gebhart/patrepeval huggingface dataset:
Full‐length bovine spp24 [spp24 (24‐203)] inhibits BMP‐2 induced bone formation (2008)

Secreted phosphoprotein 24 kDa (spp24) is a bone matrix protein. It contains a TGF-beta receptor II homology 1 (TRH1) domain. A cyclic, synthetic 19 amino acid peptide (bone morphogenetic protein binding peptide or BBP) based on the sequence of the TRH1 domain enhances BMP-2 induced osteogenesis. Many observations suggest that different size forms of this protein have very different effects (inhibiting or enhancing) on BMP-2 induced osteogenesis. Using the stable recombinant Met(His)(6)-tagged secretory form of full-length (fl) bovine spp24 [Met(His)(6)-spp24 (residues 24-203)] and transgenic (TG) mice expressing fl bovine spp24 (residues 1-203), we have demonstrated that spp24 inhibits BMP-2 induced bone formation. The effects of Met(His)(6)-spp24 (24-203) were determined in the ectopic bone-forming bioassay in male mice. Implantation of 5 microg of BMP-2 stimulated bone formation, assessed densitometrically as bone area and mineral content. When Met(His)(6)-spp24 (24-203) was implanted with BMP-2, it elicited a dose-dependent decrease in BMP-2-medicated ectopic bone formation. When added at a 50-fold excess (w/w), Met(His)(6)-spp24 (24-203) completely ablated the effects of BMP-2, while addition of a 10-fold excess had no effect. Constitutive expression of fl bovine spp24 (1-203) under the control of the osteocalcin promoter in TG female mice reduced femoral and vertebral bone mineral density at 3 months of age and reduced femoral BMD at 8 months of age, but had no effects in male mice, which can exhibit less osteocalcin-promoter driven gene transcription than females. Histomorphometric analysis demonstrated that bone volume and trabecular thickness were lower in TG female mice at 3 months of age than in sex- and age-matched wild type (WT) controls. Thus, fl spp24 and its secretory isoform (Met(His)(6)-spp24 [24-203]), which contain a BMP-binding or TRH1 motif, inhibit ectopic bone formation in male mice and adversely affects BMD and histological parameters related to bone mass and formation in female mice expressing the human transgene. Under these conditions, fl spp24 acts as a BMP antagonist in vivo.
Noncatalytic Organic Synthesis Using Supercritical Water: The Peculiarity Near the Critical Point (1999)

Pinacol and Beckmann rearrangements can be carried out effectively by using supercritical water (scH2O) both as an acid catalyst as well as a medium. In the near-critical region not only are the rates significantly accelerated (see picture), but the nature of supercritical water can be adjusted to give weak acidity, which opens a new reaction pathway to a Diels–Alder adduct between dehydrated products.
On a self-tuning impact vibration damper for rotating turbomachinery (2000)

A self-tuning impact damper is investigated analytically and experimentally as a device to inhibit vibration and increase the fatigue life of rotating components in turbomachinery. High centrifugal loads in rotors can inactivate traditional impact dampers because of friction or misalignment of the damper in the g-field. Giving an impact damper characteristics of an acceleration tuned-mass damper enables the resulting device to maintain damper mass motion and effectiveness during high-g loading. Experimental results presented here verify that this self-tuning impact damper can be designed to follow an engine order line. damping rotor component resonance crossings.
A Fluorescent Rosamine Compound Selectively Stains Pluripotent Stem Cells (2010)

The cell-by date: The fluorescent compound CDy1 selectively stains embryonic stem cells (see scheme). CDy1 was used to identify fibroblasts undergoing reprogramming to induced pluripotent stem cells prior to the expression of green fluorescent protein under the control of the Oct4 promoter. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
MICROWAVE IMAGING VIA SPACE-TIME BEAMFORMING FOR EARLY DETECTION OF BREAST CANCER: BEAMFORMER DESIGN IN THE FREQUENCY DOMAIN (2003)

Abstract Microwave imaging via space-time beamforming has been proposed recently for early-stage breast cancer detection. In this paper we present an efficient frequency-domain approach to designing the beamformers. The low-power signal sequentially transmitted into the breast by each antenna in an array may be either an ultrawideband pulse or a sequence of sinusoidal signals with carrier frequencies corresponding to the discrete design frequencies. Backscattered waveforms collected at each transmitting antenna are processed in the frequency domain using beamformers designed to compensate for frequency-dependent propagation effects in normal breast tissue. Backscattered signal energy is computed and imaged as a function of location. We demonstrate the capability of this method to detect millimeter-sized tumors using representative backscattered waveforms computed from a two-dimensional anatomically realistic FDTD breast model. These simulation results show that localized regions of high energy levels in the images consistently correspond to small malignant tumors present in the breast. Keywords:
Conformationally Defined Retinoic Acid Analogues. 5. Large-Scale Synthesis and Mammary Cancer Chemopreventive Activity for (2<i>E</i>,4<i>E</i>,6<i>Z</i>,8<i>E</i>)-8- (3‘,4‘-Dihydro-1‘(2‘<i>H</i>)-naphthalen-1‘-ylidene)-3,7-dimethyl-2,4,6-octatrienoic Acid (9cUAB30) (2003)

Retinoids that activate the nuclear retinoid X receptors (RXRs) display potential for chemoprevention of breast cancer. We previously reported that 9cUAB30 (1) is an RXR-selective retinoid. To explore its in vivo chemopreventive activity, multigram quantities of 1 were needed. Here, we describe a modified synthesis that yields up to 100 g of 1. We further demonstrate that 1 is very effective in the prevention of N-methyl-N-nitrosourea induced mammary cancers in rats without signs of toxicity.
Novel Fibrous Lost Circulation Materials Derived from Deceased Date Tree Waste (2017)

Abstract A novel fibrous eco-friendly lost circulation material (LCM) has been developed using natural date tree waste as raw material. As the source of raw material is sustainable and available in huge quantity in the Kingdom of Saudi Arabia and in the Middle Eastern Region, it has a great potential to be used as a raw material for the manufacturing of local made fibrous lost circulation material for the application during drilling and cementing to mitigate loss of circulation. This paper describes the properties of fibrous lost circulation material in different water based drilling mud systems. The raw material for the fibrous LCM is deceased date tree waste that are available in huge quantity every year. Deceased date tree trunk has been used to produce fibers for the application in drilling industry. The trunk has been subjected to crushing and grinding process to generate fibrous materials of different sizes and aspect ratio. The fibrous material has been incorporated in different water based mud systems such as gel polymer (bentonite) mud, KCl polymer mud, NaCl polymer mud and CaCl2 polymer mud. These fiber containing muds have been tested using pore plugging test (PPT) apparatus for evaluating the sealing efficiency of the fibrous material. 2 mm slotted disk has been used as filter medium simulating fractured formation of the wellbore. Experiments carried out at high pressure and high temperature (HPHT) conditions prove that the fibrous material is a perfect choice to be used to as lost circulation material for combating moderate type of lost circulation.
Acoustic confinement and waveguiding with a line-defect structure in phononic crystal slabs (2010)

We present a new way of forming phononic crystal waveguides by coupling a series of line-defect resonators. The dispersion proprieties of these coupled resonator acoustic waveguides (CRAW) can be engineered by using their geometrical parameters. We show that single-mode guiding over a large bandwidth is possible in CRAW formed in a honeycomb-lattice phononic crystal slab of holes in zinc oxide. In addition, a finite length of CRAW structure acts as an efficient selective acoustic filter for Lamb waves.
Mitigation of Stress Corrosion Cracking Based on Residual Stress Improvement by Water Jet Peening (WJP) (2011)

We have developed a practical peening technology using cavitating water jet. Water jet peening (WJP) is a preventive maintenance technology for nuclear power plants. WJP changes the residual stress on weld surfaces of reactor internals from tensile to compressive to mitigate the stress corrosion cracking (SCC). The operating conditions of WJP are controlled on the basis of ‘JSME Codes for Nuclear Power Generation Facilities.’ WJP has several advantages of operation, especially no foreign material is left in the reactor vessel since only water is injected, and wide range of the residual stress improvement is obtained since the cavitating flow spreads along the weld surface. We have also developed a prediction method of the residual stress improvement by WJP using a combination of a cavitating jet simulation and a residual stress simulation. We numerically simulated impulsive bubble pressure that varied in microseconds in the cavitating jet with ‘bubble flow model’. The bubble collapse energy was estimated by the bubble pressure. The residual stress simulation was conducted under the input conditions obtained from the bubble collapse energy. The residual stress distributions on and under the weld surface were predicted. The distributions were compared with measured data, and the result confirmed that the developed method for predicting the compressive residual stress after WJP was valid.
Novel Hybrid Materials Consisting of Regioregular Poly(3‐octylthiophene)s Covalently Attached to Single‐Wall Carbon Nanotubes (2008)

Facile routes for the synthesis of hybrid materials consisting of regioregular poly(3-octylthiophene)s covalently attached to single-wall carbon nanotubes are presented for the first time. These materials are easily processable using common organic solvents, and at the same time combine the properties of regioregular poly(3-alkylthiophene)s with those of single-wall carbon nanotubes. Moreover, studies of the properties of these materials have provided strong evidence for an electron transfer from the regioregular poly(3-octylthiophene) to the single-wall carbon nanotube.
Dynamic Characteristics of Magnetically Levitated Conveyer Using High $T_{c}$ SMB (2013)

Our group has developed a new conveyer using superconducting levitation. The conveyer is composed of a levitated table and a conveying table. The gap between levitated table and conveying table is detected by using a Hall sensor on the superconductor. The position of the table is controlled by using the PD control. In this paper, we discuss a superconducting magnetic bearing with a central superconductor. A central superconductor improves stiffness of each direction. In addition, the characteristics of magnetically levitated superconducting conveyer are studied when the levitated table moves in the horizontal direction.
Effects of Biological Reactions and Modifications on Conductance of Nanofluidic Channels (2005)

Conductance characteristics of nanofluidic channels (nanochannels) fall into two regimes: at low ionic concentrations, conductance is governed by surface charge while at high ionic concentrations it is determined by nanochannel geometry and bulk ionic concentration. We used aminosilane chemistry and streptavidin-biotin binding to study the effects of surface reactions on nanochannel conductance at different ionic concentrations. Immobilization of small molecules such as aminosilane or biotin mainly changes surface charge, affecting conductance only in the low concentration regime. However, streptavidin not only modifies surface charge but also occludes part of the channel, resulting in observable conductance changes in both regimes. Our observations reflect the interplay between the competing effects of charge and size of streptavidin on nanochannel conductance.
Eggshell membrane hydrolyzates activate NF-&kappa;B in vitro: possible implications for in vivo efficacy (2015)

Results from our studies provide evidence that ESM hydrolyzates significantly activate NF-κB, and the source of this activity was investigated to confirm that it is inherent to ESM and not derived from bacterial contamination. Based on our findings, we propose a plausible hypothesis as to how increased NF-κB activity might translate into the in vivo efficacy that has been observed with ESM via an "oral tolerance" mechanism.
Recent Advances in Ultra Long Distance Soliton Transmission (1992)

The last few years have seen a veritable explosion of ideas for the better implementation of ultra long distance soliton transmission. Experimental proof is only just now beginning to catch up. For example, by using a recirculating loop, we have recently been able to demonstrate "error-free" (measured bit error rate ≤10 –10 ) soliton transmission over more than 15,000 km at 5 Gbit/s, single channel, and over more than 12,000 km at 10 Gbit/s in a two-channel WDM (wavelength-division-multiplexing) [1]; see Fig. 1. These results, however auspicious, represent just a beginning. With the implementation of certain ideas, tested so far only in simulation, the bit rate for such error-free, ultra long distance transmission is expected soon to rise to several tens of Gbit/s.
Exploiting Atropisomerism to Increase the Target Selectivity of Kinase Inhibitors (2015)

Abstract Many biologically active molecules exist as rapidly interconverting atropisomeric mixtures. Whereas one atropisomer inhibits the desired target, the other can lead to off‐target effects. Herein, we study atropisomerism as a possibility to improve the selectivities of kinase inhibitors through the synthesis of conformationally stable pyrrolopyrimidines. Each atropisomer was isolated by HPLC on a chiral stationary phase and subjected to inhibitor profiling across a panel of 18 tyrosine kinases. Notably different selectivity patterns between atropisomers were observed, as well as improved selectivity compared to a rapidly interconverting parent molecule. Computational docking studies then provided insights into the structure‐based origins of these effects. This study is one of the first examples of the intentional preorganization of a promiscuous scaffold along an atropisomeric axis to increase target selectivity, and provides fundamental insights that may be applied to other atropisomeric target scaffolds.
Development of a Sensitive Enzyme-Linked Immunosorbent Assay for the Determination of Ochratoxin A (2005)

Polyclonal antibodies for ochratoxin A (OTA) were generated from rabbits after the animals had been immunized with either OTA-gamma-globulin or OTA- keyhole limpet hemocyanin (KLH). A competitive direct enzyme-linked immunosorbent assay (cdELISA) and a competitive indirect ELISA (ciELISA) were used for the characterization of the antibodies and for analysis of OTA in various agricultural commodities. The antibody titers in the serum of rabbits immunized with OTA-gamma-globulin were considerably higher than those in rabbits immunized with OTA-KLH. The antibodies from the rabbits immunized with OTA-gamma-globulin were further characterized. In the cdELISA, the concentrations causing 50% inhibition (IC(50)) of binding of OTA-horseradish peroxidase to the antibodies by OTA, ochratoxin B (OTB), and ochratoxin C (OTC) were found to be 0.90, 110, and 0.54 ng/mL, respectively. When 10 to 250 ng/g of standard OTA was spiked to soybean samples and then extracted with 50% aqueous methanol, the recovery rate of OTA was found to be 85.9% in the cdELISA. Analysis of OTA in various agricultural commodities showed that 12 of the 20 examined samples were contaminated with OTA at levels from 16 to 160 ng/g. The efficacy of cdELISA was also confirmed by the high-performance liquid chromatography method.
Purification and characterization of indolepyruvate decarboxylase. A novel enzyme for indole-3-acetic acid biosynthesis in Enterobacter cloacae. (1992)

Indolepyruvate decarboxylase, a key enzyme for indole-3-acetic acid biosynthesis, was found in extracts of Enterobacter cloacae. The enzyme catalyzes the decarboxylation of indole-3-pyruvic acid to yield indole-3-acetaldehyde and carbon dioxide. The enzyme was purified to apparent homogeneity from Escherichia coli cells harboring the genetic locus for this enzyme obtained from E. cloacae. The results of gel filtration experiments showed that indolepyruvate decarboxylase is a tetramer with an M(r) of 240,000. In the absence of thiamine pyrophosphate and Mg2+, the active tetramers dissociate into inactive monomers and dimers. However, the addition of thiamine pyrophosphate and Mg2+ to the inactive monomers and dimers results in the formation of active tetramers. These results indicate that the thiamine pyrophosphate-Mg2+ complex functions in the formation of the tetramer, which is the enzymatically active holoenzyme. The enzyme exhibited decarboxylase activity with indole-3-pyruvic acid and pyruvic acid as substrates, but no decarboxylase activity was apparent with L-tryptophan, indole-3-lactic acid, beta-phenylpyruvic acid, oxalic acid, oxaloacetic acid, and acetoacetic acid. The Km values for indole-3-pyruvic acid and pyruvic acid were 15 microM and 2.5 mM, respectively. These results indicate that indole-3-acetic acid biosynthesis in E. cloacae is mediated by indolepyruvate decarboxylase, which has a high specificity and affinity for indole-3-pyruvic acid.
Human Monoclonal Antibodies That Inhibit Binding of Hepatitis C Virus E2 Protein to CD81 and Recognize Conserved Conformational Epitopes (2000)

The intrinsic variability of hepatitis C virus (HCV) envelope proteins E1 and E2 complicates the identification of protective antibodies. In an attempt to identify antibodies to E2 proteins from divergent HCV isolates, we produced HCV E2 recombinant proteins from individuals infected with HCV genotypes 1a, 1b, 2a, and 2b. These proteins were then used to characterize 10 human monoclonal antibodies (HMAbs) produced from peripheral B cells isolated from an individual infected with HCV genotype 1b. Nine of the antibodies recognize conformational epitopes within HCV E2. Six HMAbs identify epitopes shared among HCV genotypes 1a, 1b, 2a, and 2b. Six, including five broadly reactive HMAbs, could inhibit binding of HCV E2 of genotypes 1a, 1b, 2a, and 2b to human CD81 when E2 and the antibody were simultaneously exposed to CD81. Surprisingly, all of the antibodies that inhibited the binding of E2 to CD81 retained the ability to recognize preformed CD81-E2 complexes generated with some of the same recombinant E2 proteins. Two antibodies that did not recognize preformed complexes of HCV 1a E2 and CD81 also inhibited binding of HCV 1a virions to CD81. Thus, HCV-infected individuals can produce antibodies that recognize conserved conformational epitopes and inhibit the binding of HCV to CD81. The inhibition is mediated via antibody binding to epitopes outside of the CD81 binding site in E2, possibly by preventing conformational changes in E2 that are required for CD81 binding.
Grid-scale fluctuations and forecast error in wind power (2016)

Wind power fluctuations at the turbine and farm scales are generally not expected to be correlated over large distances. When power from distributed farms feeds the electrical grid, fluctuations from various farms are expected to smooth out. Using data from the Irish grid as a representative example, we analyze wind power fluctuations entering an electrical grid. We find that not only are grid-scale fluctuations temporally correlated up to a day, but they possess a self-similar structure-a signature of long-range correlations in atmospheric turbulence affecting wind power. Using the statistical structure of temporal correlations in fluctuations for generated and forecast power time series, we quantify two types of forecast error: a timescale error (e t ) that quantifies deviations between the high frequency components of the forecast and generated time series, and a scaling error (e z ) that quantifies the degree to which the models fail to predict temporal correlations in the fluctuations for generated power. With no a priori knowledge of the forecast models, we suggest a simple memory kernel that reduces both the timescale error (e t ) and the scaling error (e z ).
Status Of The Hughes Charge-Coupled-Device-Addressed Liquid Crystal Light Valve (1987)

This paper discusses the present state of development of the Hughes charge-coupled-device-addressed liquid crystal light valve (CCD LCLV). The device is based on the photoactivated silicon LCLV and is suitable for a range of applications, including adaptive optics and as a programmable mask for optical data processing systems.
Microfluidic Device for Aptamer-Based Cancer Cell Capture and Genetic Mutation Detection (2018)

We present a microfluidic device for specifically capturing cancer cells and isolating their genomic DNA (gDNA) for specific amplification and sequence analysis. To capture cancer cells within the device, nucleic acid aptamers that specifically bind to cancer cells were immobilized within a channel containing micropillars designed to increase capture efficiency. The captured cells were lysed in situ, and their gDNA was isolated by physical entanglement within a second smaller-dimensioned micropillar array. This type of isolation allows the gDNA to be retained and purified within the channel and enables amplification and analysis to be performed on the gDNA without the loss of the original template. We developed a technique for selectively amplifying genes from whole gDNA using multiple displacement amplification. The amplified gene samples were sequenced, and the resulting sequence information was compared against the known wild-type gene to identify any mutations. We have tested cervical and ovarian cancer cells for mutations in the TP53 gene using this technology. This approach offers a way to monitor multiple genetic mutations in the same small population of cells, which is beneficial given the wide diversity in cancer cells, and therefore it requires very few cells to be extracted from a patient sample.
Estimation of Jones matrix, birefringence and entropy using Cloude-Pottier decomposition in polarization-sensitive optical coherence tomography (2016)

Estimation of polarimetric parameters has been a fundamental issue to assess biological tissues that have form birefringence or polarization scrambling in polarization-sensitive optical coherence tomography (PS-OCT). We present a mathematical framework to provide a maximum likelihood estimation of the target covariance matrix and its incoherent target decomposition to estimate a Jones matrix of a dominant scattering mechanism, called Cloude-Pottier decomposition, thereby deriving the phase retardation and the optic axis of the sample. In addition, we introduce entropy that shows the randomness of the polarization property. Underestimation of the entropy at a low sampling number is mitigated by asymptotic quasi maximum likelihood estimator. A bias of the entropy from random noises is corrected to show only the polarization property inherent in the sample. The theory is validated with experimental measurements of a glass plate and waveplates, and applied to the imaging of a healthy human eye anterior segment as an image filter.