Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental signals controlling expression of virulence determinants in bacteria

The study of microbial pathogenesis offers many unique research opportunities. The interaction between host and pathogen during disease is a dynamic battlefield where the microbe's clever strategies for survival and multiplication meet head on with the formidable defenses of the immune system. It is no wonder that the tactics employed by both participants in this struggle provide such interesting research topics for scientists of diverse disciplines. Major advances, fueled largely by the application of a genetic approach, have been made in the biochemistry, immunology, and cell biology of the host-parasite interaction. Among the many new insights is the recognition that bacterial pathogens have evolved highly sophisticated signal transduction systems controlling the coordinate expression of virulence determinants. In this minireview, I will discuss emerging themes that characterize these virulence regulatory systems and speculate on how these control strategies might contribute to the overall success of the microbe during pathogenesis. I refer the reader to several other full-length reviews and minireviews of areas related to microbial virulence and coordinate regulation (21, 24, 27, 28, 30, 52, 74). Because of
Fitting ordinary differential equations to short time course data

Ordinary differential equations (ODEs) are widely used to model many systems in physics, chemistry, engineering and biology. Often one wants to compare such equations with observed time course data, and use this to estimate parameters. Surprisingly, practical algorithms for doing this are relatively poorly developed, particularly in comparison with the sophistication of numerical methods for solving both initial and boundary value problems for differential equations, and for locating and analysing bifurcations. A lack of good numerical fitting methods is particularly problematic in the context of systems biology where only a handful of time points may be available. In this paper, we present a survey of existing algorithms and describe the main approaches. We also introduce and evaluate a new efficient technique for estimating ODEs linear in parameters particularly suited to situations where noise levels are high and the number of data points is low. It employs a spline-based collocation scheme and alternates linear least squares minimization steps with repeated estimates of the noise-free values of the variables. This is reminiscent of expectation–maximization methods widely used for problems with nuisance parameters or missing data.
A multi-component intervention to promote hearing protector use among construction workers

Abstract Hearing protection devices (HPD) remain a primary method of prevention of noise-induced hearing loss despite their well-known limitations. A three-pronged intervention to increase HPD use was conducted among construction workers and included a baseline hearing loss prevention training, follow-up ‘toolbox’ (TB) reinforcement trainings, and use of a personal noise level indicator (NLI). A total of 176 subjects on eight sites completed three assessments. Prior to intervention, HPDs were used an average of 34.5% of the time and increased significantly, up about 12.1% after intervention and 7.5% two months after interventions were completed. The increase in HPD use was greatest among the group receiving both TB and NLI interventions; up about 25% from baseline, and this group was about two times more likely to use HPDs than the BL (baseline) training only group. This study demonstrates the mild impact of a well-constructed HPD use training and provides support for the additional use of a personal NLI to increase use of HPDs among construction workers. The most effective procedures for using such instruments require further exploration. Sumario Los instrumentos para la protección de la audición (HPD) siguen siendo el método primordial para la prevención de las pérdidas auditivas inducidas por ruido, a pesar de sus bien conocidas limitaciones. Se ha propiciado una intervención de tres facetas para incrementar el uso de los HPD por parte de los trabajadores de la construcción que incluyen un entrenamiento básico para la prevención de problemas auditivos, un conjunto de herramientas (TB) de seguimiento para reforzar los entrenamientos y el uso de un indicador personal de niveles de ruido (NLI). Completaron las tres evaluaciones un total de 176 sujetos en ocho sedes. Antes de la intervención, se usaron los HPD con un promedio de 34.5% del tiempo y aumentaron significativamente hasta alrededor del 12.1% después de la intervención y 7.5% dos meses después de que se completaron las intervenciones. El incremento en el uso de HPD fue mayor entre el grupo que recibió las intervenciones TB y NLI, hasta cerca del 25% a partir de la línea de base y este grupo fue usuario de HPD, cerca de dos veces más que el grupo que solo recibió el entrenamiento BL. Este estudio demuestra el ligero impacto de un entrenamiento bien estructurado del HPD y proporciona apoyo para el uso adicional de un NLI personal para incrementar el uso de HPDs en trabajadores de la construcción. Los procedimientos más efectivos para el uso de estos instrumentos, requiere un análisis adicional.
Dietary patterns and breast cancer risk: a systematic review and meta-analysis.

BACKGROUND Dietary patterns, which represent whole-diet and possible food and nutrient interactions, have been linked to the risk of various cancers. However, the associations of these dietary patterns with breast cancer remain unclear. OBJECTIVE We critically appraised the literature and conducted meta-analyses to pool the results of studies to clarify the relation between dietary patterns and breast cancer risk. DESIGN MEDLINE and EMBASE were searched for relevant articles that identified common dietary patterns published up to November 2009. Multivariable-adjusted odds ratios (ORs) comparing highest and lowest categories of dietary pattern scores and multivariable-adjusted ORs for a 20th-percentile increase in dietary pattern scores were combined by using random-effects meta-analyses. RESULTS Case-control and cohort studies were retrieved that identified prudent/healthy (n = 18), Western/unhealthy (n = 17), and drinker (n = 4) dietary patterns. There was evidence of a decrease in the risk of breast cancer in the highest compared with the lowest categories of prudent/healthy dietary patterns (OR = 0.89; 95% CI: 0.82, 0.99; P = 0.02) in all studies and in pooled cohort studies alone. An increase in the risk of breast cancer was shown for the highest compared with the lowest categories of a drinker dietary pattern (OR = 1.21; 95% CI: 1.04, 1.41; P = 0.01). There was no evidence of a difference in the risk of breast cancer between the highest and the lowest categories of Western/unhealthy dietary patterns (OR = 1.09; 95% CI: 0.98, 1.22; P = 0.12). CONCLUSION The results of this systematic review and meta-analysis indicate that some dietary patterns may be associated with breast cancer risk.
Snore sound recognition: On wavelets and classifiers from deep nets to kernels

In this paper, we present a comprehensive comparison of wavelet features for the classification of snore sounds. Wavelet features have proven to be efficient in our previous work; however, the benefits of wavelet transform energy (WTE) and wavelet packet transform energy (WPTE) features were not clearly established. In this study, we firstly present our updated snore sounds database, expanded from 24 patients (collected by one medical centre) to 40 patients (collected by three medical centres). We then study the effects of varying frame sizes and overlaps for extraction of the wavelet low-level descriptors, the effect of which have yet to be fully established. We also compare the performance of the WTE and WPTE features when fed into multiple classifiers, namely, Support Vector Machines (SVM), K-Nearest Neighbours, Linear Discriminant Analysis, Random Forests, Extreme Learning Machines, Kernel Extreme Learning Machines, Multilayer Perceptron, and Deep Neural Networks. Key results presented indicate that, when fed into a SVM, WTE outperforms WPTE (one-tailed z-test, p<0.002). Further, WPTE can achieve a significant improvement when trained by a k-nearest neighbours classifier (one-tailed z-test, p < 0.001).
Affine plane curves with one place at infinity

is also a non-constant function on E (σ) σ . Therefore, ψ has also the pole of order qkδk on E (σ) σ . On the other hand, since degy(ψ) < nk+1 = nkqk, nk = degy(gk), by the division of ψ by gqk−1 k , we get ψ = c1g qk−1 k + ψ1 with degy(c1) < nk, degy(ψ1) < nk(qk−1). Dividing ψi−1 by gqk−i k successively for i = 2, · · · , qk − 1, we get ψi−1 = cig qk−i k + ψi, where degy(c1) < nk, degy(ψi) < nk(qk − i). Thus, setting cqk = ψqk−1, we get
Forensic analysis of BiP Messenger on android smartphones

ABSTRACT Nowadays, social media applications and communication tools are utilized as communication platforms and the vast majority of communication is performed using these tools. The instant messaging applications have been widely used for peer to peer communication worldwide and BiP Messenger (BM) is one of them. BM has been generally used in Turkey. The BM was presented by Turkcell mobile GSM carrier offers many services such as messaging, video chatting, data transfer to smartphone users and approximately 10 million people have been used BM. Hence, it is one of the most encountered applications in forensics examinations. In this study, the BM is analysed using a mobile forensics methodology for the Android phones and this work presents the methodology of what artefacts produced by BM is, how to analyse them and how to show their relations with each other is presented. The proposed analysis methodology shows contact analyses, communication information, message information, deleted messages, group messages, message sending and receiving processes, the chronology of multimedia files and how to reconstruct them. The proposed methodology analysed data structure, communication protocols, permissions, user information, contact information, message information and log analyses of the BM. “wct 2 Comprehensively mobile forensics examinations of BM were presented using these analyses in this paper.
Encoding of Motor Behaviors by Cortical Neuronal Networks

Performance of motor behavior requires complex coordination of neural activity across diverse regions of cortex at multiples scales. At the level of coordination across large areas of cortex, this activity is thought to be related to similarly broad concepts of movement from goal identification to motor planning to generation of motor commands. At smaller scales on the level of local populations of individual neurons in motor and premotor cortex, we observe complex non-stationary firing patterns that appear to be related to the movement itself. Our understanding of the details of this relationship are incomplete, however. Earlier work by the community largely focused on the analysis of individual units in isolation. Technological advances and changes in experimental paradigms have led to the simultaneous recording of hundreds of neurons simultaneously. Approaches to analysis must also adapt and embrace a shift in focus from the behavior of individual neurons to the interactions of the population as a whole. This work presents a number of techniques developed to address challenges and opportunities associated with the simultaneous recordings of large populations of neuii
Correlation-based direct tuning of MIMO controllers by least-squares and its application to tension-and-speed control apparatus

This paper proposes the correlation-based model-free controller design method for the tuning of linear time invariant multivariable controllers. In the proposed method, the controller parameters are tuned directly by using the input/output data obtained as often as the input dimension of the controlled plant. In addition, if the controllers are parameterized linearly with respect to the controller parameters, the optimal control parameters can be estimated by least-squares. The effectiveness of the proposed method is experimentally confirmed with the tension-and-speed control apparatus.
The personality of familiar and significant people: the lay perceiver as a social-cognitive theorist.

When are perceivers guided more by implicit social-cognitive theories of personality and when more by trait theories? As perceivers become more familiar with a person they infer relatively more psychological mediating variables (e.g., construals, goals) that underlie the person's behavior and relatively fewer broad, uncontextualized traits such as aggressive or friendly (Study 1). The effects of familiarity are moderated by the importance of the target to perceivers (Study 2). Specifically, perceivers make relatively more inferences using mediating variables and fewer inferences with traits as the target becomes more familiar, if and only if the target plays an important role in their lives. The findings indicate that psychological mediating variables play a significant role in lay perceptions of people and specify conditions in which perceiver's function like implicit social-cognitive theorists, namely, when the perceived is familiar and important to the perceiver.
The ybiT Gene of Erwinia chrysanthemi Codes for a Putative ABC Transporter and Is Involved in Competitiveness against Endophytic Bacteria during Infection

ABSTRACT We investigated the role in bacterial infection of a putative ABC transporter, designated ybiT, of Erwinia chrysanthemi AC4150. The deduced sequence of this gene showed amino acid sequence similarity with other putative ABC transporters of gram-negative bacteria, such as Escherichia coli and Pseudomonas aeruginosa, as well as structural similarity with proteins of Streptomyces spp. involved in resistance to macrolide antibiotics. The gene contiguous to ybiT, designated as pab (putative antibiotic biosynthesis) showed sequence similarity with Pseudomonas and Streptomyces genes involved in the biosynthesis of antibiotics. A ybiT mutant (BT117) was constructed by marker exchange. It retained full virulence in potato tubers and chicory leaves, but it showed reduced ability to compete in planta against the wild-type strain or against selected saprophytic bacteria. These results indicate that the ybiT gene plays a role in the in planta fitness of the bacteria.
Identification of aqueous pollen extracts using surface enhanced Raman scattering (SERS) and pattern recognition methods

Aqueous pollen extracts of varying taxonomic relations were analyzed with surface enhanced Raman scattering (SERS) by using gold nanoparticles in aqueous suspensions as SERS substrate. This enables a selective vibrational characterization of the pollen water soluble fraction (mostly cellular components) devoid of the spectral contributions from the insoluble sporopollenin outer layer. The spectra of the pollen extracts are species‐specific, and the chemical fingerprints can be exploited to achieve a classification that can distinguish between different species of the same genus. In the simple experimental procedure, several thousands of spectra per species are generated. Using an artificial neural network (ANN), it is demonstrated that analysis of the intrinsic biochemical information of the pollen cells in the SERS data enables the identification of pollen from different plant species at high accuracy. The ANN extracts the taxonomically‐relevant information from the data in spite of high intra‐species spectral variation caused by signal fluctuations and preparation specifics. The results show that SERS can be used for the reliable characterization and identification of pollen samples. They have implications for improved investigation of pollen physiology and for allergy warning.
An AC Pioneer: United Electric Light & Power Company [History]

It often appears that everything that could be written has been written with regard to the 1890s competition between alternating current (ac) and direct current (dc) electric power systems. Much is inaccurate and, unfortunately, is repeated ad infinitum. One factor that all writers, both popular and scholarly, overlook is that the issue was not resolved in a single event nor was it immediate. The ac systems that ultimately prevailed required decades of research and development prior to universal application.
Modeling and control of primary parallel isolated boost converter

In this paper state space modeling and closed loop controlled operation have been presented for primary parallel isolated boost converter (PPIBC) topology as a battery charging unit. Parasitic resistances have been included to have an accurate dynamic model. The accuracy of the model has been tested by comparing the calculated and measured loop gains. The designed controller has been implemented in a DSP based control circuit and stable operation of the converter has been achieved.
Determination of dazomet in basamid granulat using reversed phase HPLC

The reverse phase HPLC determination of dazomet (tetrahydro-3,5-dimethyl-1,3,5-thiadiazine-2-tione) in a pesticide formulation has been studied. HS Pecosphere 3 x 3 C8 (3 pm, 3.3 x 0.46 cm) and LiChrosorb C8 (5 μm, 25 x 0.4 cm) analytical columns were tested at a flow rate of 1.0 cm 3 min - 1 , column temperature of 25 °C and UV detection at 280 nm. The best separation of dazomet from its dehydro-dimer forms was achieved with a mobile phase containing acetonitrile-water in the volume ratio 15: 85 on a HS Pecosphere column, and acetonitrile-water in the volume ratio 30: 70 on a LiChrosorb C8 column. The HS Pecosphere column showed a better peak symmetry, separation factor, and multiple correlation coefficient. The retention time and peak area for the HS Pecosphere column were precise within a day and between days as indicated by the ANOVA test, in contrast to the LiChrosorb column, which showed lost of efficiency.
Role of P-glycoprotein in restricting the brain penetration of tanshinone IIA, a major active constituent from the root of Salvia miltiorrhiza Bunge, across the blood–brain barrier

Tanshinone IIA (TSA) is a major constituent of Salvia miltiorrhiza Bunge widely used in the treatment of stroke. This current study aimed to investigate the nature of brain penetration of TSA using several in vitro and in vivo models. The uptake and efflux of TSA in primary rat brain microvascular endothelial cells (RBMVECs) were altered in the presence of a PgP inhibitor or multidrug-resistance-associated protein (Mrp1/2) inhibitor. A polarized transport of TSA was found in RBMVEC monolayers with facilitated efflux from the abluminal to the luminal side. The polarized transport of TSA was attenuated by PgP or Mrp1/2 inhibitors. In an in situ rat brain perfusion model, TSA crossed the blood–brain barrier at a greater rate than that for sucrose, and the brain penetration was increased in the presence of a PgP or Mrp1/2 inhibitor. The brain levels of TSA were only about 31% of that in the plasma and it increased to 74–77% of plasma levels when verapamil or quinidine was coadministered in rats. The entry of TSA to the central nervous system (CNS) significantly increased in rats subjected to middle cerebral artery occlusion or treatment with quinolinic acid. The normalized brain penetration of TSA in mdr1a(−/−) mice was much higher than the wild-type mice. Taken collectively, these findings provide evidence that TSA has limited brain penetration through the blood–brain barrier owing to the contribution of PgP and possibly Mrp1/2.
A CMOS, fully integrated sensor for electronic detection of DNA hybridization

An integrated field-effect device for fully electronic deoxyribonucleic acid (DNA) detection was realized in a standard CMOS process. The device is composed of a floating-gate MOS transistor, a control-capacitor acting as integrated counterelectrode, and an exposed active area for DNA immobilization. The drain-current of the transistor is modulated by the electric charge carried by the DNA molecules. After DNA hybridization, this charge increases and a change in the output current is measured. Experimental results are provided. Full compatibility with a standard CMOS process opens the way to the realization of low-cost large-scale integration of fast electronic DNA detectors.
Assessing individual risk for high‐risk colorectal adenoma at first‐time screening colonoscopy

Assessing risk of colorectal adenoma at first‐time colonoscopy that are of higher likelihood of developing advanced neoplasia during surveillance could help tailor first‐line colorectal cancer screening. We developed prediction models for high‐risk colorectal adenoma (at least one adenoma ≥1 cm, or with advanced histology, or ≥3 adenomas) among 4,881 asymptomatic white men and 17,970 women who underwent colonoscopy as their first‐time screening for colorectal cancer in two prospective US studies using logistic regressions. C‐statistics and Hosmer–Lemeshow tests were used to evaluate discrimination and calibration. Ten‐fold cross‐validation was used for internal validation. A total of 330 (6.7%) men and 678 (3.8%) women were diagnosed with high‐risk adenoma at first‐time screening colonoscopy. The model for men included age, family history of colorectal cancer, BMI, smoking, sitting watching TV/VCR, regular aspirin/NSAID use, physical activity, and a joint term of multivitamin and alcohol. For women, the model included age, family history of colorectal cancer, BMI, smoking, alcohol, beef/pork/lamb as main dish, regular aspirin/NSAID, calcium, and oral contraceptive use. The C‐statistic of the model for men was 0.67 and 0.60 for women (0.64 and 0.57 in cross‐validation). Both models calibrated well. The predicted risk of high‐risk adenoma for men in the top decile was 15.4% vs. 1.8% for men in the bottom decile (Odds Ratio [OR] = 9.41), and 6.6% vs. 2.1% for women (OR = 3.48). In summary, we developed and internally validated an absolute risk assessment tool for high‐risk colorectal adenoma among the US population that may provide guidance for first‐time colorectal cancer screening.
CMOS phase frequency detector for high speed applications

A simple new phase frequency detector design is presented in this paper. Falling-Edge PFD uses only 12 transistors and preserves the main characteristics of the conventional PFD. It is implemented using Silterra 0. 18μm CMOS Process. It consumes 6. 6μW when operating at 50 MHz clock frequency with 1.8V voltage supply. It has free dead zone and operates up to 2.5 GHz. It can be used in high speed and low power consumption applications. A single ended switch at source charge pump is presented as well. It is compatible with the FE-PFD outputs characteristics.