Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteriophage Ecology in Escherichia coli and Pseudomonas aeruginosa Mixed-Biofilm Communities

ABSTRACT Phage therapy is being reexamined as a strategy for bacterial control in medical and other environments. As microorganisms often live in mixed populations, we examined the effect of Escherichia coli bacteriophage λW60 and Pseudomonas aeruginosa bacteriophage PB-1 infection on the viability of monoculture and mixed-species biofilm and planktonic cultures. In mixed-species biofilm communities, E. coli and P. aeruginosa maintained stable cell populations in the presence of one or both phages. In contrast, E. coli planktonic populations were severely depleted in coculture in the presence of λW60. Both E. coli and P. aeruginosa developed phage resistance in planktonic culture; however, reduced resistance was observed in biofilm communities. Increased phage titers and reduced resistance in biofilms suggest that phage can replicate on susceptible cells in biofilms. Infectious phage could be released from mixed-culture biofilms upon treatment with Tween 20 but not upon treatment with chloroform. Tween 20 and chloroform treatments had no effect on phage associated with planktonic cells, suggesting that planktonic phage were not cell or matrix associated. Transmission electron microscopy showed bacteriophage particles to be enmeshed in the extracellular polymeric substance component of biofilms and that this substance could be removed by Tween 20 treatment. Overall, this study demonstrates how mixed-culture biofilms can maintain a reservoir of viable phage and bacterial populations in the environment.
An Improved Finite Difference Approach to Fitting the Initial Term Structure

This paper describes an alternative discretization strategy for mean-reverting models which permits the use of implicit finite difference methods along lines developed for explicit methods by Hull and White (1990a). This provides significant benefits in terms of stability, convergence, and flexibility. A technique for fitting the initial term structure is developed which is similar to that proposed by Uhrig and Walter (1996), but much more efficient computationally. The approach is illustrated with applications to three common single factor models and two factor stochastic volatility extensions of these models.
Food habits and food choice motives among university students settled in London : The role of gender and culture

This paper reports findings from a survey carried out in April-May 2009 among English and Portuguese university students in London. The aim of this study was to assess the effect of temporary translocation from Portugal to London and the influence of gender and culture on food habits and food choice motives of university students. In total, 101 university students (55 Portuguese – 26 males and 29 females and 46 English – 15 males and 31 females) from 12 London universities were interviewed and a questionnaire comprising of three major sections: (1) food habits; (2) food choice motives; (3) food preparation and purchasing behaviours was completed. In the case of Portuguese students, the questionnaire asked about their food practices in Portugal and since their arrival in London. In general, women showed healthier food habits than men by consuming more fruit and vegetables. With temporary translocation to a new country, males were more likely to make dietary changes whereas females were more likely to maintain their food habits but showed some modifications in an undesirable direction. English consumed more crisps, chips, cooked vegetables, fresh fruit juice and chocolate and Portuguese consumed more rice, red meat, fish and vegetable soup. These differences between nationalities were higher than between genders. So, gender and cultural differences existed in these university students with regard to food habits and food choice motives. Resumo O presente trabalho sumariza os resultados de um estudo realizado de Abril a Maio de 2009 em estudantes universitários ingleses e Portugueses a viver em Londres. O objectivo deste estudo era avaliar o efeito da translocação temporária de Portugal para Londres e a influência do género e da cultura nos
The Fuzzy Fixed Charge Transportation Problem and Genetic Algorithm

The fixed charge transportation problem is an extension of the traditional transportation problem in which two kinds of costs, say direct cost and fixed charge, are taken into consideration. The direct cost is the cost associated with each source-destination pair, and the fixed charge occurs when the transportation activity takes place in the corresponding source-destination pair. In this paper, the fuzzy fixed charge transportation problem is modeled as chance-constrained programming by using the possibility measure and credibility measure firstly. Then a heuristic genetic algorithm is designed.
Simulation and analysis of optical skin lesion images

Background/purpose: In order to properly analyse the effectiveness of methods for optically differentiating malignant from benign skin lesions, it is necessary to have a set of images for which the ground truth is known. However, aspects of the ground truth of clinical images such as true lesion boundary position are unknown or not known precisely. Therefore, a skin/lesion image simulation with known features including boundary location, skin pattern and lesion colour is needed to enable accurate assessment of feature estimation algorithms for lesion classification.
Charge-assisted hydrogen bonding in salts of 2-amino-1H-benzimidazole with 3-phenylpropynoic acid and oct-2-ynoic acid.

The 100 K structures of two salts, namely 2-amino-1H-benzimidazolium 3-phenylpropynoate, C7H8N3(+)·C9H5O2(-), (I), and 2-amino-1H-benzimidazolium oct-2-ynoate, C7H8N3(+)·C8H11O2(-), (II), both have monoclinic symmetry (space group P21/c) and display N-H.O hydrogen bonding. Both structures show packing with corrugated sheets of hydrogen-bonded molecules lying parallel to the [001] direction. Two hydrogen-bonded ring motifs can be identified and described with graph sets R(2)(2)(8) and R(4)(4)(16), respectively, in both (I) and (II). Computational chemistry calculations performed on both compounds show that the hydrogen-bonded ion pairs are more energetically favourable in the crystal structure than their hydrogen-bonded neutral molecule counterparts.
Efficient Package Pin-Out Planning With System Interconnects Optimization for Package-Board Codesign

In conventional package design, engineers designate the ball grid array (BGA) pin-out manually, this always postpones the time-to-market (TTM) of products due to the turn-around between package and design houses. Recent papers propose a method of automatically generating the pin-out and taking signal integrity (SI), power delivery integrity (PI), and routability (RA) into account simultaneously by pin-block design and floorplanning, thus dramatically speeding up the developing time. However, this approach ignores the considerations of shorter path length and equilength/length matching in routing printed circuit board (PCB) trace and pin-out assignment for high-speed interface IP designs, such as USB and PCI Express. Since these features are the most important performance metrics during chip-package-board codesign, in this paper we propose the ideas to optimize the system interconnects during package pin-out design. These ideas keep the same minimized package size as aforementioned recent work and ensure that SI, PI, and RA can still be considered with significant reduction in design cost. It is achieved by relaxing the restriction of pin-block side and order on the package, usually specified by package designers. The experimental results on industrial chipset design cases show that the average improvement of our pin-block planner is over 40% when comparing the design cost with the previous work, among which we have one case accommodated over a thousand pins. Our ideas also work for any kind of pin-block or pin-group configurations.
Improved infrared thermal imaging of a CMOS MEMS device

We report a technique which can be used to improve the accuracy of infrared (IR) surface temperature measurements made on MEMS (Micro-Electro-Mechanical-Systems) devices. The technique was used to thermally characterize a SOI (Silicon-On-Insulator) CMOS (Complementary Metal Oxide Semiconductor) MEMS thermal flow sensor. Conventional IR temperature measurements made on the sensor were shown to give significant surface temperature errors, due to the optical transparency of the SiO2 membrane layers and low emissivity/high reflectivity of the metal. By making IR measurements on radiative carbon micro-particles placed in isothermal contact with the device, the accuracy of the surface temperature measurement was significantly improved.
The mismatch-noise PSD from a tree-structured DAC in a second-order /spl Delta//spl Sigma/ modulator with a midscale input

Mismatch-shaping DAC have become widely used in high-performance delta-sigma data converters in recent years. Nevertheless, no theoretical results have been published to date that quantify their performance, so designers have been forced to rely on simulation-based analyses. This paper presents the first theoretical performance analysis of a mismatch-shaping DAC. Specifically, the PSD of the mismatch noise introduced by a first-order tree-structured DAC within a second-order ADC delta-sigma modulator with a midscale constant input signal is derived. This particular mismatch-shaping DAC and delta-sigma modulator configuration was chosen for analysis because it has been demonstrated experimentally to achieve state-of-the-art ADC performance. The choice of a constant midscale input was made because simulation and experimental results suggest that it yields the worst-case performance.
Molecular epidemiology of Escherichia coli diarrhea in children in Hong Kong

This pediatric hospital-based study of 388 diarrhea cases and 306 controls analyzed predominant E. coli colonies from primary culture (253 cases and 177 controls) with eight DNA probes for enteropathogenic, enterotoxigenic, enteroaggregative, and diffusely adherent E. coli. Only enteropathogenic E. coli adherence factor was identified significantly more frequently in cases (10) than in controls (0).
Peroxisome Proliferator-activated Receptor Co-activator 1 (PGC-1 ) and Sirtuin 1 (SIRT1) Reside in Mitochondria POSSIBLE DIRECT FUNCTION IN MITOCHONDRIAL BIOGENESIS*□

The transcriptional co-activator PGC-1 and the NAD -dependent deacetylase SIRT1 are considered important inducers of mitochondrial biogenesis because in the nucleus they regulate transcription of nucleus-encodedmitochondrial genes. We demonstrate that PGC-1 and SIRT1 are also present inside mitochondria and are in close proximity tomtDNA. They interact with mitochondrial transcription factor A (TFAM) as assessed by confocal microscopy analysis and by blue nativePAGE. Nucleoid purification allowed us to identify SIRT1 and PGC-1 as proteins associated with native and cross-linked nucleoids, respectively. After mtDNA immunoprecipitation analysis, carried out on mitochondrial extracts, we found that PGC-1 is present on the same D-loop region recognized by TFAM. Finally, by oligonucleotide pulldown assay, we found PGC-1 and SIRT1 associated with the TFAM consensus sequence (human mitochondrial transcription factor-binding site H). The results obtained suggest that in mitochondria PGC-1 and SIRT1 may function as their nuclear counterparts and represent the genuine factors mediating the cross-talk between nuclear and mitochondrial genome. Finally, this work adds new knowledge on the function of SIRT1 and PGC-1 and highlights the direct involvement of such proteins in regulation of mitochondrial biogenesis.
Analytic Calculation of Jitter Induced by Power and Ground Noise Based on IBIS I/V Curve

Supply fluctuation is one of the most significant factors that cause jitter in high-speed I/O links. The traditional SPICE simulation or measuring method for power supply induced jitter is quite time-consuming and draining on resources. The I/O buffer information specification (IBIS) model is a popular standard for electronic behavioral specifications of digital integrated circuit I/O characteristics. Analytic jitter transfer functions for supply fluctuations are derived by solving two-order differential equations based on IBIS current versus voltage characteristics and pin package parameters. Then, the total time interval error induced by power and ground noise is obtained in both frequency domain and time domain. The method is validated by comparing the analytic calculation results with HSPICE simulated results for a DDR4 output buffer.
A Partitional Approach for Genomic-Data Clustering Combined with K-Means Algorithm

Bioinformatics is the science of managing, analyzing, extracting, and interpreting information from biological sequences and molecules. Recent advancements in microarray technology allow simultaneous monitoring of the expression levels of a large number of genes over different experiment conditions. Facing this huge amount of data, the biologist cannot simply use the traditional techniques in biology to analyze the data. In fact, information technologies are needed. Cluster analysis is of considerable interest and importance in the field of bioinformatics, either by clustering the genes or by clustering experiment conditions (samples). The clustering of genes is used to identify groups of genes with similar patterns of expression, aiming at helping to answer questions of how gene expression is affected by various diseases and which genes are responsible for specific diseases. The clustering of samples is used to organize the samples into intrinsic clusters such that samples with high similarity belong to same cluster. The significance of this clustering assists in diagnosis of the disease condition, and it discloses the effect of certain treatment on genes. In order to cluster the huge amount of gathered gene expression data, we propose a new partitional clustering-approach, combined with K-Means algorithm. The approach is compared with both K-Means and this approach before combination. The obtained results in terms of internal and external performance measures on a set of genomic benchmarks show the correctness and competence of the proposed approach.
Thiopurine metabolite levels in patients with atopic dermatitis and/or chronic hand/foot eczema treated with azathioprine

Abstract Background: Azathioprine is frequently used in severe eczema. It is converted in the liver into active metabolites, including 6-thioguanine nucleotide (6-TGN) and methylated 6-methylmercaptopurine (6-MMP). In the past, the therapeutic potential of azathioprine may have not been fully utilized. Recent investigations on inflammatory bowel disease have led to a better understanding of azathioprine metabolism and optimizing treatment. Objective: To investigate whether measuring thiopurine metabolites in circulation can improve the effectiveness and safety of azathioprine treatment in patients with atopic dermatitis and/or chronic hand/foot eczema. Methods: Azathioprine metabolite levels were measured in eczema patients during maintenance treatment (Part I) and dose escalation (Part II). Clinical effectiveness, hepatotoxicity, and bone marrow suppression were analyzed and TPMT genotype was assessed. Results: A wide variation in metabolite levels in all dose groups was observed. In Part I (32 patients), there were no significant differences in 6-TGN levels between clinical responders and non-responders (p = .806). No hepatoxicity or myelotoxicity was observed. In Part II, all 6-TGN and 6-MMP levels increased during dose escalation. Hypermethylation was observed in 2/8 patients. Conclusion: For individual eczema patients treated with azathioprine, routinely measuring 6-TGN and 6-MMP can be helpful in optimizing azathioprine dose, improving clinical effectiveness, and preventing side effects.
Multi-sensor Target Recognition Fusion Based on Fuzzy Theory

In the process of the multi-sensors target recognition fusion, focused on the problem that it is difficult to determine the reliability of each sensor and how the data measured by different sensors are fused, a multi-sensor target recognition fusion method based on fuzzy theory is proposed. The mutual supportability of multiple sensors is obtained from the correlation function. Then by the membership function, the reliability of information provide by each sensor is gained. Finally, the supposed fusion result of multi-sensors target recognition can be produced on the basis of fuzzy integration function. The method is simple computationally and can objectively reflect the reliability of each sensor and interrelationship between these sensors. By applying the method to the target recognition, the simulation experiment shows that it can identify the target accurately and is an effective and feasible multi-sensors target recognition fusion method.
Optimization of binding electrostatics: Charge complementarity in the barnase‐barstar protein complex

Theoretical and experimental studies have shown that the large desolvation penalty required for polar and charged groups frequently precludes their involvement in electrostatic interactions that contribute strongly to net stability in the folding or binding of proteins in aqueous solution near room temperature. We have previously developed a theoretical framework for computing optimized electrostatic interactions and illustrated use of the algorithm with simplified geometries. Given a receptor and model assumptions, the method computes the ligand‐charge distribution that provides the most favorable balance of desolvation and interaction effects on binding. In this paper the method has been extended to treat complexes using actual molecular shapes. The barnase‐barstar protein complex was investigated with barnase treated as a target receptor. The atomic point charges of barstar were varied to optimize the electrostatic binding free energy. Barnase and natural barstar form a tight complex (Kd ∼ 10−14 M) with many charged and polar groups near the interface that make this a particularly relevant system for investigating the role of electrostatic effects on binding. The results show that sets of barstar charges (resulting from optimization with different constraints) can be found that give rise to relatively large predicted improvements in electrostatic binding free energy. Principles for enhancing the effect of electrostatic interactions in molecular binding in aqueous environments are discussed in light of the optima. Our findings suggest that, in general, the enhancements in electrostatic binding free energy resulting from modification of polar and charged groups can be substantial. Moreover, a recently proposed definition of electrostatic complementarity is shown to be a useful tool for examining binding interfaces. Finally, calculational results suggest that wild‐type barstar is closer to being affinity optimized than is barnase for their mutual binding, consistent with the known roles of these proteins.
Mu-Zero Resonance Antenna

We present mu-zero resonance (MZR) antennas that use an artificial mu-negative (MNG) transmission line (TL). The equivalent circuit for verifying the peculiarity of the MNG TL is derived and analyzed. To operate the MZR antenna properly, the antenna is fed by magnetic coupling. The analysis and design of the MZR antenna are performed according to theory and simulation based on a dispersion diagram and field distribution. The surface current distribution shows that the radiation mechanism of the MZR antenna is essentially identical to that of a small-loop antenna. Applying the novel concept of the MZR antenna, a dual-band MZR antenna using two MZR antennas with different MZR frequencies is proposed. The radiation characteristics of the antenna are simulated and measured at two frequencies. The measured characteristics show agreement with the simulated results. It is confirmed that the characteristics of the MZR antenna, including the efficiency, gain, and fractional bandwidth, are suitable for a multiband antenna.
Lateral micro fluidic channels array chip fabrication for automated patch clamp application

Traditionally, patch-clamp recording is accomplished with a micromanipulator-positioned glass pipette under a microscope. A cell membrane patch is sucked into the glass pipette and forms a high electrical resistance seal. The high cost and labor-intensive methods of conventional patch clamp have prevented the full potential of ion channels as a drug target class being fully realized. Automated patch clamp systems have recently been developed, in order to inexpensively collect large amounts of data in a shorter period of time. More common automation patch-clamp systems use microchips with tiny (1-2μm) holes in a plate instead of pipettes to create the gigaseals and record from single cells. In our previously reported works, a lateral aperture of a buried micro channel was demonstrated, which differs from the common planar patch aperture and is easier fluidic integration and packaging, higher-density array comparing with planar patch aperture. In this paper, we present the optimized fabrication process and integrated the optimized fabrication process to a new designed lateral patch-clamp array chip with 12 independent lateral patch-clamping sites for patch clamp application. At last, the new designed lateral patch clamp devices are utilized to conduct whole cell patch clamp measurements in rat insulinoma (INS-1) cells. High gigaseals (>1 GΩ) were formed between the glass capillary apertures and INS-1 cells. Steady state I-V plots elicited characteristic ion channel properties and longevity of the whole cell mode could be maintained for 1 h without any breakage of the gigaseals, which long enough to apply various compounds and ion channel drugs.
A Review on Mechanical Properties of Natural Fiber Reinforced Hybrid Polymer Composites

The natural fiber reinforced composites are being used in various fields of applications that are contributing to the replacement of synthetic fibers composites which consists of Boron, glass fiber, carbon fiber etc. The composite natural fibers are being used due its light weight, higher specific strength and eco friendly natural, non –abrasive which also have economical value. As they are made out of natural plants they can absorb an considerable amount Carbon dioxide which the surrounding produce. Thus the hybrid composites with different fibre lengths and reinforcements may contribute a better role than those of single fiber composites. This paper provides a review on the mechanical properties (tensile, flexural, impact strength) of natural fiber reinforced hybrid composites.
Identification of the spatial impulse response of inductive loop detectors

The inductive loop detector (ILD), since its introduction in the early 1960s has become the most widely used sensor in a traffic management system. Magnetic signature of the vehicle collected from ILD may be used, among others applications, for high resolution vehicle classification or vehicle re-identification. The ILD is the example of sensor with aperture which means that the information about vehicle geometry is, “masked” in magnetic signature due to the averaging properties of ILD. Quantitatively this process is characterized by spatial transfer function (spatial impulse response) of the sensor. Recovery of information from the signal is conditioned by the knowledge of this transfer function. This paper concerns the estimation of spatial impulse response of inductive loop detectors. The correlation method and pseudorandom binary (PRB) signal was applied to find a solution to this problem. The method was verified for detector in scale, during laboratory tests. The achieved results are satisfactory and justifies the continuation of research aimed at application of the proposed method to ILDs embedded in a roadway and cooperating with the traffic parameters measurement systems.