Miracle-dz/UniFAR-FTUs huggingface dataset:
Circular R-Factor Molecules Controlling Penicillinase Synthesis, Replicating in Escherichia coli Under Either Relaxed or Stringent Control

Two infectious drug-resistance (R) factors, R28K and R6K, each conferring resistance to a number of penicillins by the synthesis of a penicillinase, were transferred to Proteus mirabilis PM1 and Escherichia coli RC85 host strains. Deoxyribonucleic acid (DNA) extracted from these strains was separated by density-gradient centrifugation and subjected to electron microscopy by use of a modification of the protein-monolayer diffusion technique. Analytical density-gradient centrifugation of the purified DNA from PM1 strains showed, in addition to the major peak at a density of 1.698 g/cm3 characteristic of Proteus chromosomal DNA, a single satellite band at a density of 1.710 g/cm3 [guanine plus cytosine (GC) base ratio 50%] for R28K and at 1.704 g/cm3 (GC base ratio 45%) for R6K. Direct CsCl density-gradient centrifugation of crude lysates of the E. coli (R28K)+ strain in the presence of ethidium bromide gave rise to a sedimentation profile with a single satellite peak containing covalently closed circular (CCC) DNA molecules with a mean contour length of 21.4 μm [44 × 106 atomic mass units (AMU)], although a minority was 13.6 μm in length. From the size of the major class, it was estimated that there were two to three copies of the R28K factor present as CCC molecules per chromosome at various phases of cellular growth. Similar studies of the E. coli (R6K)+ lysates showed two satellite peaks; peak I contained mostly CCC molecules of contour length 12.8 μm (26 × 106 AMU), and peak II, intermediate to peak I and the chromosomal peak, contained CCC molecules of a similar size, together with about equal numbers of catenated molecules, mostly dimers consisting of two interlocked monomers of 12.8 μm. A smaller number (ca. 0.1%) of higher catenanes was also seen. The number of CCC copies of the R6K factor per chromosome present in peak I was calculated as 13 at logarithmic phase and 38 at stationary phase. In peak II, a constant ratio of about one catenated dimer per chromosome was found at all phases of growth. Penicillinase assays of cultures at different phases of growth showed a correlation between the estimated number of R-factor copies present as CCC molecules and the enzyme activity per cell for both R28K and R6K.
A Formalization of Linkage Analysis

In this report a formalization of genetic linkage analysis is introduced. Linkage analysis is a computationally hard biomathematical method, which purpose is to locate genes on the human genome. It is rooted in the new area of bioinformatics and no formalization of the method has previously been established. Initially, the biological model is presented. On the basis of this biological model we establish a formalization that enables reasoning about algorithms used in linkage analysis. The formalization applies both for single and multi point linkage analysis. We illustrate the usage of the formalization in correctness proofs of central algorithms and optimisations for linkage analysis. A further use of the formalization is to reason about alternative methods for linkage analysis. We discuss the use of MTBDDs and PDGs in linkage analysis, since they have proven efficient for other computationally hard problems involving large state spaces. We conclude that none of the techniques discussed are directly applicable to linkage analysis, however further research is needed in order to investigated whether a modified version of one or more of these are applicable.
The effect of elemene on lung adenocarcinoma A549 cell radiosensitivity and elucidation of its mechanism

OBJECTIVE: To investigate the effect of elemene on the radiosensitivity of A549 cells and its possible molecular mechanism. METHODS: Apoptosis of A549 cells was detected by flow cytometry and fluorescence microscopy. The effect of double-strand break (DSB) damage repair in A549 cells was evaluated using the neutral comet assay. Protein expression levels were detected using western blotting, and the correlation between protein levels was analyzed. RESULTS: Elemene exhibited a radiosensitizing effect on A549 cells. The level of apoptosis induced by elemene combined with radiation was significantly greater (p<0.01) than that elicited by either radiation or elemene alone. Following radiation and subsequent repair for 24 h, the tail intensity of A549 cells treated with a combination of elemene and radiation was greater than that of cells treated with either elemene or radiation alone (p<0.01). This result indicates that elemene inhibits cellular DSB repair. Both elemene combined with radiation and radiation alone decreased the protein expression of DNA-PKcs and Bcl-2 compared to elemene alone (p<0.01), while p53 protein expression was increased (p<0.01). A negative correlation was observed between DNA-PKcs and p53 expression (r=-0.569, p=0.040), while a positive correlation was found between DNA-PKcs and Bcl-2 expression (r=0.755, p=0.012). CONCLUSIONS: Elemene exhibits a radiosensitizing effect on A549 cells, and its underlying molecular mechanism of action may be related to the downregulation of DNA-PKcs gene expression.
The effects of regular hot black tea consumption on nasal carriage of methicillin-resistant Staphylococcus aureus.

OBJECTIVES This study aims to evaluate the possible relationship between oral consumption of hot black tea and methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage in a mid-sized town population in central Anatolia. PATIENTS AND METHODS Nasal swabs were taken from a total of 109 subjects (53 females, 56 males; mean age 34.4 years; range 18 to 65 years) including 55 non-tea drinkers and 54 subjects consuming more than 10 cups of tea a day. The MRSA positivity in the nasal cultures was investigated. RESULTS In the tea consumer group MRSA was cultured in 10 subjects. Twenty-one subjects' nasal cultures were positive for MRSA in the non-tea drinkers. We found a statistically significant difference in the nasal MRSA carriage among tea drinkers and non-tea drinkers. CONCLUSION Our study findings indicate a lower incidence of nasal MRSA carriage in tea drinkers, suggesting that certain soluble tea compounds may exhibit some antibacterial properties when consumed orally.
A model of gamma‐frequency network oscillations induced in the rat CA3 region by carbachol in vitro

Carbachol (> 20 μm) and kainate (100 nm) induce, in the in vitro CA3 region, synchronized neuronal population oscillations at ≈ 40 Hz having distinctive features: (i) the oscillations persist for hours; (ii) interneurons in kainate fire at 5–20 Hz and their firing is tightly locked to field potential maxima (recorded in s. radiatum); (iii) in contrast, pyramidal cells, in both carbachol and kainate, fire at frequencies as low as 2 Hz, and their firing is less tightly locked to field potentials; (iv) the oscillations require GABAA receptors, AMPA receptors and gap junctions. Using a network of 3072 pyramidal cells and 384 interneurons (each multicompartmental and containing a segment of unmyelinated axon), we employed computer simulations to examine conditions under which network oscillations might occur with the experimentally determined properties. We found that such network oscillations could be generated, robustly, when gap junctions were located between pyramidal cell axons, as suggested to occur based on studies of spontaneous high‐frequency (> 100 Hz) network oscillations in the in vitro hippocampus. In the model, pyramidal cell somatic firing was not essential for the oscillations. Critical components of the model are (i) the plexus of pyramidal cell axons, randomly and sparsely interconnected by gap junctions; (ii) glutamate synapses onto interneurons; (iii) synaptic inhibition between interneurons and onto pyramidal cell axons and somata; (iv) a sufficiently high rate of spontaneous action potentials generated in pyramidal cell axons. This model explains the dependence of network oscillations on GABAA and AMPA receptors, as well as on gap junctions. Besides the existence of axon–axon gap junctions, the model predicts that many of the pyramidal cell action potentials, during sustained gamma oscillations, are initiated in axons.
Impact of Retrieval Precision on Perceived Dif fi culty and Other User Measures

When creating interactive retrieval systems, we want to reduce the perceived difficulty of finding relevant documents. We conducted a user study that controlled retrieval precision. We found that a higher retrieval precision caused a reduction in perceived difficulty compared to a lower retrieval precision. We also found that higher precision increases enjoyment and has some influence on ability to concentrate, but we found no evidence that precision keeps the user engaged vs. bored with the search.
Oil Spill Detection by SAR Images: Dark Formation Detection, Feature Extraction and Classification Algorithms

This paper provides a comprehensive review of the use of Synthetic Aperture Radar images (SAR) for detection of illegal discharges from ships. It summarizes the current state of the art, covering operational and research aspects of the application. Oil spills are seriously affecting the marine ecosystem and cause political and scientific concern since they seriously effect fragile marine and coastal ecosystem. The amount of pollutant discharges and associated effects on the marine environment are important parameters in evaluating sea water quality. Satellite images can improve the possibilities for the detection of oil spills as they cover large areas and offer an economical and easier way of continuous coast areas patrolling. SAR images have been widely used for oil spill detection. The present paper gives an overview of the methodologies used to detect oil spills on the radar images. In particular we concentrate on the use of the manual and automatic approaches to distinguish oil spills from other natural phenomena. We discuss the most common techniques to detect dark formations on the SAR images, the features which are extracted from the detected dark formations and the most used classifiers. Finally we conclude with discussion of suggestions for further research. The references throughout the review can serve as starting point for more intensive studies on the subject.
Prioritising use cases and scenarios

Use cases (J. Rumbaugh et al., 1997) are currently used in requirements elicitation and analysis. They describe in natural language the complete functionality of a proposed system. In most projects, the amount of detail put into eliciting and documenting a use case is usually dependent on the time and resources available. Seldom is there enough time to fully expand all the use cases. Thus, only a small number of the use cases are ever fully expanded. The paper delves into the structure and importance of use cases, the importance of prioritising requirements and use cases, and then describes a framework that can manage the multi-faceted issues that need to be considered when prioritising use cases. The various components of the tool that are used to prioritise use cases are described, and examples of how the various components assist in ranking use cases are presented.
A Distribution Separation Method Using Irrelevance Feedback Data for Information Retrieval

In many research and application areas, such as information retrieval and machine learning, we often encounter dealing with a probability distribution that is mixed by one distribution that is relevant to our task in hand and the other that is irrelevant and that we want to get rid of. Thus, it is an essential problem to separate the irrelevant distribution from the mixture distribution. This article is focused on the application in Information Retrieval, where relevance feedback is a widely used technique to build a refined query model based on a set of feedback documents. However, in practice, the relevance feedback set, even provided by users explicitly or implicitly, is often a mixture of relevant and irrelevant documents. Consequently, the resultant query model (typically a term distribution) is often a mixture rather than a true relevance term distribution, leading to a negative impact on the retrieval performance. To tackle this problem, we recently proposed a Distribution Separation Method (DSM), which aims to approximate the true relevance distribution by separating a seed irrelevance distribution from the mixture one. While it achieved a promising performance in an empirical evaluation with simulated explicit irrelevance feedback data, it has not been deployed in the scenario where one should automatically obtain the irrelevance feedback data. In this article, we propose a substantial extension of the basic DSM from two perspectives: developing a further regularization framework and deploying DSM in the automatic irrelevance feedback scenario. Specifically, in order to avoid the output distribution of DSM drifting away from the true relevance distribution when the quality of seed irrelevant distribution (as the input to DSM) is not guaranteed, we propose a DSM regularization framework to constrain the estimation for the relevance distribution. This regularization framework includes three algorithms, each corresponding to a regularization strategy incorporated in the objective function of DSM. In addition, we exploit DSM in automatic (i.e., pseudo) irrelevance feedback, by automatically detecting the seed irrelevant documents via three different document reranking methods. We have carried out extensive experiments based on various TREC datasets, in order to systematically evaluate the proposed methods. The experimental results demonstrate the effectiveness of our proposed approaches in comparison with various strong baselines.
On the selection of optimal nonlinearities for stochastic gradient adaptive algorithms

This paper derives an expression for the optimal error nonlinearity in adaptive filter design. Using an energy conservation relation, and some typical assumptions, the choice of the error function is optimized by minimizing the mean-square deviation subject to a fixed rate of convergence. The resulting optimal choice is shown to subsume earlier results as special cases.
Using Acoustic Structure in a Hand-Held Audio Playback Device

This paper discusses issues in navigation and presentation of voice documents, and their application to a particular hand-held audio playback device, called NewsComm. It discusses situations amenable to auditory information retrieval, techniques for deriving document structure based on acoustical cues, and techniques for interactive presentation of digital audio. NewsComm provides a portable user interface to digitized radio news and interview programs, and it allows occasional connectivity to a networked audio server with disconnected playback.
Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Ion Channel Activity Promotes Virus Fitness and Pathogenesis

Deletion of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) envelope (E) gene attenuates the virus. E gene encodes a small multifunctional protein that possesses ion channel (IC) activity, an important function in virus-host interaction. To test the contribution of E protein IC activity in virus pathogenesis, two recombinant mouse-adapted SARS-CoVs, each containing one single amino acid mutation that suppressed ion conductivity, were engineered. After serial infections, mutant viruses, in general, incorporated compensatory mutations within E gene that rendered active ion channels. Furthermore, IC activity conferred better fitness in competition assays, suggesting that ion conductivity represents an advantage for the virus. Interestingly, mice infected with viruses displaying E protein IC activity, either with the wild-type E protein sequence or with the revertants that restored ion transport, rapidly lost weight and died. In contrast, mice infected with mutants lacking IC activity, which did not incorporate mutations within E gene during the experiment, recovered from disease and most survived. Knocking down E protein IC activity did not significantly affect virus growth in infected mice but decreased edema accumulation, the major determinant of acute respiratory distress syndrome (ARDS) leading to death. Reduced edema correlated with lung epithelia integrity and proper localization of Na+/K+ ATPase, which participates in edema resolution. Levels of inflammasome-activated IL-1β were reduced in the lung airways of the animals infected with viruses lacking E protein IC activity, indicating that E protein IC function is required for inflammasome activation. Reduction of IL-1β was accompanied by diminished amounts of TNF and IL-6 in the absence of E protein ion conductivity. All these key cytokines promote the progression of lung damage and ARDS pathology. In conclusion, E protein IC activity represents a new determinant for SARS-CoV virulence.
The role of surface functionality on acute cytotoxicity, ROS generation and DNA damage by cationic gold nanoparticles.

Gold nanoparticles (AuNPs) are promising materials for biomedical applications [1,2] due to their tunable surface properties [3] and extraordinary stability. [4] Additionally, the inert core material reduces the potential for toxicity issues arising from particle degradation. [5] The size regime and concomitant geometrical outcomes including high degree of curvature, however, generates the potential for toxicity. [6,7] Generally, the toxicity of AuNPs depends on size, shape, the degree to which they aggregate, and their surface properties[8,9] Recently, several studies on the short-term cytotoxicity of AuNPs[10] and quantum dots[11] have focused on size,[12,13] shape,[14,15] and charge. [16] To date, however, issues such as ligand hydrophobicity have not been systematically explored.
The plastid outer envelope protein OEP16 affects metabolic fluxes during ABA-controlled seed development and germination

Previously, the OEP16.1 channel pore in the outer envelope membrane of mature pea (Pisum sativum) chloroplasts in vitro has been characterized to be selective for amino acids. Isolation of OEP16.2, a second OEP16 isoform from pea, in the current study allowed membrane localization and gene expression of OEP16 to be followed throughout seed development and germination of Arabidopsis thaliana and P. sativum. Thereby it can be shown on the transcript and protein level that the isoforms OEP16.1 and OEP16.2 in both plant species are alternating: whereas OEP16.1 is prominent in early embryo development and first leaves of the growing plantlet, OEP16.2 dominates in late seed development stages, which are associated with dormancy and desiccation, as well as early germination events. Further, OEP16.2 expression in seeds is under control of the phytohormone abscisic acid (ABA), leading to an ABA-hypersensitive phenotype of germinating oep16 knockout mutants. In consequence, the loss of OEP16 causes metabolic imbalance, in particular that of amino acids during seed development and early germination. It is thus concluded that in vivo OEP16 most probably functions in shuttling amino acids across the outer envelope of seed plastids.
Corneal higher order aberrations after myopic wavefront-optimized ablation.

PURPOSE To analyze the induced corneal higher order aberrations (HOAs) after wavefront-optimized ablation. METHODS Sixty-four myopic eyes that underwent wavefront-optimized myopic LASIK were divided into three groups based on spherical equivalent (SE): low myopia group (23 eyes with SE <-3.00 diopters [D]); moderate myopia group (27 eyes with SE between -3.00 and -6.00 D); and high myopia group (14 eyes with SE >-6.00 D). Total corneal HOA, corneal spherical aberrations, corneal coma through a 6-mm pupil size, and corneal eccentricity were measured with a dual Scheimpflug imaging device preoperatively and 3 months after surgery. RESULTS An overall increase in total corneal HOA was observed with a mean of 0.18±0.18 μm (P<.01), although this induction was not statistically significant in the low myopic group with a mean of 0.006±0.15 μm (P=.85). Root-mean-square spherical aberration varied the most after myopic ablation, with an overall induction of positive spherical aberration of 0.27±0.25 μm (P<.001). CONCLUSIONS Although the wavefront-optimized profile was designed to preserve the preoperative HOAs of the total eye, a significant induction of the corneal HOAs after myopic treatment was observed. The magnitude of the induced corneal HOA was related to the amount of intended correction. Corneal wavefront profiles do not reflect the visual performance; however, they provide relevant information, which may help in optimizing new laser treatment algorithms.
Square-root adaptive Wave Filtering for marine vessels

In this paper, the problem of designing numerically stable recursive estimators for adaptive Wave Filtering (WF) of marine vessels is addressed. The WF technique consists of a recursive optimization procedure to identify the dominant wave frequency (the uncertain parameter) by minimizing an appropriate defined performance index and the application of the Kalman filter for dynamic positioning purpose. The computational approach yields to a set of the filter sensitivity equations and a set of matrix Riccati-type sensitivity equations. Recently proposed WF methodology [1] is based on the conventional Kalman filter and its derivatives (with respect to unknown system parameters) that is known to be numerically unstable. To improve the numerical stability we are focusing in the techniques developed in the Kalman filtering community to solve ill conditioned problems. More precisely, here the square-root variant of the adaptive WF scheme is designed to improve accuracy and robustness for a finite-precision computer arithmetics. Then, it is examined on the dynamic positioning model of marine vessels.
Haptic interfaces and devices

Haptic interfaces enable person‐machine communication through touch, and most commonly, in response to user movements. We comment on a distinct property of haptic interfaces, that of providing for simultaneous information exchange between a user and a machine. We also comment on the fact that, like other kinds of displays, they can take advantage of both the strengths and the limitations of human perception. The paper then proceeds with a description of the components and the modus operandi of haptic interfaces, followed by a list of current and prospective applications and a discussion of a cross‐section of current device designs.
Estimation of possibility of multiple scattering medium optical parameters determination by backscattered light

The dependence of intensity distribution of diffusely reflected light during medium irradiation with narrow laser beam on optical parameters of multiple scattering media such as tissue has been investigated. The dependence of backscattered spot size on penetration depth as well as dependence of sensitivity on absorption and scattering coefficients have been analyzed by Monte Carlo simulation. Experiments in model multiple scattering media which determine the dependence between the spot size of backscattered radiation and optical characteristics have been carried out. Scanning with optical fibers have been used for measurements of intensity distribution.