gebhart/patrepeval huggingface dataset:
Influence of polarization on pump-signal RIN transfer and cross-phase modulation in copumped Raman amplifiers (2006)

Pump-to-signal relative intensity noise (RIN) transfer in copumped Raman amplifiers is analyzed. By means of simulations and experiments, the authors call attention to the impact of the polarized nature of stimulated Raman scattering on RIN transfer. Although depolarizing the Raman pump enables polarization-independent signal gain, the authors demonstrate that proper modeling of RIN transfer requires including the polarization dependence of the Raman effect and the polarization mode dispersion of the fiber. A second key phenomenon is emphasized. Besides the RIN transfer induced by Raman gain, pump RIN is also transferred to the signal via nonlinear gain. This phenomenon can be addressed as pump-signal cross-phase modulation since it essentially generates phase noise on the signal. For the first time, in this paper, a model of pump-to-signal RIN transfer that includes polarization and nonlinear gain is presented. The authors reveal the key influence of these factors that had been uncared for so far. Their analysis is supported by experimental data. Signal noise characteristics (RIN spectrum and high-resolution optical power spectrum) measured at the output of a copumped Raman amplifier were presented. The Raman pump is a pair of semiconductor diodes in the first two experiments and then a Raman fiber laser. For these two kinds of depolarized or unpolarized Raman pumps that are commonly used in the field, the authors emphasize the necessity of considering polarization for the good assessment of RIN transfer.
Multiexcitation fluorescence and reflectance spectroscopy as a real-time guide to biopsy in vivo (2001)

A compact excitation-emission spectrofluorimeter system used to acquire tissue fluorescence and reflectance with fiber optic light delivery and collection is presented. Ten dye cells are pumped by a XeC1 excimer laser, creating laser excitation from 308 nm to 505nm, which is used to excite tissue fluorescence. A xenon-flash lamp is employed to obtain the reflectance spectrum of the corresponding tissue spot. Eleven fluorescence spectra and one white light diffuse reflectance spectrum are collected in vivo in 0.2 seconds and can be potentially analyzed in real time to obtain diagnostic information. The instrument can be used for early cancer detection. The measured fluorescence and reflectance spectra are used to model the intrinsic fluorescence of the tissue, which gives important insight into its biochemical composition (tryptophan, collagen, elastin, NADH, etc.) and metabolic state. Diffuse reflectance provides information about tissue morphology, in terms of the scatterhig and absorption coefficient. By subtracting the diffusely reflected component from the measured reflectance, light scattering spectroscopic (LSS) information due to single backscattering from epithelial cell nuclei can be obtained. LSS provides information about the size distribution of cell nuclei. The parameters give diagnostic information, which can be used to guide the physician in real time while taking biopsies of invisible tissue abnormalities.
Building a Simulation Grid for Large Scale Reservoir Simulation (2013)

Abstract Large scale reservoir simulation is essential to understand various flow processes inside the reservoir. With the advent of high performance computing (HPC), it is now possible to simulate models larger than even one billion cells. Because of its cost effectiveness, Linux clusters are very popular for large scale reservoir simulations. Many large clusters have been built by connecting processors via state-of-the-art high speed networks like Infiniband (IB), which can add considerable cost for the hardware. It is possible to connect multiple computer clusters to build a simulation grid, to simulate giant models, which may be difficult to do on a single cluster because of the size limitation. The network connecting clusters should be capable of supporting the needed data transfer rate to avoid performance degradation. Communication and computational load in a simulation depends on various parameters of the model, including size, underlying physics, mathematical formulation, etc. Our focus in this study is to examine HPC architectures, which may be used for large scale reservoir simulation in a cost-effective manner. Our design was made following extensive benchmark studies. We designed the network configuration, which is blocking in design to reduce the cost of hardware associated with the network. Our tests with large models indicate that there is only minor degradation in performance because of the new design, while significantly saving in hardware cost. We followed the Hyperscale design principle in constructing the cluster, eliminating all unnecessary components and keeping only essential ones. In this paper, we present results of our simulation grid and discuss scalability of such simulations. We also discuss benefits of a simulation grid in increasing utilization of hardware resources.
Enhancement of Thermostability of Firefly Luciferase from<i>Luciola lateralis</i>by a Single Amino Acid Substitution (1994)

We constructed firefly luciferase mutants from Luciola lateralis in which Ala at position 217 was replaced by each of three hydrophobic amino acid residues (Ile, Leu, and Val). These mutants were superior to the wild-type in thermostability. Especially, the purified Ala217Leu mutant still maintained over 70% of the initial activity after 60 min at 50 degrees C. This mutant is the most thermostable firefly luciferase obtained.
Structural basis for HIV-1 gp120 recognition by a germ-line version of a broadly neutralizing antibody (2013)

Efforts to design an effective antibody-based vaccine against HIV-1 would benefit from understanding how germ-line B-cell receptors (BCRs) recognize the HIV-1 gp120/gp41 envelope spike. Potent VRC01-like (PVL) HIV-1 antibodies derived from the VH1-2*02 germ-line allele target the conserved CD4 binding site on gp120. A bottleneck for design of immunogens capable of eliciting PVL antibodies is that VH1-2*02 germ-line BCR interactions with gp120 are uncharacterized. Here, we report the structure of a VH1-2*02 germ-line antibody alone and a germ-line heavy-chain/mature light-chain chimeric antibody complexed with HIV-1 gp120. VH1-2*02 residues make extensive contacts with the gp120 outer domain, including all PVL signature and CD4 mimicry interactions, but not critical CDRH3 contacts with the gp120 inner domain and bridging sheet that are responsible for the improved potency of NIH45-46 over closely related clonal variants, such as VRC01. Our results provide insight into initial recognition of HIV-1 by VH1-2*02 germ-line BCRs and may facilitate the design of immunogens tailored to engage and stimulate broad and potent CD4 binding site antibodies.
Evaluation of the Estrogenic Effects of Legume Extracts Containing Phytoestrogens (2003)

Seven legume extracts containing phytoestrogens were analyzed for estrogenic activity. Methanol extracts were prepared from soybean (Glycine max L.), green bean (Phaseolus vulgaris L.), alfalfa sprout (Medicago sativa L.), mung bean sprout (Vigna radiata L.), kudzu root (Pueraria lobata L.), and red clover blossom and red clover sprout (Trifolium pratense L.). Extracts of kudzu root and red clover blossom showed significant competitive binding to estrogen receptor beta (ERbeta). Estrogenic activity was determined using an estrogen-dependent MCF-7 breast cancer cell proliferation assay. Kudzu root, red clover blossom and sprout, mung bean sprout, and alfalfa sprout extracts displayed increased cell proliferation above levels observed with estradiol. The pure estrogen antagonist, ICI 182,780, suppressed cell proliferation induced by the extracts, suggesting an ER-related signaling pathway was involved. The ER subtype-selective activities of legume extracts were examined using transiently transfected human embryonic kidney (HEK 293) cells. All seven of the extracts exhibited preferential agonist activity toward ERbeta. Using HPLC to collect fractions and MCF-7 cell proliferation, the active components in kudzu root extract were determined to be the isoflavones puerarin, daidzin, genistin, daidzein, and genistein. These results show that several legumes are a source of phytoestrogens with high levels of estrogenic activity.
Language Weaver: The Next Generation of Machine Translation (2003)

We introduce a new generation of commercial translation software, based primarily on statistical learning and statistical language models.
A novel architecture low data rate full duplex optical communications link between Earth and LEO (2003)

We present a model which shows that a data rate of 10-kbps to LEO is possible with a 4 watt transmitter. Furthermore, we have presented for the first time the use of circular polarization keying for free-space optical communications and the "Lightwire" concept that allows full-duplex communications using a single optical beam.
A new camera calibration method for robotic applications (2002)

In this paper, we present a camera calibration method using two views of three pairs of concentric circles with known sizes. A new invariant property for circle is introduced to determine the position of the center of the projected circle. Given two image ellipses and their corresponding centers, a cross-ratio based method estimates the center of projected circles using the new invariant property. The accurate center of projected concentric circles provides correct correspondences between ellipses in the image plane and circles in 3D plane. We also demonstrate that two views of three pairs of coplanar concentric circles are enough to determine the intrinsic camera parameters, such as the focal length, the aspect ratio, and the principal point. We validate the performance of the method using both synthetic and real images. Our method shows a comparable performance with respect to similar calibration methods using planes. The use of concentric circles, however, provides correct correspondences between 3D target points and their image points, and greatly simplifies the calibration problem.
Two novel phosphatidylinositol-4-phosphate 5-kinase type Iγ splice variants expressed in human cells display distinctive cellular targeting (2009)

The generation of various phosphoinositide messenger molecules at distinct locations within the cell is mediated via the specific targeting of different isoforms and splice variants of phosphoinositide kinases. The lipid messenger PtdIns(4,5)P(2) is generated by several of these enzymes when targeted to distinct cellular compartments. Several splice variants of the type Igamma isoform of PIPK (PtdIns4P 5-kinase), which generate PtdIns(4,5)P(2), have been identified, and each splice variant is thought to serve a unique functional role within cells. Here, we have identified two novel C-terminal splice variants of PIPKIgamma in human cells consisting of 700 and 707 amino acids. These two splice variants are expressed in multiple tissue types and display PIPK activity in vitro. Interestingly, both of these novel splice variants display distinct subcellular targeting. With the addition of these two new splice isoforms, there are minimally five PIPKIgamma splice variants that have been identified in mammals. Therefore, we propose the use of the HUGO (Human Genome Organization) nomenclature in the naming of the splice isoforms. PIPKIgamma_i4 (700 amino acids) is present in the nucleus, a targeting pattern that has not been previously observed in any PIPKIgamma splice variant. PIPKIgamma_i5 (707 amino acids) is targeted to intracellular vesicle-like structures, where it co-localizes with markers of several types of endosomal compartments. As occurs with other PIPKIgamma splice variants, the distinctive C-terminal sequences of PIPKIgamma_i4 and PIPKIgamma_i5 may facilitate association with unique protein targeting factors, thereby localizing the kinases to their appropriate cellular subdomains for the site-specific generation of PtdIns(4,5)P(2).
Microbial Consortium with High Cellulolytic Activity (MCHCA) for Enhanced Biogas Production (2016)

The use of lignocellulosic biomass as a substrate in agricultural biogas plants is very popular and yields good results. However, the efficiency of anaerobic digestion, and thus biogas production, is not always satisfactory due to the slow or incomplete degradation (hydrolysis) of plant matter. To enhance the solubilization of the lignocellulosic biomass various physical, chemical and biological pretreatment methods are used. The aim of this study was to select and characterize cellulose-degrading bacteria, and to construct a microbial consortium, dedicated for degradation of maize silage and enhancing biogas production from this substrate. Over 100 strains of cellulose-degrading bacteria were isolated from: sewage sludge, hydrolyzer from an agricultural biogas plant, cattle slurry and manure. After physiological characterization of the isolates, 16 strains (representatives of Bacillus, Providencia, and Ochrobactrum genera) were chosen for the construction of a Microbial Consortium with High Cellulolytic Activity, called MCHCA. The selected strains had a high endoglucanase activity (exceeding 0.21 IU/mL CMCase activity) and a wide range of tolerance to various physical and chemical conditions. Lab-scale simulation of biogas production using the selected strains for degradation of maize silage was carried out in a two-bioreactor system, similar to those used in agricultural biogas plants. The obtained results showed that the constructed MCHCA consortium is capable of efficient hydrolysis of maize silage, and increases biogas production by even 38%, depending on the inoculum used for methane fermentation. The results in this work indicate that the mesophilic MCHCA has a great potential for application on industrial scale in agricultural biogas plants.
The Mushroom Marasmius oreades Lectin Is a Blood Group Type B Agglutinin That Recognizes the Galα1,3Gal and Galα1,3Galβ1,4GlcNAc Porcine Xenotransplantation Epitopes with High Affinity (2002)

A blood group B-specific lectin from the mushroom Marasmius oreades (MOA) was investigated with respect to its molecular structure and carbohydrate binding properties. SDS-PAGE mass spectrometric analysis showed it to consist of an intact (H; 33 kDa) and truncated (L; 23 kDa) subunit in addition to a small polypeptide (P; 10 kDa). Isolation in the presence of EDTA produced only the H subunits, indicating that the latter two are formed by metalloprotease cleavage of the intact H subunit. Tryptic digestion of the H, L, and P polypeptide chains followed by mass spectral analysis supports this view. The lectin strongly precipitated blood group type B substance, was nonreactive with type A substance, and reacted weakly with type H substance. Carbohydrate binding studies reveal a high affinity for Galalpha1,3Gal (but not for the isomeric alpha1,2-, alpha1,4-, and alpha1,6-disaccharides); Galalpha1,3Galbeta1,4GlcNAc; and the type B branched trisaccharide. MOA also reacts strongly with murine laminin from the Engelbreth-Holm-Swarm sarcoma and bovine thyroglobulin, both of which contain multiple Galalpha1,3Galbeta1,4GlcNAc end groups. This linear B trisaccharide is a component of porcine tissues and organs, preventing their transplantation into humans. MOA also shares carbohydrate recognition of this trisaccharide with toxin A elaborated by Clostridium difficile.
Instant spectral assignment for advanced decision tree-driven mass spectrometry (2012)

We have developed and implemented a sequence identification algorithm (inSeq) that processes tandem mass spectra in real-time using the mass spectrometer's (MS) onboard processors. The inSeq algorithm relies on accurate mass tandem MS data for swift spectral matching with high accuracy. The instant spectral processing technology takes ∼16 ms to execute and provides information to enable autonomous, real-time decision making by the MS system. Using inSeq and its advanced decision tree logic, we demonstrate (i) real-time prediction of peptide elution windows en masse (∼3 min width, 3,000 targets), (ii) significant improvement of quantitative precision and accuracy (~3x boost in detected protein differences), and (iii) boosted rates of posttranslation modification site localization (90% agreement in real-time vs. offline localization rate and an approximate 25% gain in localized sites). The decision tree logic enabled by inSeq promises to circumvent problems with the conventional data-dependent acquisition paradigm and provides a direct route to streamlined and expedient targeted protein analysis.
Abstract 206: A New MicroRNA Family Regulating Cardiac Autophagy and Hypertrophy (2012)

Pathologic growth of cardiomyocytes and derailed autophagy are major determinants for the development of heart failure, one of the leading medical causes of mortality worldwide. Here, we show the microRNA (miRNA)-212/132 family to regulate hypertrophy and autophagy in cardiomyocytes. Hypertrophic stimuli lead to the upregulation of miR-212 and miR-132 expression in cardiomyocytes, which are both necessary and sufficient to drive the hypertrophic growth of cardiomyocytes. MiR-212/132 null mice are protected from pressure-overload induced heart failure, whereas cardiomyocyte-specific overexpression of the miR-212/132 family leads to pathological cardiac hypertrophy, heart failure and lethality in mice. Mechanistically, both miR-212 and miR-132 directly target the anti-hypertrophic and pro-autophagic FoxO3 transcription factor and overexpression of these miRNAs leads to hyperactivation of pro-hypertrophic calcineurin/NFAT signalling and impaired autophagic response upon starvation. Pharmacologic miRNA inhibition by antagomir injection rescues cardiac hypertrophy and heart failure in mice, offering a possible therapeutic approach for cardiac failure.
Cloning and Characterization of Multigenes Encoding the Immunodominant 30-Kilodalton Major Outer Membrane Proteins of <i>Ehrlichia canis</i> and Application of the Recombinant Protein for Serodiagnosis (1998)

A 30-kDa major outer membrane protein of Ehrlichia canis, the agent of canine ehrlichiosis, is the major antigen recognized by both naturally and experimentally infected dog sera. The protein cross-reacts with a serum against a recombinant 28-kDa protein (rP28), one of the outer membrane proteins of a gene (omp-1) family of Ehrlichia chaffeensis. Two DNA fragments of E. canis were amplified by PCR with two primer pairs based on the sequences of E. chaffeensis omp-1 genes, cloned, and sequenced. Each fragment contained a partial 30-kDa protein gene of E. canis. Genomic Southern blot analysis with the partial gene probes revealed the presence of multiple copies of these genes in the E. canis genome. Three copies of the entire gene (p30, p30-1, and p30a) were cloned and sequenced from the E. canis genomic DNA. The open reading frames of the two copies (p30 and p30-1) were tandemly arranged with an intergenic space. The three copies were similar but not identical and contained a semivariable region and three hypervariable regions in the protein molecules. The following genes homologous to three E. canis 30-kDa protein genes and the E. chaffeensis omp-1 family were identified in the closely related rickettsiae: wsp from Wolbachia sp. , p44 from the agent of human granulocytic ehrlichiosis, msp-2 and msp-4 from Anaplasma marginale, and map-1 from Cowdria ruminantium. Phylogenetic analysis among the three E. canis 30-kDa proteins and the major surface proteins of the rickettsiae revealed that these proteins are divided into four clusters and the two E. canis 30-kDa proteins are closely related but that the third 30-kDa protein is not. The p30 gene was expressed as a fusion protein, and the antibody to the recombinant protein (rP30) was raised in a mouse. The antibody reacted with rP30 and a 30-kDa protein of purified E. canis. Twenty-nine indirect fluorescent antibody (IFA)-positive dog plasma specimens strongly recognized the rP30 of E. canis. To evaluate whether the rP30 is a suitable antigen for serodiagnosis of canine ehrlichiosis, the immunoreactions between rP30 and the whole purified E. canis antigen were compared in the dot immunoblot assay. Dot reactions of both antigens with IFA-positive dog plasma specimens were clearly distinguishable by the naked eye from those with IFA-negative plasma specimens. By densitometry with a total of 42 IFA-positive and -negative plasma specimens, both antigens produced results similar in sensitivity and specificity. These findings suggest that the rP30 antigen provides a simple, consistent, and rapid serodiagnosis for canine ehrlichiosis. Cloning of multigenes encoding the 30-kDa major outer membrane proteins of E. canis will greatly facilitate understanding pathogenesis and immunologic study of canine ehrlichosis and provide a useful tool for phylogenetic analysis.
Sorting colloidal particles into multiple channels with optical forces: Prismatic optical fractionation (2010)

Brownian particles drifting through a periodically structured force landscape can become entrained by the landscape's symmetries. What direction a particular particle takes can depend strongly on subtle variations in its physical properties. Consequently, a homogeneously structured force field can sort a mixture of particles into spatially separated fractions, much as an optical prism refracts light into its component wavelengths. When the force landscape is implemented with structured light fields, such continuous multichannel sorting may be termed prismatic optical fractionation. We describe experimental and numerical studies of colloidal spheres' transport through periodic arrays of optical tweezers, which reveal an important role for three-dimensional motion in determining a drifting particle's fate. These studies also demonstrate sorting on the basis of statistically locked-in transport, in which brownian fluctuations contribute to direction selection.
Structure and Control of Thermoacoustic Instabilities in a Gas-turbine Combustor (1998)

Thermoacoustic instability was investigated and controlled in an experimental low-emission swirl stabilized combustor, in which the acoustic boundary conditions were modified to obtain combustion instability. Several axisymmetric and helical unstable modes were identified for fully premixed and partially premixed/diffusion combustion. These unstable modes were associated with flow instabilities related to the recirculation region on the combustor axis and shear layer instabilities at the sudden expansion (dump plane). The spatial locations of the intense combustion regions associated with the different unstable modes were visualized by phase locked images of OH chemiluminescence. The axisymmetric mode showed large variation of the heat release during one cycle, while the helical modes showed variations in the radial location of maximal heat release. A closed loop active control system was employed to suppress the thermoacoustic pressure oscillations and to reduce NO x emissions. Microphone and OH emission sensors were utilized to monitor the combustion process and provide input to the control system. Acoustic actuation was utilized to modulate the air flow to aflect the mixing process and the combustion. Suppression levels of up to 5 dB in the pressure oscillations and a concomitant reduction of NO x emissions were obtained using an acoustic power of less than 0.002% of the combustion power. The microphone based controller was slightly more efficient than the OH-based controller. This was due to the reduced coherence of the combusting large-scale structures which resulted in a deterioration of the OH signal when the controller became effective.