in culture, cells in explants of epiblast exhibited the typical close-packed morphology of epithelia, and the tissue remained as a coherent patch of cells that were shown to express transcripts of the cytokeratin Endo B by in situ analysis. In contrast, cells in explants of primitive streak mesoderm exhibited a greatly flattened, fibroblastic morphology, did not express Endo B transcripts, and migrated away from the center of the explant. As epiblast cells in vivo undergo the epithelial-mesenchymal transition at the primitive streak, they cease expressing the prominent calcium-sensitive cell adhesion molecule E-cadherin (uvomorulin, Cell-CAM 120/80). We asked whether the loss of E-cadherin expression was a passive result of differentiation or if it might play a more causative role in mesoderm differentiation and migration. Culture with function-perturbing antibodies against E-cadherin caused cells within epiblast explants to lose cell-cell contacts, to flatten, and to assume a mesenchymal morphology; they were also induced to migrate. Anti-E-cadherin antibodies had no effect on explants of primitive streak mesoderm. In immunofluorescence studies, anti-E-cadherin-treated epiblast cells ceased to express SSEA-1, a carbohydrate moiety that is lost as mesoderm differentiates from the epiblast in vivo, and they also ceased to express E-cadherin itself. In contrast, these cells began to express the intermediate filament protein vimentin, a cytoskeletal protein characteristic of the primitive streak mesoderm at this stage of development. As epiblast cells differentiate into mesoderm, their predominant adhesive interactions change from cell-cell to cell-substratum. Therefore, we also investigated the adhesive interactions between primitive streak tissues and extracellular matrix (ECM) components. Epiblast explants adhered well to fibronectin, more poorly to laminin and type IV collagen, and not at all to vitronectin. In contrast, mesoderm explants attached well to all these proteins. Furthermore, epiblast, but not mesoderm, displayed an anchorage-dependent viability in culture. After anti-E-cadherin treatment, epiblast cells that had assumed the mesenchymal morphology did attach to vitronectin, another characteristic shared with primitive streak mesoderm. (ABSTRACT TRUNCATED AT 400 WORDS)