gebhart/patrepeval huggingface dataset:
On the origins of esterases. (1988)

Comparisons among the primary sequences of five cloned eukaryotic esterases reveal two distinct lineages, neither bearing any significant overall sequence similarity to the functionally related serine protease multigene family. We have not eliminated the possibility that the esterases may have residual conformational similarities to the serine proteases. However, our profile analysis and analyses of the predicted conformations of the esterases reveal little similarity to the serine proteases. Four of the esterase proteins share 27%-53% overall sequence similarity and evidence of a catalytic mechanism involving the same Arg-Asp-Ser or His-Asp-Ser charge relay. We propose that these four esterases, three of them cholinesterases, form part of a multigene family essentially separate from the serine proteases.
Carotid plaque computed tomography imaging in stroke and nonstroke patients (2008)

Patients with acute carotid stroke demonstrate significant differences in the appearance of their carotid wall ipsilateral to the side of their infarct, when compared with either nonacute carotid stroke patients or the carotid wall contralateral with the infarct side.
Identification and Characterization of a Novel Gene, C13orf25 , as a Target for 13q31-q32 Amplification in Malignant Lymphoma (2004)

The amplification at 13q31-q32 has been reported in not only hematopoietic malignancies but also in other solid tumors. We identified previously frequent amplification of chromosomal band 13q31-q32 in 70 cases of diffuse large B-cell lymphoma patients by conventional comparative genomic hybridization analysis. In an attempt to identify a candidate gene within this region, we used array comparative genomic hybridization and fluorescent in situ hybridization to map the 13q31-q32 amplicon. We then screened the 65 expressed sequence tags and Glypican 5 (GPC5) by reverse transcription-PCR and Northern blotting. As a result, we identified a novel gene, designated Chromosome 13 open reading frame 25 (C13orf25), which was overexpressed in B-cell lymphoma cell lines and diffuse large B-cell lymphoma patients with 13q31-q32 amplifications. However, GPC5, which has been reported to be a target gene for 13q31-q32 amplification, was truncated in one cell line, Rec1, possessing the amplification, and its expression in various cell lines with amplification at 13q31-q32 was not significantly different from that in other cell lines without amplification, suggesting that GPC5 is not likely to be the candidate gene. Additional analysis identified two major transcripts in the C13orf25 gene. The two transcripts A and B predicted open reading frames of 32 and 70-amino acid polypeptides, respectively. The former has been reported as bA121J7.2, which is conserved among species. Transcript-B also contained seven mature microRNAs in its untranslated region. These results suggest that the C13orf25 gene is the most likely candidate gene for the 13q31-q32 amplicon found in hematopoietic malignancies.
Wearable and wireless time-domain near-infrared spectroscopy system for brain and muscle hemodynamic monitoring (2020)

We present a wearable time-domain near infrared spectroscopy (TD-NIRS) system (two wavelengths, one detection channel), which fits in a backpack and performs real-time hemodynamic measurements on the brain and muscle tissues of freely moving subjects. It can provide concentration values of oxygenated hemoglobin (O<sub>2</sub>Hb), deoxygenated hemoglobin (HHb), total hemoglobin (tHb = O<sub>2</sub>Hb + HHb) and tissue oxygen saturation (StO<sub>2</sub>). The system is battery-operated and can be wirelessly controlled. By following established characterization protocols for performance assessment of diffuse optics instruments, we achieved results comparable with state-of-the-art research-grade TD-NIRS systems. We also performed <i>in-vivo</i> measurements such as finger tapping (motor cortex monitoring), breath holding (prefrontal cortex monitoring and forearm muscle monitoring), and outdoor bike riding (vastus lateralis muscle monitoring), in order to test the system capabilities in evaluating both muscle and brain hemodynamics.
<title>Optical coherence tomography based projected index computed tomography</title> (2007)

Projected index computed tomography (PICT) is an emerging noninvasive imaging technique that can provide tomographic mapping of sample's refractive index. In this paper, we report a PICT system developed on the basis of a fiber-optic OCT system. The tomographic mapping is reconstructed with convolution back projection algorithm using a series of angular projection data collected by optical coherence tomography (OCT) at sequential orientations. Measurement of refractive index distribution of a glass tube is carried out. The result shows that the developed system has high resolution and sensitivity to discriminate tube boundaries. With index information involved, the reconstructed PICT image is free of distortions, which are inherent artifacts of conventional OCT image.
Preparation of block copolymer vesicles in solution (2004)

Abstract Block copolymer vesicles can be prepared in solution from a variety of different amphiphilic systems. Polystyrene‐ block ‐poly(acrylic acid), polystyrene‐ block ‐poly(ethylene oxide), and many other block copolymer systems can produce vesicles of a wide range of sizes; those in the range of 100–1000 nm have been explored extensively. Different factors, such as the absolute and relative block lengths, the presence of additives (ions, homopolymers, and surfactants), the water content in the solvent mixture, the nature and composition of the solvent, the temperature, and the polydispersity of the hydrophilic block, provide control over the types of vesicles produced. Their high stability, resistance to many external stimuli, and ability to package both hydrophilic and hydrophobic compounds make them excellent candidates for use in the medical, pharmaceutical, and environmental fields. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 923–938, 2004
Reduction of insulin gene transcription in HIT-T15 beta cells chronically exposed to a supraphysiologic glucose concentration is associated with loss of STF-1 transcription factor expression. (1995)

Chronic exposure of HIT-T15 beta cells to elevated glucose concentrations leads to decreased insulin gene transcription. The reduction in expression is accompanied by diminished binding of a glucose-sensitive transcription factor (termed GSTF) that interacts with two (A+T)-rich elements within the 5' flanking control region of the insulin gene. In this study we examined whether GSTF corresponds to the recently cloned insulin gene transcription factor STF-1, a homeodomain protein whose expression is restricted to the nucleus of endodermal cells of the duodenum and pancreas. We found that an affinity-purified antibody recognizing STF-1 supershifted the GSTF activator complex formed from HIT-T15 extracts. In addition, we demonstrated a reduction in STF-1 mRNA and protein levels that closely correlated with the change in GSTF binding in HIT-T15 cells chronically cultured under supraphysiologic glucose concentrations. The reduction in STF-1 expression in these cells could be accounted for by a change in the rate of STF-1 gene transcription, suggesting a posttranscriptional control mechanism. In support of this hypothesis, no STF-1 mRNA accumulated in HIT-T15 cells passaged in 11.1 mM glucose. The only RNA species detected was a 6.4-kb STF-1 RNA species that hybridized with 5' and 3' STF-1-specific cDNA probes. We suggest that the 6.4-kb RNA represents an STF-1 mRNA precursor and that splicing of this RNA is defective in these cells. Overall, this study suggests that reduced expression of a key transcriptional regulatory factor, STF-1, contributes to the decrease in insulin gene transcription in HIT-T15 cells chronically cultured in supraphysiologic glucose concentration.
In vivo suppression of injury-induced vascular smooth muscle cell accumulation using adenovirus-mediated transfer of the herpes simplex virus thymidine kinase gene. (1994)

Restenosis, a process characterized in part by excessive smooth muscle cell (SMC) proliferation in areas of vascular injury, occurs in up to 50% of patients undergoing balloon angioplasty. In an effort to develop a treatment strategy for restenosis, we constructed a replication-deficient recombinant adenovirus (AdMLP.HSTK) containing the herpes simplex virus thymidine kinase gene (HSV tk). This viral gene product phosphorylates the prodrug ganciclovir to form a nucleoside analog that inhibits DNA synthesis. Cultured primary rat SMCs infected with AdMLP.HSTK were completely growth-inhibited by incubation in ganciclovir-containing medium. In addition, when only a portion of the SMC population received the HSV tk transgene, an inhibitory effect on neighboring SMCs was evident. Evaluation of this strategy in vivo using a rat carotid balloon injury model demonstrated that local infection of injured arteries with AdMLP.-HSTK followed by 2 weeks of systemic ganciclovir treatment significantly (P < 0.01) reduced injury-induced SMC accumulation. In contrast, there was no suppression of injury-induced SMC accumulation in animals infected with AdMLP.HSTK but not receiving ganciclovir or in those animals infected with a control adenovirus and either treated or not treated with ganciclovir. These results demonstrate the potential utility of adenovirus-mediated gene transfer for treatment of restenosis after balloon injury.
Upregulation of Reg 1α and GW112 in the epithelium of inflamed colonic mucosa (2001)

Selective expression of Reg 1alpha and GW112 genes in the crypt epithelium of inflamed colonic mucosa suggests the important regulatory functions of these genes.
Ischaemic preconditioning for liver transplantation (2008)

There is currently no evidence to support or refute the use of ischaemic preconditioning in donor liver retrievals. Further studies are necessary to identify the optimal ischaemic preconditioning stimulus. Further randomised clinical trials are necessary to evaluate the role of ischaemic preconditioning in donor liver retrievals involving a period of warm reperfusion, following ischaemic preconditioning during donor liver retrieval.
Real-time deformation and fracture in a game environment (2009)

This paper describes a simulation system that has been developed to model the deformation and fracture of solid objects in a real-time gaming context. Based around a corotational tetrahedral finite element method, this system has been constructed from components published in the graphics and computational physics literatures. The goal of this paper is to describe how these components can be combined to produce an engine that is robust to unpredictable user interactions, fast enough to model reasonable scenarios at real-time speeds, suitable for use in the design of a game level, and with appropriate controls allowing content creators to match artistic direction. Details concerning parallel implementation, solver design, rendering method, and other aspects of the simulation are elucidated with the intent of providing a guide to others wishing to implement similar systems. Examples from in-game scenes captured on the Xbox 360, PS3, and PC platforms are included.
The use of deconvolution and total least squares in recovering a radiation detector line spread function (1998)

We present a method for obtaining the line spread function (LSF) of any radiation detector from measured data. The problem of finding a LSF is essentially a discrete deconvolution from known values of the input (Monte Carlo generated data) and the output (measured data) which can be put into matrix form. We applied the total least squares (TLS) method which is particularly useful when there are errors in both the input and output data. Results from computer simulation as well as from actual data are shown. In a practical application, however, our technique is currently limited by the ability of the Monte Carlo data to simulate correctly the inherent data from the head of the linear accelerator (linac). To overcome this difficulty we have solved by deconvolution and TLS for a more realistic inherent beam profile of our linac using the information from both profile data as measured with film and the film densitometer response function. The LSF of the densitometer was estimated with a simple method of direct measurement of a slit image and a full width at half maximum (FWHM) of 0.997 mm was recorded. Additionally, using the knowledge of this realistic inherent profile of the linac, a blurring function representing the finite source size effect missing in our current Monte Carlo profile simulation was determined. Finally, with the realistic inherent beam profile we have applied the deconvolution and TLS method to find a LSF for the Markus chamber and found a resulting FWHM of 5.39 mm. The TLS approach for deconvolving can find a useful application for both finding the LSF and correcting for the detector size effect once its LSF is known. This type of correction is required when a high spatial resolution is needed (e.g., in small field off-axis measurements). Convolved and measured profiles are also presented to illustrate the effect of the blurring due to different LSFs.
Stearoyl-coenzyme A desaturase 1 inhibition and the metabolic syndrome: considerations for future drug discovery (2010)

SCD1 inhibitors continue to hold promise as metabolic syndrome therapeutics; yet consideration must be taken to avoid the proinflammatory side-effects secondary to accumulation SCD1 substrates (SFAs).
Stock Index Options Pricing Models (2013)

The purpose of this research is to apply stochastic modeling methods to determine the prices of stock index options. In this paper, three models are implemented and compared for accuracy based on the S&P 500 index (SPX) options data for 1996. These models include the Black-Scholes Model (BS), a stochastic volatility model (SV) which accounts for volatility in the underlying stock price, and a stochastic volatility model with jump in the underlying stock price (SVJ). This jump in the stock index prices is accounted for in the SVJ model using a compound Poisson distribution. The SV model is nested in the SVJ model, with jump-related parameters being set to zero. These three mathematical models are implemented in MATLAB. The models are calibrated using data from one day at a time for the SPX options on the Chicago Board Options Exchange based on the criteria of the least sum of squared errors. The models are tested for consistency by calibrating and measuring the squared error for each day in an entire year's worth of option price data.
Asthma Control during and after Cessation of Regular Beta 2 -Agonist Treatment (1993)

It has been suggested that regular treatment with high doses of beta 2-agonists might result in poorer control of asthma and increased bronchial responsiveness. We have examined change in FEV1 (delta FEV1), bronchial reactivity, peak expiratory flow (PEF), and symptoms during and after 3 wk of regular treatment with a relatively low dose of albuterol and broxaterol, a new beta 2-agonist. Eleven subjects 18 to 50 yr of age with mild asthma inhaled albuterol (200 micrograms), broxaterol (400 micrograms), or placebo three times a day for 3 wk with a 2- to 4-wk run-in/washout period between treatments. Ipratropium bromide was allowed for symptomatic relief. The PD20 (dose of histamine causing a 20% fall in FEV1) was measured before and 11, 35, and 59 h after cessation of treatment and a bronchodilator dose-response study before and 83 h after cessation of treatment. Change from baseline after albuterol and broxaterol are compared with change after placebo. Diurnal change in PEF (amplitude % mean) increased during treatment with albuterol by 6.5% (95% CI, 1.7-12.3; p < 0.02) mainly because of a fall in morning PEF. Cessation of treatment with both beta 2-agonists was associated with a fall in FEV1 and PD20 compared with placebo.(ABSTRACT TRUNCATED AT 250 WORDS)
Gas-Phase Substituent Effects in Highly Electron-Deficient Systems. I. Intrinsic Stabilities of 1-Aryl-1-(trifluoromethyl)ethyl Cations (1996)

Abstract The relative stabilities of 1-aryl-1-(trifluoromethyl)ethyl cations were determined by measuring the proton-transfer equilibria of 1-aryl-1-(trifluoromethyl)ethylenes or the chloride-transfer equilibria of 1-aryl-1-(trifluoromethyl)ethyl chlorides in the gas phase. The stability of 1-phenyl-1-(trifluoromethyl)ethyl cation was found to be 16 kcal mol−1 lower than that of the α-cumyl (1-phenyl-1-methylethyl) cation. The substituent effect on the stability of this cation can be correlated in terms of the Yukawa–Tsuno equation, giving an r+ of 1.41 and a ρ of −10.0 (in log K/Ko−1 unit). While the ρ value is nearly identical to that of the α-cumyl cation series, the r+ value is remarkably higher than the value of unity for the α-cumyl cation, indicating that such a highly electron-deficient carbocation system should be characterized by an extremely large r+ value compared with that of the stable α-cumyl cation. In addition, this r+ value agrees with that for the SN1 solvolysis of 1-aryl-1-(trifluoromethyl)ethyl tosylates. Such agreement of the r+ values between the gas phase and solvolysis reactions has been generally observed for the benzylic carbocation systems. It is concluded that the enhanced r+ value for the solvolysis of 1-aryl-1-(trifluoromethyl)ethyl tosylates must reflect the intrinsic resonance demand characteristic of the parent 1-phenyl-1-(trifluoromethyl)ethyl cation, itself, and that the extremely large ρ+ values given by a simple correlation with σ+ (r+ = 1) are an artifact due to an improper analysis of underestimating the resonance demand for such highly deactivated substrates.
3D Porosity Modeling of a Carbonate Reservoir Using Continuous Multiple-Point Statistics Simulation (2006)

Summary Training images are numerical representations of geological conceptual models that provide prior information on reservoir architecture. A new emerging geostatistical approach named multiple-point statistics (MPS) simulation allows extracting multiple-point structures from such training images and anchoring these structures to the data actually observed in the reservoir. By reproducing multiple-point statistics inferred from training images, MPS enables the modeling of complex curvilinear structures (e.g., sinuous channels) in a much more geologically realistic way than traditional two-point statistics (variogram-based) techniques. However, in the original MPS implementation, all MPS moments computed from the training image are exported to the reservoir model without processing, which allows simulating only categorical or discretized variables. This implementation is appropriate with clastic reservoirs for which, typically, depositional facies are simulated first using MPS, then porosity and permeability are distributed within each simulated facies using traditional variogram-based techniques. But for reservoirs, in particular in carbonate environments, where porosity and permeability trends/cycles are not closely tied to any facies distribution, simulating porosity/permeability directly using corresponding continuous training images appears to be a more suitable approach. In this paper, a new filter-based implementation of MPS, named filtersim, is proposed to reproduce features from continuous variable training images. First, a set of general filters is applied to the training image to transform (summarize) each training pattern into a set of scores accounting for different aspects of the pattern, such as north-south and east-west gradients and curvatures. The training patterns are classified in the score space and grouped into a small number of similarity classes. The simulation consists then of visiting each grid node along a random path, identifying the similarity class that best fits to the local conditioning data, and patching a pattern drawn from that selected similarity class. In our study, this new approach was applied to model the 3D porosity distribution of a carbonate reservoir in Kazakhstan. First, the original "categorical" MPS program snesim was used to model the two main reservoir regions, platform and slope, where the spatial porosity distribution is characterized by significantly different features. Interpreted well markers and seismic data were used to condition the modeling of these two regions. Then porosity was distributed in the platform region using the "continuous" filter-based MPS program filtersim, as described previously. The 3D training images used in that second step displayed porosity trends/cycles controlled by the type of geological sedimentation process believed to have occurred in the reservoir.
Directed evolution of a genetic circuit (2002)

The construction of artificial networks of transcriptional control elements in living cells represents a new frontier for biological engineering. However, biological circuit engineers will have to confront their inability to predict the precise behavior of even the most simple synthetic networks, a serious shortcoming and challenge for the design and construction of more sophisticated genetic circuitry in the future. We propose a combined rational and evolutionary design strategy for constructing genetic regulatory circuits, an approach that allows the engineer to fine-tune the biochemical parameters of the networks experimentally in vivo. By applying directed evolution to genes comprising a simple genetic circuit, we demonstrate that a nonfunctional circuit containing improperly matched components can evolve rapidly into a functional one. In the process, we generated a library of genetic devices with a range of behaviors that can be used to construct more complex circuits.
Charge‐Conversional Polyionic Complex Micelles—Efficient Nanocarriers for Protein Delivery into Cytoplasm (2009)

Abstract Special delivery! Polyionic complex (PIC) micelles that contain the charge‐conversional moieties citaconic amide or cis ‐aconitic amide were developed for cytoplasmic protein delivery. The increase of the charge density on the protein cargo helped the stability of the PIC micelles without cross‐linking, and the charge‐conversion in endosomes induced the dissociation of the PIC micelles to result in efficient endosomal release (see picture). magnified image
New and emerging HDAC inhibitors for cancer treatment (2014)

Epigenetic enzymes are often dysregulated in human tumors through mutation, altered expression, or inappropriate recruitment to certain loci. The identification of these enzymes and their partner proteins has driven the rapid development of small-molecule inhibitors that target the cancer epigenome. Herein, we discuss the influence of aberrantly regulated histone deacetylases (HDACs) in tumorigenesis. We examine HDAC inhibitors (HDACis) targeting class I, II, and IV HDACs that are currently under development for use as anticancer agents following the FDA approval of two HDACis, vorinostat and romidepsin.