gebhart/patrepeval huggingface dataset:
Extracellular Proteases of Staphylococcus spp. (2002)

Bacterial proteases secreted into an infected host may exhibit a wide range of pathogenic potentials. Staphylococci, in particular Staphylococcus aureus, are known to produce several extracellular proteases, including serine-, cysteine- and metalloenzymes. Their insensitivity to most human plasma protease inhibitors and, even more, the ability to inactivate some of these make the proteases potentially harmful. Indeed, several recent studies have shown that staphylococcal proteases are able to interact with the host defense mechanisms and tissue components as well as to modify other pathogen-derived virulence factors. A tight, cell density-dependent control of proteolytic activity expression, similar to that of the well-defined virulence determinants, further suggests the role of staphylococcal proteases in the infection process. Consistently, alterations in coordinated expression of extracellular proteins markedly diminished the virulence. However, despite these data and the fact that a strain deficient in sspABC operon coding for serine (sspA) and cysteine (sspB) proteases was highly attenuated in virulence in the animal infection model, it was impossible to unambiguously demonstrate the importance of any particular protease as a virulence factor. Therefore, it can be assumed that the orchestrated expression and interaction of a variety of extracellular and cell surface proteins rather than any particular one is responsible for the staphylococcal pathogenicity and that the proteases apparently play an important role in this complex process. Such redundant mechanism is very well suited for promoting the survival of staphylococci under diverse environmental conditions encountered in the infected host.
An investigation into the real-time manipulation and control of three-dimensional sound fields (2004)

This thesis describes a system that can be used for the decoding of a three dimensional audio recording over headphones or two, or more, speakers. A literature review of psychoacoustics and a review (both historical and current) of surround sound systems is carried out. The need for a system which is platform independent is discussed, and the proposal for a system based on an amalgamation of Ambisonics, binaural and transaural reproduction schemes is given. In order for this system to function optimally, each of the three systems rely on providing the listener with the relevant psychoacoustic cues. The conversion from a five speaker ITU array to binaural decode is well documented but pair-wise panning algorithms will not produce the correct lateralisation parameters at the ears of a centrally seated listener. Although Ambisonics has been well researched, no one has, as yet, produced a psychoacoustically optimised decoder for the standard irregular five speaker array as specified by the ITU as the original theory, as proposed by Gerzon and Barton (1992) was produced (known as a Vienna decoder), and example solutions given, before the standard had been decided on. In this work, the original work by Gerzon and Barton (1992) is analysed, and shown to be suboptimal, showing a high/low frequency decoder mismatch due to the method of solving the set of non-linear simultaneous equations. A method, based on the Tabu search algorithm, is applied to the Vienna decoder problem and is shown to provide superior results to those shown by Gerzon and Barton (1992) and is capable of producing multiple solutions to the Vienna decoder problem. During the write up of this report Craven (2003) has shown how 4th order circular harmonics (as used in Ambisonics) can be used to create a frequency independent panning law for the five speaker ITU array, and this report also shows how the Tabu search algorithm can be used to optimise these decoders further. A new method is then demonstrated using the Tabu search algorithm coupled with lateralisation parameters extracted from a binaural simulation of the Ambisonic system to be optimised (as these are the parameters that the Vienna system is approximating). This method can then be altered to take into account head rotations directly which have been shown as an important psychoacoustic parameter in the localisation of a sound source (Spikofski et al., 2001) and is also shown to be useful in differentiating between decoders optimised using the Tabu search form of the Vienna optimisations as no objective measure had been suggested. Optimisations for both Binaural and Transaural reproductions are then discussed so as to maximise the performance of generic HRTF data (i.e. not individualised) using inverse filtering methods, and a technique is shown that minimises the amount of frequency dependant regularisation needed when calculating cross-talk cancellation filters.
Volume regulatory influx of electrolytes from plasma to brain during acute hyperosmolality (1987)

Brain volume is regulated during acute hyperosmolal states based, in part, on the tissue gain of Na, Cl, and K [H. F. Cserr, M. DePasquale, and C.S. Patlak, Am. J. Physiol. 253 (Renal Fluid Electrolyte Physiol. 22): F522-F529, 1987]. This study evaluates the contribution of influx from plasma to the volume regulatory gain of electrolyte. Blood-to-brain transfer constants, K1, were measured as a function of plasma osmolality, over the range 300-385 mosmol/kg, for sodium (22Na) and potassium (42K or 86Rb) and as a marker for nonselective changes in permeability for [14C]mannitol. Osmolality was elevated by intraperitoneal injection of hypertonic NaCl, mannitol, or sucrose. K1 for Na, K, and mannitol each increased linearly with plasma osmolality. Increases in K1 for Na and mannitol were small and were proportional to their respective diffusion coefficients, consistent with the development of a small leak pathway. Increases in K1 for K were much larger, consistent with osmotic stimulation of a selective permeability pathway. Quantitative analysis of the results suggests that uptake from plasma accounts for most of the K gained by brain tissue in response to acute hyperosmolality but for only a small fraction of the Na. This provides indirect evidence for an additional source of Na, presumably from cerebrospinal fluid.
Ion implantation model considering crystal structure effects (2003)

An ion implantation model for crystalline targets, based on the Monte Carlo method, is proposed. Crystal structure effects on ion channeling are directly modeled by taking into account simultaneous collisions with multitarget atoms. The model can reproduce an experimental boron distribution profile in crystalline silicon. Some important effects on distribution profile, such as thermal lattice vibrations, tilted implantation, and surface imperfection, have been investigated. It is found that a subchannelling effect is important in determining the boron distribution profile.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Assessing Ovarian Cancer Risk When Considering Elective Oophorectomy at the Time of Hysterectomy (2011)

We developed a risk-assessment tool that can quantify women's risk for ovarian cancer and should be validated in other data sets.
Expression Pattern of Kv11 (Ether à-go-go-Related Gene; erg) K+ Channels in the Mouse Retina (2011)

In response to light, most retinal neurons exhibit gradual changes in membrane potential. Therefore K+ channels that mediate threshold currents are well-suited for the fine-tuning of signal transduction. In the present study we demonstrate the expression of the different Kv11 (ether-à-go-go related gene; erg) channel subunits in the human and mouse retina by RT PCR and quantitative PCR, respectively. Immunofluorescence analysis with cryosections of mouse retinae revealed the following local distribution of the three Kv11 subunits: Kv11.1 (m-erg1) displayed the most abundant expression with the strongest immunoreactivity in rod bipolar cells. In addition, immunoreactivity was found in the inner part of the outer plexiform layer (OPL), in the inner plexiform layer (IPL) and in the inner segments of photoreceptors. Immunoreactivity for Kv11.2 (m-erg2) was observed in the outer part of the OPL and throughout the IPL. Double-labeling for vGluT1 or synaptophysin indicated a mainly presynaptic localization of Kv11.2. While no significant staining for Kv11.3 (m-erg3) was detected in the neuronal retina, strong Kv11.3 immunoreactivity was present in the apical membrane of the retinal pigment epithelium. The different expression levels were confirmed by real-time PCR showing almost equal levels of Kv11.1 and Kv11.2, while Kv11.3 mRNA expression was significantly lower. The two main splice variants of Kv11.1, isoforms a and b were detected in comparable levels suggesting a possible formation of cGMP/cGK-sensitive Kv11.1 channels in photoreceptors and rod bipolar cells. Taken together, the immunohistological results revealed different expression patterns of the three Kv11 channels in the mouse retina supposing distinct physiological roles.
Smooth sampling trajectories for sparse recovery in MRI (2011)

Recent attempts to apply compressed sensing to MRI have resulted in pseudo-random k-space sampling trajectories which, if applied naïvely, may do little to decrease data acquisition time. This paper shows how an important indicator of CS performance guarantees, the Restricted Isometry Property, holds for deterministic sampling trajectories corresponding to radial and spiral sampling patterns in common use. These theoretical results support several empirical studies in the literature on compressed sensing in MRI. A combination of Geršgorin's Disc Theory and Weyl's sums lead to performance bounds on sparse recovery algorithms applied to MRI data collected along short and smooth sampling trajectories.
Fusion spliceable and highly efficient Bi/sub 2/O/sub 3/-based EDF for short-length and broadband application pumped at 1480 nm (2002)

A conventional fusion splicing to SiO/sub 2/ fiber was achieved in W/sub 2/O/sub 3/-based Er doped fibers (EDF). High slope efficiency of 43 % and broadband gain spectrum were achieved at 1490 nm pumping amplification for only 26 cm-length.
Fabrication, current density and strain dependence of sintered, Ag-sheathed BiSrCaCuO (2212) single filament and multifilamentary tape superconductors (1991)

Bi/sub 2/Sr/sub 2/CaCu/sub 2/O/sub x/ (2212) superconductors have been fabricated into silver (Ag)-sheathed single-filament, multifilament, and wire-in-tube (WIT) tapes. Calcining, annealing and sintering conditions have been studied to improve the critical current density J/sub c/(B, 4.2 K) at high magnetic field (B). The optimization is discussed, and resulting properties are related to the microstructure of the superconductor. Superconductor J/sub c/ approximately 1-5*10/sup 4/ A/cm/sup 2/ has been obtained in fields >20 T at 4.2 K in both single and multifilamentary tapes. The dependence of J/sub c/ upon mechanical strain ( in ) has been investigated. No prestraining of the superconductor occurred in any of the samples, most likely due to yielding of the Ag sheath. Although strain resistance was good in all samples, the WIT tapes were significantly more resistant than the single-filament tapes. For the single-filament tapes, in /sub irr/ approximately 0.24%, while for the WIT tapes, in /sub irr/ approximately 0.36%, where in /sub irr/ is the irreversible strain limit.
Grover’s quantum search algorithm for an arbitrary initial amplitude distribution (1999)

Grover's algorithm for quantum searching is generalized to deal with arbitrary initial complex amplitude distributions. First-order linear difference equations are found for the time evolution of the amplitudes of the marked and unmarked states. These equations are solved exactly. New expressions are derived for the optimal time of measurement and the maximal probability of success. They are found to depend on the averages and variances of the initial amplitude distributions of the marked and unmarked states, but not on higher moments. Our results imply that Grover's algorithm is robust against modest noise in the amplitude initialization procedure.
Demonstration of reverse symmetry waveguide sensing in aqueous solutions (2002)

A reverse symmetry waveguide is presented for evanescent wave sensing in aqueous solutions. The waveguide consists of a thin polystyrene film, supported by a thicker substrate layer of nanoporous silica on glass. The nanoporous substrate layer has a refractive index of nS=1.193, hence, with an aqueous cover refractive index of nC=1.331, a reverse symmetry (nS&lt;nC) is obtained. A surface relief grating formed in the polystyrene film is used as a coupling element. Sensitivities considerably higher than for a conventional waveguide sensor are demonstrated.
Ceritinib in <i>ALK</i> -Rearranged Non–Small-Cell Lung Cancer (2014)

Ceritinib was highly active in patients with advanced, ALK-rearranged NSCLC, including those who had had disease progression during crizotinib treatment, regardless of the presence of resistance mutations in ALK. (Funded by Novartis Pharmaceuticals and others; ClinicalTrials.gov number, NCT01283516.).
First space flight of InP solar cells (2002)

A large-scale, commercial process to produce high-efficiency diffused junction InP solar cells is developed. Proton irradiation effects on InP solar cells are also studied. Superior proton resistance of InP cells is confirmed by defect analysis. 1300 pieces of InP solar cells (2*1 cm/sup 2/), with efficiencies of 16-17%, were used as the power source for the lunar orbiter of the Japanese scientific satellite MUSES-A, launched in January 1990. The InP solar cells have been demonstrated to be stable in space.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Permanent Real-Time Downhole Flow-Rate Measurements in Multilateral Wells Improve Reservoir Monitoring and Control (2007)

Abstract During the last decade, intelligent well completions have evolved to become engineered solutions widely used for both monobore and multilateral horizontal wells. However, a clear understanding of zonal or lateral branch flow contributions still remains an issue. Several SPE papers covering the issue have been published recently. This paper presents the engineered solution for a TAML level 5 dual-lateral horizontal well that was drilled and completed in the Oseberg Sør field in December 2005. The solution combines hydraulic flow control valves with advanced downhole two-phase flow and density measurement provided by a Venturi-based flowmeter with a gamma ray source and detector. Real-time data were used to optimize the settings of the downhole chokes to obtain a balanced production from the two horizontal wellbores. The completion provides the capability to control and measure, in real time, flow contributions from both laterals and is the first installation of its type. This capability is critical for production and reservoir optimization. Additional value of the technology is demonstrated by the analysis of acquired downhole data. Productivity Indices are obtained for each of the two laterals without any production loss associated with shutting down the other lateral branch. Data analysis indicated a decrease of the Productivity Index for one of the two horizontal wellbores. The successful installation of the two-phase flowmeter in an intelligent completion is a significant milestone corresponding to the general trend in the industry to improve inflow control and the understanding of flow contributions in multilateral wells. This solution for flow control and measurement can be applied effectively in both multilateral wells and monobore wells designed for commingled production from different reservoirs where accurate production allocation is a critical issue.
Watermarking three-dimensional polygonal models through geometric and topological modifications (1998)

This paper discusses techniques for embedding data into three-dimensional (3-D) polygonal models of geometry. Given objects consisting of points, lines, (connected) polygons, or curved surfaces, the algorithms described in produce polygonal models with data embedded into either their vertex coordinates, their vertex topology (connectivity), or both. Such data embedding can be used, for example, for copyright notification, copyright protection, theft deterrence, and inventory of 3-D polygonal models. A description of the background and requirements is followed by a discussion of where, and by what fundamental methods, data can be embedded into 3-D polygonal models. The paper then presents several data embedding algorithms, with examples, based on these fundamental methods. By means of these algorithms and examples, we show that the embedding of data into 3-D polygonal models is a practicable technique.
Formation and Nature of InGaN Quantum Dots in GaN Nanowires (2015)

InGaN/GaN disk-in-nanowire heterostructures on silicon substrates have emerged as important gain media for the realization of visible light sources. The nature of quantum confinement in the disks is largely unknown. From the unique nature of the measured temperature dependence of the radiative lifetime and direct transmission electron microscopy, it is evident that such self-organized islands (disks) behave as quantum dots. This is confirmed by the observation of single photon emission from a single disk-in-nanowire and the presence of a sharp minimum in the line width enhancement factor of edge emitting lasers having the InGaN disks as the gain media.
Estimation of the impact of the human immunodeficiency virus infection on tuberculosis: tuberculosis risks re-visited? (1997)

The human immunodeficiency virus (HIV) infection has both a direct and an indirect effect on the incidence of tuberculosis. The direct effect is due to the increased number of cases among HIV-infected individuals because of their enhanced susceptibility to the disease. The indirect effect is increased transmission of Mycobacterium tuberculosis infection in a community with high levels of dual infection, as a consequence of infectious cases occurring in HIV-infected persons. The risk of infection by M. tuberculosis in the population will then increase, as will the number of tuberculosis cases in the general population. According to the World Health Organization, over 4 million people are estimated to be dually infected with HIV and M. tuberculosis world-wide. In 1990, it was estimated that 300,000 new TB cases (4% of total new cases) were attributable to HIV infection; around 1.4 million cases are expected per year by 2000 (equivalent to about 14% of expected cases), thus increasing the reservoir of tuberculosis patients capable of transmitting the infection to others, and increasing the burden on the already overstretched National Tuberculosis Control Programmes, especially in resource-poor countries. This paper is a review of methods suggested to quantify the effect of the interaction between HIV infection and tuberculosis at population level, and more particularly the effect of HIV on the risk of tuberculosis infection.
Lipid Droplets and Peroxisomes: Key Players in Cellular Lipid Homeostasis <i>or</i> A Matter of Fat—Store ’em Up or Burn ’em Down (2012)

Lipid droplets (LDs) and peroxisomes are central players in cellular lipid homeostasis: some of their main functions are to control the metabolic flux and availability of fatty acids (LDs and peroxisomes) as well as of sterols (LDs). Both fatty acids and sterols serve multiple functions in the cell-as membrane stabilizers affecting membrane fluidity, as crucial structural elements of membrane-forming phospholipids and sphingolipids, as protein modifiers and signaling molecules, and last but not least, as a rich carbon and energy source. In addition, peroxisomes harbor enzymes of the malic acid shunt, which is indispensable to regenerate oxaloacetate for gluconeogenesis, thus allowing yeast cells to generate sugars from fatty acids or nonfermentable carbon sources. Therefore, failure of LD and peroxisome biogenesis and function are likely to lead to deregulated lipid fluxes and disrupted energy homeostasis with detrimental consequences for the cell. These pathological consequences of LD and peroxisome failure have indeed sparked great biomedical interest in understanding the biogenesis of these organelles, their functional roles in lipid homeostasis, interaction with cellular metabolism and other organelles, as well as their regulation, turnover, and inheritance. These questions are particularly burning in view of the pandemic development of lipid-associated disorders worldwide.
Influence of omega‐3 and omega‐6 fatty acid sources on prostaglandin levels in mice (1989)

Studies from this laboratory, employing a hairless mouse model, have indicated that a polyunsaturated fatty acid source rich in omega-3 (n-3) fatty acid (FA) inhibits ultraviolet (UV)-carcinogenic expression, when compared to that of diets containing predominantly n-6 fatty acids. Omega-3 FA is a poor substrate for cyclooxygenase, the rate-limiting step in prostaglandin (PG) synthesis--the latter, particularly PGE2, are known to influence tumor biology. Based upon this rationale, plasma and cutaneous PGE2 levels were determined from hairless mice fed diets containing either 4% or 12% corn or menhaden oil. After two weeks on the respective diets, plasma PGE2 levels of corn oil-fed animals were approximately 6-fold greater than those of the menhaden oil-fed groups. A similar response was found in the dermis. Although the relationship to carcinogenic expression is unknown, dietary n-3 FA content can have a pronounced effect upon PGE2 levels and possesses the potential for influencing other immunomodulators.
Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes (2015)

Gene fusions have been described in approximately one‐third of soft tissue tumors (STT); of the 142 different fusions that have been reported, more than half are recurrent in the same histologic subtype. These gene fusions constitute pivotal driver mutations, and detailed studies of their cellular effects have provided important knowledge about pathogenetic mechanisms in STT. Furthermore, most fusions are strongly associated with a particular histotype, serving as ideal molecular diagnostic markers. In recent years, it has also become apparent that some chimeric proteins, directly or indirectly, constitute excellent treatment targets, making the detection of gene fusions in STT ever more important. Indeed, pharmacological treatment of STT displaying fusions that activate protein kinases, such as ALK and ROS1, or growth factors, such as PDGFB, is already in clinical use. However, the vast majority (52/78) of recurrent gene fusions create structurally altered and/or deregulated transcription factors, and a small but growing subset develops through rearranged chromatin regulators. The present review provides an overview of the spectrum of currently recognized gene fusions in STT, and, on the basis of the protein class involved, the mechanisms by which they exert their oncogenic effect are discussed. © 2015 Wiley Periodicals, Inc.
[Comparative study of the effect of ecdysterone, turkesterone and nerobol on the function of rat liver mitochondria in experimental diabetes]. (1986)

Oxidative phosphorylation and Ca2+-transport functions of liver mitochondria were normalized in rats with alloxane diabetes after peroral administration of phytoecdisteroids - ecdisterone and turkesterone (5 mg/kg) or nerobol (10 mg/kg) within 15 days. These drugs normalized the activity of NADH dehydrogenase and succinate dehydrogenase in respiratory chain of mitochondria, increased distinctly stability of the enzymes to the effect of such factors as heating, effect of phospholipase A2 or trypsin.