gebhart/patrepeval huggingface dataset:
Improvement of Intestinal Absorption of Pglycoprotein Substrate by Dtartaric Acid (2006)

The purpose of the present experiment was to examine the effects of D-tartaric acid (TA) on intestinal drug absorption under both in situ and in vitro experimental conditions. In the in vitro diffusion chamber experiments, TA (10 mM) added to the mucosal side of rat colon significantly decreased rhodamine123 (Rho 123) transport from the serosal to mucosal side. Since TA has been shown to change the integrity of the epithelial tight junctions in rat colon at low pH conditions, resulting in improved paracellular drug transport, the effect of TA on membrane resistance was examined at pH 7.4 in the present study. It was found that membrane resistance, an indicator of paracellular integrity, did not change at pH 7.4. In the in situ loop method, TA (20 mM) increased the absorption of Rho123 in both ileum and colon but not in jejunum. TA (20 mM) also increased the absorption of daunorubicin in the ileum, but TA (20 mM) did not change the expression level of P-glycoprotein (P-gp). TA (20 mM) significantly inhibited excretion of i.v.-administered Rho123 and daunorubicin into the ileal lumen. In conclusion, for the first time we demonstrated that TA increases the intestinal absorption of P-gp substrates Rho123 and daunorubicin, possibly by modulating the P-gp function without changing the expression level of P-gp in the rat intestine.
Low-power programmable routing circuitry for FPGAs (2005)

We propose two new FPGA routing switch designs that are programmable to operate in three different modes: high-speed, low-power or sleep. High-speed mode provides similar power and performance to a traditional routing switch. In low-power mode, speed is curtailed in order to reduce power consumption. Our first switch design reduces leakage power consumption by 36-40% in low-power vs. high-speed mode (on average); dynamic power is reduced by up to 28%. Leakage power in sleep mode is 61% lower than in high-speed mode. A second switch design offers a 36% smaller area overhead and reduces leakage by 28-30% in low-power vs. high-speed mode. The proposed switch designs require only minor changes to a traditional routing switch, making them easy to incorporate into current FPGA interconnect. The applicability of the new switches is motivated through an analysis of timing slack in industrial FPGA designs. Specifically, we show that a considerable fraction of routing switches may be slowed down (operate in low-power mode), without impacting overall design performance.
Clinical and genetic delineation of neurodegeneration with brain iron accumulation (2008)

Neurodegeneration with brain iron accumulation (NBIA) describes a group of progressive neurodegenerative disorders characterised by high brain iron and the presence of axonal spheroids, usually limited to the central nervous system. Mutations in the PANK2 gene account for the majority of NBIA cases and cause an autosomal recessive inborn error of coenzyme A metabolism called pantothenate kinase associated neurodegeneration (PKAN). More recently, it was found that mutations in the PLA2G6 gene cause both infantile neuroaxonal dystrophy (INAD) and, more rarely, an atypical neuroaxonal dystrophy that overlaps clinically with other forms of NBIA. High brain iron is also present in a portion of these cases. Clinical assessment, neuroimaging, and molecular genetic testing all play a role in guiding the diagnostic evaluation and treatment of NBIA.
Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl- d -erythritol kinase (2003)

4-Diphosphocytidyl-2C-methyl-d-erythritol kinase, an essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis, catalyzes the single ATP-dependent phosphorylation stage affording 4-diphosphocytidyl-2C-methyl-d-erythritol-2-phosphate. The 2-A resolution crystal structure of the Escherichia coli enzyme in a ternary complex with substrate and a nonhydrolyzable ATP analogue reveals the molecular determinants of specificity and catalysis. The enzyme subunit displays the alpha/beta fold characteristic of the galactose kinase/homoserine kinase/mevalonate kinase/phosphomevalonate kinase superfamily, arranged into cofactor and substrate-binding domains with the catalytic center positioned in a deep cleft between domains. Comparisons with related members of this superfamily indicate that the core regions of each domain are conserved, whereas there are significant differences in the substrate-binding pockets. The nonmevalonate pathway is essential in many microbial pathogens and distinct from the mevalonate pathway used by mammals. The high degree of sequence conservation of the enzyme across bacterial species suggests similarities in structure, specificity, and mechanism. Our model therefore provides an accurate template to facilitate the structure-based design of broad-spectrum antimicrobial agents.
Aryl Trihydroxyborates:  Easily Isolated Discrete Species Convenient for Direct Application in Coupling Reactions (2006)

A conceptually and practically simple alternative approach to the use of arylboron species as the organometallic component in cross-coupling processes is described whereby trihydroxyborate salts are isolated and directly employed. The protocol derives practical benefit from the ease and convenience of the isolation and subsequent use of the discrete borate salts, eliminates the need for additional base, and aids the use of correct reaction stoichiometry.
Side-Chain-Grafted Random Copolymer Brushes as Neutral Surfaces for Controlling the Orientation of Block Copolymer Microdomains in Thin Films (2006)

Random copolymers of P(S-r-MMA-r-HEMA)s with a distribution of surface reactive hydroxyl groups were synthesized to formulate neutral surface layers on a SiO2 substrate. The layers were designed to drive vertical orientation of lamellar microdomains in a top P(S-b-MMA) thin film. Copolymers with a styrene weight fraction (f(St)) of 0.58 and a HEMA fraction (f(HEMA)) ranging from 0.01 to 0.03, with a corresponding MMA fraction (f(MMA)) ranging from 0.41 to 0.39, in the P(S-r-MMA-r-HEMA) copolymer showed neutral surface characteristics. The morphology of block copolymer thin films was studied by scanning electron microscopy (SEM). P(S-r-MMA-r-HEMA) copolymers prepared by both living and classical free-radical polymerizations were equally effective in demonstrating the neutrality of the surface. These side-chain-grafted random copolymer brushes showed faster grafting kinetics than the end-chain-grafted P(S-r-MMA) because of multipoint attachment to the surface. The modified surfaces had a very thin layer of random copolymer brush (5-7 nm), which is desirable for effective pattern transfer. Furthermore, neutral surfaces could be obtained even when the grafting time was reduced to 3 h. These results indicate that the composition of the random copolymer brush, rather than its PDI or molecular weights, is the most important factor in controlling the neutrality of the surface. These results also demonstrate the feasibility of using a third comonomer (C) in the random copolymer brush P(A-r-B-r-C) to alter the interfacial and surface energies of a diblock copolymer (A-b-B).
Assigning distinct identities to sites on an anonymous distributed system (2003)

A distributed algorithm that assigns distinct and ordered identities to the sites of a connect anonymous distributed system is presented. The basis for this algorithm is the sequential distributed traversal scheme, the sequential aspect of which ensures that all sites are systematically visited in mutual exclusion. Such an algorithm allows the definition of sites to be independent of particular of initial values (as far as identities are concerned).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Content-based multimedia information retrieval (2006)

Extending beyond the boundaries of science, art, and culture, content-based multimedia information retrieval provides new paradigms and methods for searching through the myriad variety of media all over the world. This survey reviews 100+ recent articles on content-based multimedia information retrieval and discusses their role in current research directions which include browsing and search paradigms, user studies, affective computing, learning, semantic queries, new features and media types, high performance indexing, and evaluation techniques. Based on the current state of the art, we discuss the major challenges for the future.
Cell Surface Proteoglycans Are Necessary for A27L Protein-Mediated Cell Fusion: Identification of the N-Terminal Region of A27L Protein as the Glycosaminoglycan-Binding Domain (1998)

We previously showed that vaccinia virus infection of BSC40 cells was blocked by soluble heparin, suggesting that cell surface heparan sulfate mediates vaccinia virus binding (C.-S. Chung, J.-C. Hsiao, Y. -S. Chang, and W. Chang, J. Virol. 72:1577-1585, 1998). In this study, we extended our previous work and demonstrated that soluble A27L protein bound to heparan sulfate on cells and interfered with vaccinia virus infection at a postbinding step. In addition, we investigated the structure of A27L protein that provides for its binding to heparan sulfate on cells. A mutant of A27L protein, named D-A27L, devoid of a cluster of 12 amino acids rich in basic residues, was constructed. In contrast to the soluble A27L protein, purified D-A27L protein was inactive in all of our assays, including binding to heparin in vitro, binding to heparan sulfate on cells, and the ability to block virus infection. These data demonstrated that the N-terminal region acts as a glycosaminoglycan (GAG)-binding domain critical for A27L protein binding to cells. Previously A27L protein was thought to be involved in fusion of virus-infected cells induced by acid treatment. When we investigated whether cell surface GAGs also participate in A27L-dependent fusion, our results indicated that soluble A27L protein blocked cell fusion, whereas D-A27L protein did not. Taken together, the results therefore demonstrated that A27L-mediated cell fusion is triggered by its interaction with cell surface GAGs through the N-terminal domain.
Fabrication and Characterization of CMOS-MEMS Thermoelectric Micro Generators (2010)

This work presents a thermoelectric micro generator fabricated by the commercial 0.35 μm complementary metal oxide semiconductor (CMOS) process and the post-CMOS process. The micro generator is composed of 24 thermocouples in series. Each thermocouple is constructed by p-type and n-type polysilicon strips. The output power of the generator depends on the temperature difference between the hot and cold parts in the thermocouples. In order to prevent heat-receiving in the cold part in the thermocouples, the cold part is covered with a silicon dioxide layer with low thermal conductivity to insulate the heat source. The hot part of the thermocouples is suspended and connected to an aluminum plate, to increases the heat-receiving area in the hot part. The generator requires a post-CMOS process to release the suspended structures. The post-CMOS process uses an anisotropic dry etching to remove the oxide sacrificial layer and an isotropic dry etching to etch the silicon substrate. Experimental results show that the micro generator has an output voltage of 67 μV at the temperature difference of 1 K.
Defining the Bilin Lyase Domain:  Lessons from the Extended Phytochrome Superfamily (2000)

Through pattern searches of genomic databases, new members of the growing family of phytochrome-related genes were identified and used to construct a 130-180 amino acid motif that delimits the bilin lyase domain, a subdomain of the extended phytochrome family that is sufficient for covalent attachment of linear tetrapyrroles (bilins). To test this hypothesis, portions of locus sll0821, a novel phytochrome-related gene from Synechocystis sp. PCC6803 that encodes a large protein with two potential bilin binding sites, were amplified, and the recombinant apoproteins were tested for bilin binding and phytochrome photoactivity. Our experiments indicated that both sites of this protein, termed Cph2 for cyanobacterial phytochrome 2, possessed bilin lyase activity, revealing two distinct classes of bilin lyase domains--those whose bilin adducts are red, far-red reversible and a second class whose bilin adducts are nonphotochromic. Spectroscopic analysis of photochromic phycocyanobilin and fluorescent phycoerythrobilin adducts of a 24-kDa fragment of Cph2 definitively established that the motif identified by pattern searches represents a bona fide bilin lyase domain. Site-directed mutagenesis of highly conserved charged residues within bilin lyase domains of nearly all members of the extended phytochrome superfamily has identified a glutamate residue critical for bilin binding.
A decoupled coil detector array for fast image acquisition in magnetic resonance imaging (1991)

A method for magnetic resonance imaging (MRI) is investigated here, whereby an object is put under a homogeneous magnetic field, and the image is obtained by applying inverse source procedures to the data collected in an array of coil detectors surrounding the object. The induced current in each coil due to the precession of the magnetic dipole in each voxel depends on the characteristics of both the magnetic dipole frequency and strength, together with its distance from the coil, the coil direction in space, and the electrical properties of the coils. By calculating the induced current signals over an array of coil detectors, a relationship is established between the set of signals and the structure of the body under investigation. The linear relation can then be represented in matrix notation, and inversion of this matrix will produce an image of the body. Important problems which must be considered in the proposed method are signal-to-noise ratio (SNR) and coupling between adjacent coils. Solutions to these problems will provide a new method for obtaining an instantaneous image by NMR, with no need for gradient switching for encoding. A general algorithm for decoupling of the coils is presented and fast sampling of the signal, instead of filtering, is used in order to reduce both noise and numerical roundoff errors at the same time. Sensitivity considerations are made with respect to the number of coils that is required and its connection with coil radius and SNR. A computer simulation demonstrates the feasibility of this new modality. Based on the solutions presented here for the problems involved in the use of a large number of coils for a simultaneous recording of the signal, an improved method of multicoil recording is suggested, whereby it is combined with the conventional zeugmatographic method with read and phase gradients, to result in a novel method of magnetic resonance imaging. In the combined method, there are no phase-encoding gradients. Only a single slice-selecting gradient, to be followed by a single read-gradient. Instead of phase-encoding gradients, use is made of an equivalent number of coils. The number of coils now is reduced significantly. This method suggests a single slice image taken within a single echo time, and where a 128 x 128 resolution is possible with only 128 coils. The applicability of the method is based on a successful decoupling procedure for the detectors (coils and cables) and the availability of highly accurate, high-gain, low-noise amplifiers with a broad dynamic range.
Isolation and Partial Characterization of Three Cryptic Plasmids from Strains of Clostridium butyricum (1981)

Of seven strains of Clostridium butyricum examined, four contained covalently closed circular DNA molecules. The bacteriocinogenic strain C. butyricum NCIB 7423 carried two plasmids: pCB101 of molecular mass 3·9 megadaltons (5·6 × 103 bases) and pCB102 of molecular mass 5·2 megadaltons (7·4 × 103 bases). Plasmid pCB101 was not restricted by EcoRI which cleaved pCB102 at two sites; both plasmids were restricted by HindIII. The three other plasmid-bearing strains of C. butyricum (SA1, SA11 and NCTC 6084) each carried a single plasmid of molecular mass 4·3 megadaltons (6·2 × 103 bases) with a single cleavage site for EcoRI and four sites for HindIII, the fragments so produced from the three plasmids being indistinguishable on agarose gel electrophoretograms. It was concluded that the three strains harboured a common plasmid - pCB103.
Site-directed mutagenesis of conserved serines in rat histidase. Identification of serine 254 as an essential active site residue. (1994)

We have identified serine 254 as an essential residue in rat histidase (histidine ammonia-lyase, EC 4.3.1.3). Histidase and phenylalanine ammonia-lyase are the only two enzymes that have been postulated to require the modified amino acid, dehydroalanine, for enzyme activity. In the bacterial peptides nisin and subtilin, and in the pyruvoyl enzymes, the precursor for dehydroalanine is a serine. To determine whether serine may be the dehydroalanine precursor in rat histidase, we substituted four highly conserved serines with alanines, and expressed the mutated histidase cDNAs in COS cells, which have no endogenous histidase activity. Substitution of serines 223, 254, 508, and 533 resulted in the production of approximately equal amounts of histidase protein with histidase activities of 2.4, 0.0, 75, and 16%, respectively. The abrogation of histidase activity by the substitution of alanine for serine 254, together with the modification by L-cysteine of the corresponding residue in Pseudomonas putida histidase (Hernandez, C., Stroh, J. G., and Phillips, A. T. (1993) Arch. Biochem. Biophys. 307, 126-132), is strong evidence that this residue is the precursor of the essential electrophilic moiety of histidase.
Usage Based Life Prediction Uncertainty Assessments and Fleet Management Impact For Gas Turbine Engines (2010)

With the evolution of more sophisticated digital electronic engine controls (DEEC) and databased logistic systems the ability to track asset consumption in aero engine across all its major rotating components has evolved to become dramatically more accurate, allowing for usage-specific engine, part, and location-specific life calculations. Considerable prior work regarding the deterministic usage based calculation of life consumed has been published but the development of a methodology to manage the uncertainty in the life calculation has not been equally explored. This paper will discuss an approach to managing the intrinsic uncertainty within the calculation of stresses and temperatures within the usage algorithms and their associated impact on life.
The use of active shape models for making thickness measurements of articular cartilage from MR images (1997)

Previously reported studied to quantify articular cartilage have used labor-intensive manual or semi-automatic data-driven techniques, demonstrating high accuracy and precision. However, none has been able to automate the segmentation process. This paper describes a fast, automatic, model-based approach to segmentation and thickness measurement of the femoral cartilage in 3D T1-weighted images using active shape models (ASMs). Systematic experiments were performed to assess the accuracy and precision of the technique with in vivo images of both normal and abnormal knees. Segmentation accuracy was determined by comparing the results of the segmentation with the boundaries delineated by a radiologist. The mean error in locating the boundary was 0.57 pixels. To assess the precision of the measurement technique, the mean thickness of the femoral cartilage was calculated for repeated scans of five healthy volunteers. A mean coefficient of variation (CV) of 2.8% was obtained for the thickness measurements.
Pseudomonas aeruginosa 142 uses a three-component ortho-halobenzoate 1,2-dioxygenase for metabolism of 2,4-dichloro- and 2-chlorobenzoate (1994)

Cell extracts of Pseudomonas aeruginosa 142, which was previously isolated from a polychlorinated biphenyl-degrading consortium, were shown to degrade 2,4-dichlorobenzoate, 2-chlorobenzoate, and a variety of other substituted ortho-halobenzoates by a reaction that requires oxygen, NADH, Fe(II), and flavin adenine dinucleotide. By using extracts that were chromatographically depleted of chlorocatechol and catechol 1,2-dioxygenase activities, products of the initial reaction with 2,4- or 2,5-dichlorobenzoate and 2-chlorobenzoate were identified by mass spectrometry as 4-chlorocatechol and catechol. In contrast to the well-characterized benzoate dioxygenases or the recently described 2-halobenzoate 1,2-dioxygenase from P. cepacia 2CBS (S. Fetzner, R. Müller, and F. Lingens, J. Bacteriol. 174:279-290, 1992) that possess two protein components, the P. aeruginosa enzyme was resolved by ion-exchange chromatography into three components, each of which is required for activity. To verify the distinct nature of this enzyme, we purified, characterized, and identified one component as a ferredoxin (M(r), approximately 13,000) containing a single [2Fe-2S] Rieske-type cluster (electron paramagnetic resonance spectroscopic values of gx = 1.82, gy = 1.905, and gz = 2.02 in the reduced state) that is related in sequence to ferredoxins found in the naphthalene and biphenyl three-component dioxygenase systems. By analogy to these enzymes, we propose that the P. aeruginosa ferredoxin serves as an electron carrier between an NADH-dependent ferredoxin reductase and the terminal component of the ortho-halobenzoate 1,2-dioxygenase. The broad specificity and high regiospecificity of the enzyme make it a promising candidate for use in the degradation of mixtures of chlorobenzoates.
Scientific approach to the 1-h cycling world record: a case study (2000)

The purpose of this study was to describe the physiological and aerodynamic characteristics and the preparation for a successful attempt to break the 1-h cycling world record. An elite professional road cyclist (30 yr, 188 cm, 81 kg) performed an incremental laboratory test to assess maximal power output (W(max)) and power output (W(OBLA)), estimated speed (V(OBLA)), and heart rate (HR(OBLA)) at the onset of blood lactate accumulation (OBLA). He also completed an incremental velodrome (cycling track) test (VT1), during which V(OBLAVT1) and HR(OBLAVT1) were measured and W(OBLAVT1) was estimated. W(max) was 572 W, W(OBLA) 505 W, V(OBLA) 52.88 km/h, and HR(OBLA) 183 beats/min. V(OBLAVT1), HR(OBLAVT1), and W(OBLAVT1) were 52.7 km/h, 180 beats/min, and 500.6 W, respectively. Drag coefficient and shape coefficient, measured in a wind tunnel, were 0. 244 and 0.65 m(2), respectively. The cyclist set a world record of 53,040 m, with an estimated average power output of 509.5 W. Based on direct laboratory data of the power vs. oxygen uptake relationship for this cyclist, this is slightly higher than the 497. 25 W corresponding to his oxygen uptake at OBLA (5.65 l/min). In conclusion, 1) the 1-h cycling world record is the result of the interaction between physiological and aerodynamic characteristics; and 2) performance in this event can be predicted using mathematical models that integrate the principal performance-determining variables.
Visualizing and Understanding Convolutional Networks (2013)

Large Convolutional Network models have recently demonstrated impressive classification performance on the ImageNet benchmark. However there is no clear understanding of why they perform so well, or how they might be improved. In this paper we address both issues. We introduce a novel visualization technique that gives insight into the function of intermediate feature layers and the operation of the classifier. We also perform an ablation study to discover the performance contribution from different model layers. This enables us to find model architectures that outperform Krizhevsky \etal on the ImageNet classification benchmark. We show our ImageNet model generalizes well to other datasets: when the softmax classifier is retrained, it convincingly beats the current state-of-the-art results on Caltech-101 and Caltech-256 datasets.