Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Approach for the Rapid Mutagenesis and Directed Evolution of the Structural Genes of West Nile Virus

ABSTRACT Molecular clone technology has proven to be a powerful tool for investigating the life cycle of flaviviruses, their interactions with the host, and vaccine development. Despite the demonstrated utility of existing molecular clone strategies, the feasibility of employing these existing approaches in large-scale mutagenesis studies is limited by the technical challenges of manipulating relatively large molecular clone plasmids that can be quite unstable when propagated in bacteria. We have developed a novel strategy that provides an extremely rapid approach for the introduction of mutations into the structural genes of West Nile virus (WNV). The backbone of this technology is a truncated form of the genome into which DNA fragments harboring the structural genes are ligated and transfected directly into mammalian cells, bypassing entirely the requirement for cloning in bacteria. The transfection of cells with this system results in the rapid release of WNV that achieves a high titer (∼107 infectious units/ml in 48 h). The suitability of this approach for large-scale mutagenesis efforts was established in two ways. First, we constructed and characterized a library of variants encoding single defined amino acid substitutions at the 92 residues of the “pr” portion of the precursor-to-membrane (prM) protein. Analysis of a subset of these variants identified a mutation that conferred resistance to neutralization by an envelope protein-specific antibody. Second, we employed this approach to accelerate the identification of mutations that allow escape from neutralizing antibodies. Populations of WNV encoding random changes in the E protein were produced in the presence of a potent monoclonal antibody, E16. Viruses resistant to neutralization were identified in a single passage. Together, we have developed a simple and rapid approach to produce infectious WNV that accelerates the process of manipulating the genome to study the structure and function of the structural genes of this important human pathogen.
N ov 2 00 9 Beliaev technique for a weakly interacting Bose gas

Aiming for simplicity of explicit equations and at the same time controllable accuracy of the theory we present results for all thermodynamic quantities and correlation functions for the weakly interacting Bose gas at short-to-intermediate distances obtained within an improved version of Beliaev’s diagrammatic technique. With a small symmetry breaking term Beliaev’s diagrammatic technique becomes regular in the infrared limit. Up to higher-order terms (for which we present order-of-magnitude estimates), the partition function and entropy of the system formally correspond to those of a non-interacting bosonic (pseudo-)Hamiltonian with a temperature dependent Bogoliubov-type dispersion relation. Away from the fluctuation region, this approach provides the most accurate—in fact, the best possible within the Bogoliubov-type pseudoHamiltonian framework—description of the system with controlled accuracy. It produces accurate answers for the off-diagonal correlation functions up to distances where the behaviour of correlators is controlled by generic hydrodynamic relations, and thus can be accurately extrapolated to arbitrarily large scales. In the fluctuation region, the non-perturbative contributions are given by universal (for all weakly interacting U(1) systems) constants and scaling functions, which can be obtained separately—by simulating classical U(1) models—and then used to extend the description of the weakly interacting Bose gas to the fluctuation region. The theory works in all spatial dimensions and we explicitly check its validity against first-principle Monte Carlo simulations for various thermodynamic properties and the single-particle density matrix. PACS numbers: 05.30. Jp, 03.75. Hh, 67.10. -j Beliaev technique for a weakly interacting Bose gas 2
Toward a Medipix2 coded aperture gamma microscope

We report on tests of a radionuclide imaging system for in vivo investigations in small animals with low energy gamma-rays as from /sup 125/I (27-35 keV). The system imaging optics features a high resolution coded aperture mask and a fine pitch silicon hybrid pixel detector of the Medipix2 series (55 /spl mu/m pitch). The coded aperture (no-two-holes-touching MURA 62/spl times/62) had 70 /spl mu/m holes in 75 /spl mu/m tungsten, and was used in a 2:1 magnification for a field of view of about 7 mm. Laboratory tests with a /sup 109/Cd 22-keV source and in vivo mouse thyroid imaging tests with /sup 125/I show a system resolution of about 110 /spl mu/m. This low energy, semiconductor-based, compact gamma camera is the basic imaging unit of a small animal single photon emission computed tomography system with deep sub-millimeter resolution.
AN ENHANCED FRAMEWORK FOR MULTI-MODULE EMBEDDED RECONFIGURABLE SYSTEMS

Reconfigurable logic facilitates dynamic adaptation of hardware and ensures better utilization of hardware space as desired in embedded applications. Partial reconfiguration of hardware is a recent trend where a portion of the reprogrammable logic can be altered without affecting other portions. Host-based multiple-module reconfigurable hardware fabric, such as Field Programmable Gate Arrays (FPGAs), can potentially employ partial reconfiguration for embedded applications where a FPGA-resident or external host controls the application execution and reconfiguration. Although this technique minimizes area requirements and potential energy requirements for applications, it may result in a disparity in usage of different reconfigurable modules. This disparity may cause localized temperature build-up and failure. Moreover, in such a host-based system, a subjective load distribution between the host and the reconfigurable module could result in performance improvement through parallelism. In this paper, policies are presented that ensure uniform utilization of reconfigurable modules, while implementing load-balancing between the host and the reconfigurable module for better performance. Experimental results involving benchmark kernels with these policies show a reduction in disparity of more than 40% of module usage as well as improvements in an application execution time of about 35%, as compared to a reference algorithm. In general, though, these policies are minimal when compared with the execution time for applications.
DeepEye : Visualizing Your Data by Keyword Search [ Visionary Paper ]

Do you dream to create good visualizations for your dataset simply like a Google search? If yes, our visionary systemDeepEye is committed to fulfill this task. Given a dataset and a keyword query, DeepEye understands the query intent, generates and ranks good visualizations. The user can pick the one he likes and do a further faceted search to easily navigate the visualizations. We detail the architecture of DeepEye, key components, as well as research challenges and opportunities.
Posted Prices vs. Negotiations

We consider two alternatives to optimal auctions: posted-price mechanisms and dynamic auctions. In posted-price mechanisms, the seller posts a single price and sells to some bidder that accepts it. In a dynamic auction, bidders arrive sequentially and observe take-it-or-leave-it offers. We establish an exact characterization of the optimal revenue in each of these mechanisms for general distributions, under a mild condition taken from extreme-value theory. We also devise mechanisms that achieve this optimal revenue. Intuitively, auctions should perform better than posted prices for more dispersed values; We show that this stops at a point where more value dispersion causes an opposite phenomenon. keywords: Auctions. Posted prices. Secretary problems. Stopping rules. Dynamic auctions. Extreme Value Theory. ∗Corresponding author. blumrosen@huji.ac. il. Fax: 972-2-5883244. Phone: 972-2-5883065. The authors are grateful to Matthias Degen, Bobby Kleinberg, Ilya Segal and to seminar participants at Berkeley, Brown, Northwestern, Tel Aviv and the Hebrew University for helpful discussions and comments. The paper was accepted for presentation at the ACM conference on Electronic Commerce but was not published in the proceedings of the conference, except for a brief description in a single paragraph. (The authors hold copyrights for the paper.) This research was made in part when both authors have been post-doctoral researchers at Microsoft Research, Silicon Valley. The work of Liad Blumrosen was also supported in part by the Israeli Science Foundation grant number 230/10 and by the Google Inter-university center for Electronic Markets and Auctions.
Spectral-domain optical coherence tomography and adaptive optics may detect hydroxychloroquine retinal toxicity before symptomatic vision loss.

PURPOSE To describe spectral-domain optical coherence tomography (SD-OCT) and adaptive optics (AO) imaging in hydroxychloroquine retinal toxicity. METHODS Two patients with long-term hydroxychloroquine use, subtle perifoveal ophthalmoscopic pigmentary changes, and bilateral perifoveal defects on automated Humphrey visual field (HVF) 10-2 perimetry were imaged using SD-OCT and AO. RESULTS SD-OCT images demonstrated loss of photoreceptor inner segment/outer segment (IS/OS) junction and a downward "sink-hole" displacement of inner retinal structures in areas of hydroxychloroquine toxicity corresponding to HVF 10-2 defects and ophthalmoscopic clinical examination findings. SD-OCT irregularities in the IS/OS junction were also seen in areas not detected on HVF 10-2. AO images showed disruption of the cone photoreceptor mosaic in areas corresponding to HVF 10-2 defects and SD-OCT IS/OS junction abnormalities. Additionally, irregularities in the cone photoreceptor density and mosaic were seen in areas with normal HVF 10-2 and SD-OCT findings. CONCLUSIONS SD-OCT and AO detected abnormalities that correlate topographically with visual field loss from hydroxychloroquine toxicity as demonstrated by HVF 10-2 and may be useful in the detection of subclinical abnormalities that precede symptoms or objective visual field loss.
Relational Antecedents of Employee Engagement : A Test of the Investment Model Predictions

This study used a theoretical model from social psychological research on relationships, the investment model, to explain the engagement process. More specifically, the study examined how employee satisfaction with the relationship, quality of alternatives to the relationship (whether employees’ most important needs can be met elsewhere), investment size in the relationship, and organizational commitment contribute to employee engagement. An online survey was conducted with 314 full-time employees from various industries recruited through the Amazon Mechanical Turk (MTurk). Results of the path analysis showed that employees’ satisfaction and size of investment in the relationship with the organization positively influence employee organizational commitment and level of engagement. Employees’ organizational commitment largely influences employee engagement and partially mediates the effects of employee satisfaction and investment size on employee engagement.
Observing the forbidden zone for light

We experimentally study light propagation in novel two-dimensional and three-dimensional macroporous photonic crystals. These crystals strongly interact with light for nearinfrared frequencies. We present polarization resolved reflectivity from two-dimensional photonic crystals with a centred rectangular lattice. The reflectivity has been collected from the ΓM ′and ΓKdirections for crystals with a range of pore diameters. Stopgaps and a two-dimensional band gap for TE polarized light have been identified by comparing spectra with calculated photonic dispersion relations and Bragg conditions. In the ΓK-direction, a lowest frequency diffraction peak exists that cannot be explained with simple Bragg diffraction. Calculated dispersion relations indicate that multiple Bragg diffraction occurs on the (10) and (01) crystal planes, causing an experimentally observed distinction between a simple Bragg diffraction peak and a sub-Bragg diffraction peak. Polarization resolved reflectivity spectra are presented for three-dimensional silicon inverse woodpile photonic crystals. The reflectivity has been collected from the ΓXand ΓZ-directions for crystals with a range of pore diameters. Diffraction peaks are in reasonable agreement with calculated dispersion relations. Spectra demonstrate for several crystals overlapping diffraction peaks for different polarizations and directions, indicating the presence of a photonic band gap. A two-dimensional photonic crystal was embedded in a lead sulphide quantum dot suspension to study the crystal’s influence on spontaneous emission. Emission maxima have been observed near the high-frequency edge of the two-dimensional band gap for TE polarized light.
Markov-Switching Approach to Analyze the Inflation Hedging Potential of Copper and Gold Futures

This study incorporates the time-varying cointegration approach under the regime-switching framework to investigate inflation hedging potential of gold and copper futures for the sample period from April 2005 to June 2015. Based on the test results of Brock, Dechert and Scheinkman (BDS) and Schwarz Information Criterion (SIC), linear Vector Error-Correction Model (VECM) for gold futures and nonlinear MarkovSwitching Vector Error-Correction Model (MS-VECM) for copper futures are chosen. The results confirm the full inflation hedging potential of gold futures and partial hedging potential of copper futures. In addition, regime dependent analysis of copper futures series signifies the equal adjustment pattern of inflation index in each regime.
Magnetic vortex in color-flavor locked quark matter

Within Ginzburg-Landau theory, we study the structure of a magnetic vortex in color-flavor locked quark matter. This vortex is characterized by winding of the SU(3) phase in color-flavor space, as well as by the presence of a color-flavor unlocked condensate in the core. We estimate the upper and lower critical fields and the critical Ginzburg-Landau parameter that distinguishes between type I and type II superconductors.
NITROUS OXIDE EMISSIONS FROM ANIMAL EXCRETA DEPOSITED ON HILL COUNTRY SLOPES

The objective of this study was to conduct field measurements of nitrous oxide (N2O) emissions caused by deposition of sheep and beef cattle dung and urine on hill country pasture. This work was carried out on a free-draining volcanic soil at the Whatawhata Research Farm in the Waikato region as part of a series of nationwide field trials conducted in 2015. This research provides field data to determine background N2O emissions and the emission factor (EF3, % of the applied excreta N emitted as N2O) for animal excreta deposited in the autumn-winter on steep (>25 o ) and moderate(12-25 o ) slopes. N2O flux measurements were made using a closed chamber technique. N2O fluxes from controls on both medium and steep slopes were less than 0.55 mg N2O-N m 2 hr -1 through the four month (winter/early spring) measurement period. Greater variability in background emissions was exhibited on the steep slopes than on the medium slopes. There was a slight trend for higher total background N2O emissions from medium (average 0.035 kg N2O ha -1 ) compared to steep slope areas (average 0.021 kg N2O ha -1 ), but the difference was not significant (P>0.05). EF3 values for all excreta types were generally very low and highly variable. There was a trend for higher EF3 values on the medium slope than on the steep slope, with beef cattle dung on the medium slope having the highest EF3 value and sheep dung on the steep slope having the lowest EF3 value. There was no apparent relationship between EF3 and soil properties, including soil Olsen P, moisture and mineral nitrogen levels. Introduction In grazed hill country, there is great spatial variation in soil chemical and physical characteristics and in excreta deposition patterns due to animal behaviour, all of which are known drivers of N2O production and emissions. In the Ministry of Agriculture and Forestry (MAF)-funded studies conducted in 2008-09, a framework was developed and later refined to enable up-scaled calculations of N2O emissions in hill country (Hoogendoorn et al., 2008; de Klein et al., 2009). This framework considered the impact of topography in hill country on both the drivers of N2O emissions and on excreta nitrogen (N) deposition patterns. Results from previous studies in hill country indicate that the N2O emission factor, EF3, for sheep and cattle urine deposited on low (0 – 12°) slopes is significantly greater than from medium (12 – 25°) slopes and several studies have reported a significantly higher EF3 from cow urine deposited on relatively flat low-land sites compared to low slope/camp areas of grazed hill country (van der Weerden et al., 2011; Luo et al., 2012; 2013; Kelliher et al., 2014; Saggar et al., 2015). A previous Ministry for Primary Industries (MPI)-funded trial also suggested that EF3 values for animal dung on the medium slope were lower than those on the low slope (Hoogendoorn et al., 2013).
Cyclooxygenase‐2 modulates cellular growth and promotes tumorigenesis

Cyclooxygenase (COX)‐2 and the prostaglandins resulting from its enzymatic activity have been shown to play a role in modulating cell growth and development of human neoplasia. Evidence includes a direct relationship between COX‐2 expression and cancer incidence in humans and animal models, increased tumorigenesis after genetic manipulation of COX‐2, and significant anti‐tumor properties of non‐steroidal anti‐inflammatory drugs in animal models and in some human cancers. Recent data showed that COX‐2 and the derived prostaglandins are involved in control of cellular growth, apoptosis, and signal through a group of nuclear receptors named peroxisome proliferator‐activated receptors (PPARs). In this article we will review some of the findings suggesting that COX‐2 is involved in multiple cellular mechanisms that lead to tumorigenesis.
A Glucuronic Acid-Producing Endophyte Pseudomonas sp. MCS15 Reduces Cadmium Uptake in Rice by Inhibition of Ethylene Biosynthesis

Dynamic regulation of phytohormone levels is pivotal for plant adaptation to harmful conditions. It is increasingly evidenced that endophytic bacteria can regulate plant hormone levels to help their hosts counteract adverse effects imposed by abiotic and biotic stresses, but the mechanisms underlying the endophyte-induced stress resistance of plants remain largely elusive. In this study, a glucuronic acid-producing endophyte Pseudomonas sp. MCS15 alleviated cadmium (Cd) toxicity in rice plants. Inoculation with MCS15 significantly inhibited the expression of ethylene biosynthetic genes including OsACO3, OsACO4, OsACO5, OsACS2, and OsACS5 and thus reduced the content of ethylene in rice roots. In addition, the expression of iron uptake-related genes including OsIRT1, OsIRT2, OsNAS1, OsNAS2 and OsYSL15 was significantly downregulated in the MCS15-inoculated roots under Cd stress. Similarly, glucuronic acid treatment also remarkably inhibited root uptake of Cd and reduced the production of ethylene. However, treatment with 1-aminocyclopropyl carboxylic acid (ACC), a precursor of ethylene, almost abolished the MCS15 or glucuronic acid-induced inhibition of Cd accumulation in rice plants. Conversely, treatment with aminoethoxyvinyl glycine (AVG), an inhibitor of ethylene biosynthesis, markedly reduced the Cd accumulation in plants. Taken together, our results revealed that the endophytic bacteria MCS15-secreted glucuronic acid inhibited the biosynthesis of ethylene and thus weakened iron uptake-related systems in rice roots, which contributed to preventing the Cd accumulation.
Seed germination behavior of two Brachypodium species with a key role in the improvement of marginal areas

Brachypodium genuense (DC.) Roem. & Schult. and B. rupestre (Host) R. et S. are important components of the vegetation of some widespread secondary, semi-natural grassland habitats. Both species play a very important role in the development of vegetation series that characterize these grasslands when they are no longer subjected to grazing or cutting regimes. This led to the gradual disappearance of such habitats and the constitution
Interpolation using asymptote and apex shifted hyperbolic Radon transform

The asymptote and apex shifted hyperbolic Radon transform is an extension to the apex shifted hyperbolic Radon transform that allows shifts in both the asymptote and apex of hyperbolic events. This extension improves the transform ability to focus seismic diffractions in common shot domain. The transform kernel is implemented using Stolt migration/demigration operators in order to improve its computational speed. Our results show that the new transform can be used to efficiently interpolate data that contain seismic diffraction.
Differential Equation Models of Neoadjuvant Chemotherapeutic Treatment Strategies for Stage III Breast Cancer Patients

In this study, we investigate different neoadjuvant chemotherapy treatment strategies for patients with Stage III breast cancer. We use two deterministic models to illustrate the effect of chemotherapy on tumor growth and a patient's health. The models consist of a system of three differential equations representing (1) the tumor growth rate, (2) the change in the patient's health (a variable between 0 and 1), and (3) the rate at which the drug combination, cyclophosphamide and adriamycin, dissipates after administration. The intrinsic growth rate of the tumor is exp<;>nential in model A, and logistic in model B. In our numerical solutions, success is determined by whether the tumor can be reduced to an operable size (1 x 109 cells) before the patient's health falls to a fatal level (0.1). By varying the frequency and dosage of chemotherapy, we evaluate the effectiveness of various treatment schedules for patients beginning treatment with different sized tumors. We observe that patients diagnosed with smaller tumors show faster success if the chemotherapy dosages are kept constant. On the other hand, patients with larger tumors survive longer when the dosage at each chemotherapy session is proportional to the tumor size and the patient's health.
miR-122 Release in Exosomes Precedes Overt Tolvaptan-Induced Necrosis in a Primary Human Hepatocyte Micropatterned Coculture Model

Idiosyncratic drug-induced liver injury (IDILI) is thought to often result from an adaptive immune attack on the liver. However, it has been proposed that the cascade of events culminating in an adaptive immune response begins with drug-induced hepatocyte stress, release of exosomal danger signals, and innate immune activation, all of which may occur in the absence of significant hepatocelluar death. A micropatterned coculture model (HepatoPac) was used to explore the possibility that changes in exosome content precede overt necrosis in response to the IDILI drug tolvaptan. Hepatocytes from 3 human donors were exposed to a range of tolvaptan concentrations bracketing plasma Cmax or DMSO control continuously for 4, 24, or 72 h. Although alanine aminotransferase release was not significantly affected at any concentration, tolvaptan exposures at approximately 30-fold median plasma Cmax resulted in increased release of exosomal microRNA-122 (miR-122) into the medium. Cellular imaging and microarray analysis revealed that the most significant increases in exosomal miR-122 were associated with programmed cell death and small increases in membrane permeability. However, early increases in exosome miR-122 were more associated with mitochondrial-induced apoptosis and oxidative stress. Taken together, these data suggest that tolvaptan treatment induces cellular stress and exosome release of miR-122 in primary human hepatocytes in the absence of overt necrosis, providing direct demonstration of this with a drug capable of causing IDILI. In susceptible individuals, these early events may occur at pharmacologic concentrations of tolvaptan and may promote an adaptive immune attack that ultimately results in clinically significant liver injury.