gebhart/patrepeval huggingface dataset:
Multiplex polymerase chain reaction (PCR) assays for the detection of Enterobacteriaceae in clinical samples (2010)

The accurate and rapid identification of bacteria in the enteric tract is necessary for early treatment. In this study, we describeD a novel system which consists of a multiplex polymerase chain reaction (PCR) to simultaneously identify a group of six Enterobacteriaceae members including Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Citrobacter spp., Enterobacter cloacae and Salmonella typhi. Genus and species specific primers were designed for this group of pathogens and conventional multiplex PCR and SYBR green based real time PCR assays were performed to detect these pathogens. All the samples were analysed with a eubacterial real-time PCR assay that enables detection of bacterial DNA and then detection of the organisms was determined using genus and species specific PCR assays. This assay was evaluated using clinical specimens and was found to be quite sensitive and specific. Their PCR results matched with the conventional culture identifications. The conventional and SYBR green real time multiplex PCR assays takes only 3 h to be performed and has the potential to replace the conventional culture technique and thus can speed up the treatment process. This technique has the potential to be a valuable diagnostic tool for simultaneous identification of E. coli, K. pneumoniae, P. mirabilis, Citrobacter spp., E. cloacae and S. typhi.
A New Random Current Control Technique for a Single-Phase Inverter with Bipolar and Unipolar Modulations (2007)

Although a hysteresis current control is a simple and a reliable modulation technique in switching control systems, its spectral contents around switching sideband are not distributed broadly. Random pulse width modulation (RPWM) technique is an effective scheme which distributes the spectral contents of load current and can reduce acoustic noise and mechanical vibrations of an inverter-fed motor drive. This paper presents a random-band hysteresis current control (RBHCC) technique with bipolar and unipolar modulations. Mathematical analysis and simulation results show the RBHCC with the unipolar modulation has no considerable effect on distributing the spectral contents of the load current compared to the bipolar modulation technique. Finally, the effect of the random-band hysteresis current control is analysed to determine the best hysteresis band height variation for the bipolar modulation.
Chip Scale Atomic Clocks: Benefits to Airborne GNSS Navigation Performance (2006)

Currently available atomic clocks are too large, power hungry and costly for use onboard GNSS receivers. Chip Scale Atomic Clocks (CSACs) are a promising new technology that is expected to be commercially available in a few years time. These devices are highly-stable atomic clocks in a small, low power and low cost package that may replace less-stable crystal oscillators in GNSS receivers. Previous studies have shown that integrating an atomic clock with a GNSS receiver gives improved navigation performance. This paper presents a study into the expected level of navigation performance that may be achieved with CSACs. A theoretical CSAC error model is constructed based on published performance. The application considered in this study is "clock coasting" in airborne GPS navigation. The results show that "clock coasting" with CSACs results in an improved Dilution of Precision (DOP) for up to 55 minutes under low satellite visibility or poor geometry, compared to a typical crystal oscillator. Results also show that good navigation performance (PDOP < 6) can be achieved for up to 80 minutes in four-satellite navigation with CSAC.
Multiple mechanisms of tumorigenesis in E mu-myc transgenic mice. (1993)

Transgenic mice bearing a c-myc oncogene under control of the immunoglobulin heavy chain enhancer (E mu-myc mice) reproducibly develop and die from tumors of the B lymphocyte lineage (J.M. Adams, A.W. Harris, C.A. Pinkert, L.M. Corcoran, W.S. Alexander, S. Cory, R.D. Palmiter, and R.L. Brinster, Nature (Lond.), 318: 533-538, 1985; W.Y. Langdon, A. W. Harris, S. Cory, and J.M. Adams, Cell 47: 11-18, 1986; A.W. Harris, C.A. Pinkert, M. Crawford, W.Y. Langdon, R.L. Brinster, and J.M. Adams, J. Exp. Med., 167: 353-371, 1988; reviewed in S. Cory and J.M. Adams, Annu. Rev. Immunol., 6: 25-48, 1988). Analysis of lymphocytes obtained by serial sampling of peripheral blood from individual hemizygous (E mu-myc/0) and homozygous (E mu-myc/E mu-myc) transgenic mice indicates that proliferation in the original host and transplantability into histocompatible recipients are distinct properties that can be acquired independently and in either order. These two types of transgenic mice differ in that homozygous mice have about one-fourth the life span of hemizygous mice and develop polyclonal, non-transplantable tumors in comparison to the oligoclonal, highly transplantable malignancies seen in hemizygous animals. In conclusion, the overall concept of malignancy is best viewed as an aggregate of the separable parameters of cellular proliferation, clonality, tissue invasiveness, metastasis, and (experimental) transplantability. The E mu-myc transgenic mouse represents an attractive model in which to investigate the multistep nature and alternative pathways of tumorigenesis.
Noise injection and propagation in high performance designs (2003)

Signal integrity has become a critical issue in the design of high-performance circuits. Noise on a net arises both through propagation of noise from previous stages through the driver gate of the net and through injection of new noise through coupling capacitance with neighboring nets. Typically, propagated noise and injected noise are added linearly to simplify the analysis and increase its efficiency. In this paper, we show that this linear assumption results in a significant underestimation of the noise, due to the nonlinear behavior of the driver gate, and hence can lead to many undetected noise failures in the design. Since complete nonlinear simulation is too slow for large cell-based designs, we propose a new linear model that accurately captures the nonlinear behavior of the driver gate. We propose three iterative methods for computing the model parameters of this linear model. Results are presented to demonstrate the accuracy of the proposed approach on several industrial designs.
Abstract #2937: A purine scaffold heat shock protein 90 (Hsp90) inhibitor destabilizes BCL6 and has specific anti-tumor activity in BCL6 dependent lymphomas in vitro and in vivo (2009)

Although Hsp90 is a rational therapeutic target in cancer, the clinical use of the available quinone Hsp90 inhibitors has been challenged by their liver toxicity. We developed a non-quinone Hsp90 inhibitor named PU-H71. Relatively little is known about the efficacy of Hsp90 inhibitors in diffuse large B-cell lymphomas (DLBCL). The BCL6 transcriptional repressor is the main oncoprotein in DLBCL. The continued presence of the BCL6 is required for survival of DLBCL. Considering that Hsp90 is overexpressed in DLBCLs, we hypothesized that sustained BCL6 expression in DLBCL could be regulated by Hsp90 chaperone activity. In that case, Hsp90 inhibition would affect the maintenance of the malignant phenotype by BCL6. When screened against 12 DLBCL cell lines, PU-H71 selectively killed DLBCLs that are biologically dependent on the BCL6 activity. Cell uptake and Hsp90 inhibition were similar among the cell lines. Treatment of DLBCL cells with PU-H71 resulted in apoptosis and destabilization and subsequent degradation of BCL6. The destabilization of BCL6 occurred at the mRNA and protein levels. The BCL6 protein half-life decreased 5 times in the treated cells. PU-H71-induced downregulation of BCL6 was partially blocked by treatment with a proteasome inhibitor. By co-IP we showed that BCL6 and Hsp90 interact at the nuclear level. Moreover, ChIP assays revealed the presence of both proteins at the critical BCL6 target genes ATR and TP53. In addition, PU-H71 increased the BCL6 mRNA decay rate by 32%. PU-H71 was also active in 19 out of 21 primary DLBCL cells obtained from patient biopsies. To evaluate the in vivo effect, PU-H71 75mg/kg/day or vehicle were administered to Farage, Ly7 and SUDHL4 xenografts (n=5 per treatment and per cell line). By day 10, a 76%, 95% and 95% inhibition of tumor growth was observed in Farage, Ly7 and SUDHL4 mice respectively (p=0.002, p Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 2937.
A progammable baseband anti-alias filter for a passive-mixer-based, SAW-less, multi-band, multi-mode WEDGE transmitter (2011)

A programmable baseband anti-alias filter (AAF) for a passive-mixer-based, 1.8V, SAW-less, multi-band, multi-mode WEDGE (WCDMA/HSUPA/EGPRS) cellular transmitter (TX) is described. This paper presents an AAF which results in ultra-low, -170dBc/Hz, receive-band noise, and enables the first single-mixer-based, multi-mode, SAW-less TX. By providing the noise and linearity performance only on-demand from system requirements, the presented AAF enables power savings of 14mW, or 34% of the total 41mW TX power. The AAF has been fabricated as part of a single-chip 0.13μm CMOS transceiver.
Quantification of the left ventricular volumes and function with cine MR imaging: comparison of geometric models with three-dimensional data. (1993)

Acquisition and measurement of left ventricular (LV) volumes with a three-dimensional data set of cine magnetic resonance (MR) images from apex to base is a time-consuming process. Results of a study with 10 healthy volunteers and 10 patients with LV hypertrophy were prospectively evaluated. The heart was shown in the anatomic short- and horizontal long-axis planes with cine MR imaging. LV volumes were measured with various geometric models, and ejection fractions were calculated. In both groups, the values of LV stroke volume obtained with a modified Simpson rule and biplane ellipsoid models correlated well to the analysis of the three-dimensional data set of cine MR images. There were no significant differences for the calculated ejection fraction between values obtained with the modified Simpson rule or the biplane ellipsoid model versus the three-dimensional data set. A high inter-observer reproducibility of cine MR measurements with the two former models was found. Therefore, modified Simpson rule and biplane ellipsoid models, with their shorter acquisition and processing times, may increase the clinical utility of cine MR imaging.
A cooperative game based allocation for sharing data center networks (2013)

In current IaaS datacenters, tenants are suffering unfairness since the network bandwidth is shared in a besteffort manner. To achieve predictable network performance for rented virtual machines (VMs), cloud providers should guarantee minimum bandwidth for VMs or allocate the network bandwidth in a fairness fashion at VM-level. At the same time, the network should be efficiently utilized in order to maximize cloud providers' revenue. In this paper, we model the bandwidth sharing problem as a Nash bargaining game, and propose the allocation principles by defining a tunable base bandwidth for each VM. Specifically, we guarantee bandwidth for those VMs with lower network rates than their base bandwidth, while maintaining fairness among other VMs with higher network rates than their base bandwidth. Based on rigorous cooperative game-theoretic approaches, we design a distributed algorithm to achieve efficient and fair bandwidth allocation corresponding to the Nash bargaining solution (NBS). With simulations under typical scenarios, we show that our strategy can meet the two desirable requirements towards predictable performance for tenants as well as high utilization for providers. And by tuning the base bandwidth, our solution can enable cloud providers to flexibly balance the tradeoff between minimum guarantees and fair sharing of datacenter networks.
Easily repairable networks (2014)

We introduce a simple class of distribution networks which withstand damage by being repairable instead of redundant. We prove a lower bound for the expected cost of repair, and show that for networks on the square and triangular lattice, this bound is achievable and results in a network with exactly three levels of structural hierarchy. We extend our results to networks subject to repeated attacks, in which the repairs themselves must be repairable. We find that, in exchange for a modest increase in repair cost, such networks are able to withstand any number of attacks.
Elastic and Viscoelastic Calculations of Stresses in Sedimentary Basins (1989)

Summary This study presents a method for estimating the stress state within reservoirs at depth with a time-history approach for both elastic and viscoelastic rock behavior. The model can incorporate changes in pore pressure, temperature gradients, consolidation and diagenesis through time-varying material properties, and varying tectonic episodes. Example calculations are presented for simple cases and for a complete stress history of rocks in the Piceance basin.
Long-Range-Ordered Anodic Porous Alumina with Less-Than-30 nm Hole Interval (2006)

Long-range-ordered anodic porous alumina having hole intervals from 25 to 30 nm was prepared in H2SO4 electrolyte. Constant-voltage anodization under high temperature condition in addition to high concentration of H2SO4 generated the long-range-ordered anodic porous alumina having ideally ordered hole configuration with 25 and 30 nm hole intervals at 10 and 12 V, respectively.
Induced Ca<sup>2+</sup> uptake and callose synthesis in suspension‐cultured cells of <i>Catharanthus roseus</i> are decreased by the protein phosphatase inhibitor okadaic acid (1991)

Subtoxic concentrations of the saponin digitonin. the polyene antibiotic amphotericin B and the bacterial phytotoxin syringomycin induce increased uptake of 45 Ca 2+ into suspension‐cultured plant cells and a rapid Ca 2+ ‐dependent defense response, callose synthesis. Both reactions were inhibited by preincubation of the cells with okadaic acid, a specific inhibitor of type 1 and type 2A protein phosphatases. These results suggest that Ca 2+ uptake induced by the above agents does not occur due to unspecific perturbation of plasma membrane permeability but involves transport proteins which are controlled by protein phosphorylation/dephosphorylation. Phosphoproteins appear also to be involved in the regulation of callose synthesis, although it remains open whether this control is effected at the level of Ca 2+ transport or at the 1,3‐ß‐glucan synthase involved in deposition of the polymer.
Control hof the hyperglycemic response to hemorrhage in cats (1982)

Rapid hemorrhage to 50 mmHg (1 mmHg = 133.322 Pa) mean arterial blood pressure led to a rise in blood glucose levels that reached a level of 500 mg% by 15 min and was then maintained with minor decreases for the full period of hemorrhage (90 min). From changes in hepatic glycogen levels it is estimated that glucose from 3.1 g of glycogen was released per kilogram of body weight over the 90-min period of hemorrhage. Bilateral adrenalectomy or hepatic denervation did not reduce the hyperglycemic response significantly although adrenalectomy tended to produce a lesser response. Removal of the adrenals and the hepatic nerves (surgically or selective hepatic sympathectomy using 6-hydroxydopamine) eliminated all but a very small hyperglycemic response which was of slow onset. Thus, the hyperglycemic response to hemorrhage is controlled by a redundant control system wherein either the adrenals or the hepatic sympathetic nerves can produce the response but elimination of both systems eliminates the response. The minor hyperglycemia that occurred with both systems eliminated shows that other hormonal changes known to occur during hemorrhage play, at most, a minor role in the direct stimulation of glycogenolysis during hemorrhage.
Voronoi Diagram Based Blending of Quadratic Response Surfaces for Cumulative Global Optimization (2002)

This paper proposes a Voronoi diagram based blending scheme of local response surfaces for cumulative global optimization. In the scheme, after sample points are distributed over the design space and local function expressions are generated as quadratic polynomials for the subspaces around respective sample points, they are blended into the global approximation by using superposable function approximation based on geometric structure that is represented by Voronoi diagram, a technique of computational geometry. Under its superposability, it has an ability of cumulative function approximation, in which sample points are adaptively added based on tentative optimization results and approximation fidelity is cumulatively enhanced. Numerical examples of cumulative global optimization are given to ascertain the effectiveness and validity of the proposed blending scheme.
Determination of hierarchical relationship of Src and Rac at subcellular locations with FRET biosensors (2008)

Genetically encoded biosensors based on FRET have enabled the visualization of signaling events in live cells with high spatiotemporal resolution. However, the limited sensitivity of these biosensors has hindered their broad application in biological studies. We have paired enhanced CFP (ECFP) with YPet, a variant of YFP. This ECFP/YPet FRET pair markedly enhanced the sensitivity of biosensors (several folds enhancement without the need of tailored optimization for each individual biosensor) for a variety of signaling molecules, including tyrosine kinase Src, small GTPase Rac, calcium, and a membrane-bound matrix metalloproteinase MT1-MMP. The application of these improved biosensors revealed that the activations of Src and Rac by PDGF displayed distinct subcellular patterns during directional cell migration on micropatterned surface. The activity of Rac is highly polarized and concentrated at the leading edge, whereas Src activity is relatively uniform. These FRET biosensors also led to the discovery that Src and Rac mutually regulate each other. Our findings indicate that molecules within the same signaling feedback loop can be differentially regulated at different subcellular locations. In summary, ECFP/YPet may serve as a general FRET pair for the development of highly sensitive biosensors to allow the determination of molecular hierarchies at subcellular locations in live cells.
Grafts of adenosine-releasing cells suppress seizures in kindling epilepsy (2001)

Adenosine is an inhibitor of neuronal activity in the brain. The local release of adenosine from grafted cells was evaluated as an ex vivo gene therapy approach to suppress synchronous discharges and epileptic seizures. Fibroblasts were engineered to release adenosine by inactivating the adenosine-metabolizing enzymes adenosine kinase and adenosine deaminase. After encapsulation into semipermeable polymers, the cells were grafted into the brain ventricles of electrically kindled rats, a model of partial epilepsy. Grafted rats provided a nearly complete protection from behavioral seizures and a near-complete suppression of afterdischarges in electroencephalogram recordings, whereas the full tonic-clonic convulsions in control rats remained unaltered. Thus, the local release of adenosine resulting in adenosine concentrations <25 nM at the site of action is sufficient to suppress seizure activity and, therefore, provides a potential therapeutic principle for the treatment of drug-resistant partial epilepsies.
Injectable Cellular Aggregates Prepared from Biodegradable Porous Microspheres for Adipose Tissue Engineering (2008)

Cellular aggregates were prepared using biodegradable porous microspheres for injectable reconstruction of soft tissues in vivo. Biodegradable porous microspheres with sizes of approximately 50 microm were prepared by a porogen leaching-phase separation process in an oil-in-water single-emulsion method using poly(D,L-lactide-co-glycolide). 3T3 L1 mouse preadipocyte cells were transformed into cellular aggregates by suspension cultivation in a spinner flask using the porous microspheres as effective buoyant and cell-adhesive microcarriers. Spherically shaped aggregates were readily formed with sizes of up to 1000 microm with a higher number of viable cells compared to the nonporous microspheres. The resultant cellular aggregates exhibited far better extent of differentiation into adipocytes than the cell aggregates prepared from nonporous microspheres or monolayer cultured cells. The cellular aggregates could also be injected into nude mice using a syringe needle for adipose tissue regeneration in vivo. Immunohistochemical studies showed that the aggregate-derived tissues with porous microspheres displayed histological characteristics similar to adipose tissues 4 weeks after injection.
Synergy of tumor necrosis factor and interleukin 2 in the activation of human cytotoxic lymphocytes: effect of tumor necrosis factor alpha and interleukin 2 in the generation of human lymphokine-activated killer cell cytotoxicity. (1988)

Human lymphocytes can respond to interleukin 2 (IL-2) under serum-free conditions with generation of major histocompatibility locus-unrestricted oncolytic activity. This function has been named lymphokine activated killing (LAK). Although IL-2 is sufficient for the development of LAK, this function can be regulated positively by the addition of tumor necrosis factor alpha or beta (TNF-alpha or -beta). The cytotoxic synergy observed with TNF enables production of optimal LAK function at a 10-fold lower IL-2 concentration. Neither TNF-alpha nor -beta is able to induce LAK function in the absence of IL-2. Using TNF-alpha as a model, we demonstrate that (a) the cytotoxic synergy occurs with both fresh human tumors and cell lines; (b) the degree of IL-2/TNF-alpha synergy, for most peripheral blood lymphocyte donors, is dependent upon the IL-2 concentration used for activation with the most striking synergy observed at lower IL-2 doses; (c) synergy is specific for TNF-alpha and can be abrogated by neutralizing antibody against this cytokine; (d) addition of high-dose neutralizing antibody to IL-2 alone-stimulated peripheral blood lymphocytes can reduce the cytotoxicity capacity of these effectors suggesting an immunoregulatory role for endogenous TNF-alpha; and (e) TNF-alpha addition to IL-2-stimulated peripheral blood lymphocytes does not increase proliferation or cell recovery but does result in enhanced IL-2 receptor expression. Collectively, our results suggest that TNF-alpha (and -beta) have immunopotentiating roles in the amplification of non-major histocompatibility locus-restricted lymphocyte effector function.