gebhart/patrepeval huggingface dataset:
The functional and physical relationship between the DRA bicarbonate transporter and carbonic anhydrase II (2002)

COOH-terminal cytoplasmic tails of chloride/bicarbonate anion exchangers (AE) bind cytosolic carbonic anhydrase II (CAII) to form a bicarbonate transport metabolon, a membrane protein complex that accelerates transmembrane bicarbonate flux. To determine whether interaction with CAII affects the downregulated in adenoma (DRA) chloride/bicarbonate exchanger, anion exchange activity of DRA-transfected HEK-293 cells was monitored by following changes in intracellular pH associated with bicarbonate transport. DRA-mediated bicarbonate transport activity of 18 +/- 1 mM H+ equivalents/min was inhibited 53 +/- 2% by 100 mM of the CAII inhibitor, acetazolamide, but was unaffected by the membrane-impermeant carbonic anhydrase inhibitor, 1-[5-sulfamoyl-1,3,4-thiadiazol-2-yl-(aminosulfonyl-4-phenyl)]-2,6-dimethyl-4-phenyl-pyridinium perchlorate. Compared with AE1, the COOH-terminal tail of DRA interacted weakly with CAII. Overexpression of a functionally inactive CAII mutant, V143Y, reduced AE1 transport activity by 61 +/- 4% without effect on DRA transport activity (105 +/- 7% transport activity relative to DRA alone). We conclude that cytosolic CAII is required for full DRA-mediated bicarbonate transport. However, DRA differs from other bicarbonate transport proteins because its transport activity is not stimulated by direct interaction with CAII.
Assessment of Liver Function in Primary Cultures of Hepatocytes Using Diethoxy (5,6) Chloromethylfluorescein and Confocal Laser Scanning Microscopy (1998)

A method is presented which can be used to assess the function of hepatocytes in complex culture configurations without disrupting the integrity of the cell environment. It utilises a fluorescent probe for cytochrome P450 dependent mixed function oxidase (MFO) activity diethoxy (5,6) chloromethylfluorescein, and confocal laser scanning microscopy. The MFO activity of individual cells in primary cultures of intact hepatocytes can be detected in situ, and quantified by image analysis. This may be a valuable means of monitoring the effect of culture conditions on the function of bioartificial liver devices, and could be used to assess the need for effective oxygenation of cells, the influence of shear stress and of exposure to patient serum during clinical use.
Precise subpixel position measurement with linear interpolation of CMOS sensor image data (2011)

In the industrial automation it is often required to provide high precision measurements of objects positions and sizes. As a reasonable contactless method measurement based on digital image processing is used. In praxis the image-based measurement of physical quantities can replace expensive mechanical sensors. From the construction point of view it is reasonable to use CMOS image sensor for camera construction. The basic drawback of these sensors is not homogenous pixel photosensitivity distribution. This feature is especially crucial when sub-pixel measurement resolution required. Linear interpolation as one of possible methods results estimation on CMOS image data is discussed in this paper. Having realized a real-world experiment with a precise micro-positioning unit the practical results of measurement are presented and limitations of method discussed.
The forward EEG solutions can be computed using artificial neural networks (2000)

Study of electroencenphalography (EEG) is the one of the most utilized methods in both basic brain research and clinical diagnosis of neurological disorders. Recent technological advances in computer and electronic systems have allowed the EEG to be recorded from large electrode arrays. Modeling the brain waves using a head volume conductor model provides an effective method to localize functional generators within the brain. However, the forward solutions to this model, which represent theoretical potentials in response to current sources within the volume conductor, are difficult to compute because of time-consuming numerical procedures utilized in either the boundary element method (BEM) or the finite element method (FEM). This paper presents a novel computational approach using an artificial neural network (ANN) to map two vectors of forward solutions. These two vectors correspond to different head models but with respect to the same current source. The input vector to the ANN is based on the spherical head model, which can be computed efficiently but involves large errors. The output vector from the ANN is based on the spheroidal model, which is more precise, but difficult to compute directly using the traditional means. Our experiments indicate that this ANN approach provides a remarkable improvement over the BEM and FEM methods: 1) the mean-square error of computation was only approximately 0.3% compared to the exact solution; 2) the online computation was extremely efficient, requiring only 168 floating point operations per channel to compute the forward solution, and 10.2 K-bytes of storage to represent the entire ANN. Using this approach it is possible to perform real-time EEG modeling accurately on personal computers.
Development of a genetically engineered vaccine against feline leukemia virus infection (1991)

A genetically engineered subunit vaccine against FeLV infection was developed. The protective immunogen in the vaccine was a purified recombinant protein containing the entire amino acid sequence of FeLV subgroup A gp70 envelope protein. The optimal adjuvant was determined to be a highly purified saponin, QS-21, derived from Quillaja saponaria Molina. A vaccine formulation containing the recombinant protein, QS-21, and aluminum hydroxide was tested in specific-pathogen-free kittens and was shown to induce neutralizing antibodies as well as appreciable antibody responses to native gp70 by enzyme immunoassay and protein (western) immunoblot analysis and of whole virus preparations.
Analysis of Serum Cytokines in Patients with Severe Acute Respiratory Syndrome (2004)

Severe acute respiratory syndrome (SARS) is an acute infectious disease of the respiratory system. Although a novel coronavirus has been identified as the causative agent of SARS, the pathogenic mechanisms of SARS are not understood. In this study, sera were collected from healthy donors, patients with SARS, patients with severe SARS, and patients with SARS in convalescence. The serum concentrations of interleukin-1 (IL-1), IL-4, IL-6, IL-8, IL-10, tumor growth factor beta (TGF-beta), tumor necrosis factor alpha (TNF-alpha), and gamma interferon (IFN-gamma) were measured by enzyme-linked immunosorbent assays (ELISA). The concentrations of IL-1 and TNF-alpha were not significantly different in different groups. The IL-6 concentration was increased in SARS patients and was significantly elevated in severe SARS patients, but the IL-6 concentrations were similar in convalescent patients and control subjects, suggesting that there was a positive relationship between the serum IL-6 concentration and SARS severity. The concentrations of IL-8 and TGF-beta were decreased in SARS patients and significantly reduced in severe SARS patients, but they were comparable in convalescent SARS patients and control subjects, suggesting that there was a negative relationship between the IL-8 and TGF-beta concentrations and SARS severity. The concentrations of IFN-gamma, IL-4, and IL-10 showed significant changes only in convalescent SARS patients. The IFN-gamma and IL-4 levels were decreased, while the levels of IL-10 were increased, and the differences between convalescent SARS patients and other patient groups were statistically significant. These results suggest that there are different immunoregulatory events during and after SARS and may contribute to our understanding of the pathogenesis of this syndrome.
Several Common HLA-DR Types Share Largely Overlapping Peptide Binding Repertoires (1998)

The peptide binding specificities of HLA-DRB1*0401, DRB1*0101, and DRB1*0701 have been analyzed by the use of large collections of synthetic peptides corresponding to naturally occurring sequences. The results demonstrated that nearly all peptides binding to these DR molecules bear a motif characterized by a large aromatic or hydrophobic residue in position 1 (Y, F, W, L, I, V, M) and a small, noncharged residue in position 6 (S, T, C, A, P, V, I, L, M). In addition, allele-specific secondary effects and secondary anchors were defined, and these parameters were utilized to derive allele-specific motifs and algorithms. By the combined use of such algorithms, peptides capable of degenerate DRB1*0101, DRB1*0401, and DRB1*0701 binding were identified. Additional experiments utilizing a panel of quantitative assays specific for nine additional common DR molecules identified a large set of DR molecules, which includes at least the DRB1*0101, DRB1*0401, DRB1*0701, DRB5*0101, DRB1*1501, DRB1*0901, and DRB1*1302 allelic products, characterized by overlapping peptide-binding repertoires. These results have implications for understanding the molecular interactions involved in peptide-DR binding, as well as the genetic and structural basis of MHC polymorphism. These results also have potential practical implications for the development of epitope-based prophylactic and therapeutic vaccines.
Floating-point precision tuning using blame analysis (2016)

While tremendously useful, automated techniques for tuning the precision of floating-point programs face important scalability challenges. We present Blame Analysis, a novel dynamic approach that speeds up precision tuning. Blame Analysis performs floating-point instructions using different levels of accuracy for their operands. The analysis determines the precision of all operands such that a given precision is achieved in the final result of the program. Our evaluation on ten scientific programs shows that Blame Analysis is successful in lowering operand precision. As it executes the program only once, the analysis is particularly useful when targeting reductions in execution time. In such case, the analysis needs to be combined with search-based tools such as Precimonious. Our experiments show that combining Blame Analysis with Precimonious leads to obtaining better results with significant reduction in analysis time: the optimized programs execute faster (in three cases, we observe as high as 39.9% program speedup) and the combined analysis time is 9x faster on average, and up to 38x faster than Precimonious alone.
The Airway Epithelium is Central to the Pathogenesis of Asthma (2008)

Asthma is an inflammatory disorder principally involving the conducting airways and characterised by infiltration of the airway wall with a range of inflammatory cells driven in large part by activation of Th2-type lymphocytes, mast cells and eosinophils. However a key component of asthma is the structural change that involves all of the elements of the airway wall. Here evidence is presented to suggest that the airway epithelium in asthma is fundamentally abnormal with increased susceptibility to environmental injury and impaired repair associated with activation of the epithelial-mesenchymal trophic unit (EMTU). In addition to adopting an activated phenotype, the barrier function of the epithelium is impaired through defective tight junction formation thereby facilitating penetration of potentially toxic or damaging environmental insults. Activated and repairing epithelial cells generate a range of growth factors that are involved in the early life origins of this disease as well as its progression in the form of mucous metaplasia and airway wall remodeling. By placing the epithelium at the forefront of asthma pathogenesis, different approaches to treatment can be devised focused more on protecting vulnerable airways against environmental injury rather than focusing on suppressing airway inflammation or manipulating the immune response.
Nucleic acid analysis (1991)

It seems almost ridiculous to start this chapter by stating that there are two nucleic acids, ribo- and deoxyribo-nucleic acids, RNA and DNA respectively, as everyone knows this. However, I had to start somewhere. DNA is the custodian of all the fundamental data (but not all the information, it's that distinction again) required to construct most biological entities be these E. coli, amoebae, daffodils, elephants or humans. It is the 'Encyclopaedia Biologica' which has the inherent capacity within its structure to be replicated exactly (Watson and Crick, 1953). The retroviruses are the exceptions in which the genetic material is RNA, and these organisms use the DNA of a cell in their replicative process.
Permeation of water through some hydrogels (1965)

The permeability to water and the average pore radius of transparent hydrogels from glyceryl methacrylate (GMA), 2-hydroxyethyl methacrylate (HEMA), propylene glycol monoacrylate (PGMA), and a polyelectrolyte complex were determined. The transport process was found to be a predominantly viscous flow in the polyelectrolyte complex and in the more dilute GMA hydrogels (74–94% water), but in HEMA hydrogel (40% water), and PGMA hydrogels (40–60% water), diffusion seemed to play a more important part in the movement of water through the gel. These hydrogels are potentially useful for surgical implants in the cornea. A comparison is made with the flow conductivity of the corneal stroma at normal hydration.
Design and performance of a multiple element slab waveguide spectrograph for multimode fiber-optic WDM systems (1993)

A new type of compact (<7 cm/sup 2/) multiple element slab waveguide spectrograph suitable for medium resolution fiber-optic wavelength division multiplexing (WDM) applications in the 700 nm to 900 nm optical band is described. The spectrograph consists of a replicated diffraction grating formed on the convex edge of a multilayer glass-ceramic slab waveguide stack The grating design, based on an aberration corrected derivative of the classic Rowland spectrometer, was first verified holographically, and then implemented by replication from a ruled master grating. A combination of thick-film solder glass glazing, lamination, optical finishing and grating replication was chosen to produce a multiple element spectrograph that enables accurate spectral referencing, and can be interfaced by a passive optical fiber array and detector array alignment procedures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rationally Designed PI3Kα Mutants to Mimic ATR and Their Use to Understand Binding Specificity of ATR Inhibitors (2017)

ATR, a protein kinase in the PIKK family, plays a critical role in the cell DNA-damage response and is an attractive anticancer drug target. Several potent and selective inhibitors of ATR have been reported showing significant antitumor efficacy, with most advanced ones entering clinical trials. However, due to the absence of an experimental ATR structure, the determinants contributing to ATR inhibitors' potency and specificity are not well understood. Here we present the mutations in the ATP-binding site of PI3Kα to progressively transform the pocket to mimic that of ATR. The generated PI3Kα mutants exhibit significantly improved affinity for selective ATR inhibitors in multiple chemical classes. Furthermore, we obtained the X-ray structures of the PI3Kα mutants in complex with the ATR inhibitors. The crystal structures together with the analysis on the inhibitor affinity profile elucidate the roles of individual amino acid residues in the binding of ATR inhibitors, offering key insights for the binding mechanism and revealing the structure features important for the specificity of ATR inhibitors. The ability to obtain structural and binding data for these PI3Kα mutants, together with their ATR-like inhibitor binding profiles, makes these chimeric PI3Kα proteins valuable model systems for structure-based inhibitor design.
Isolation of Two Novel WNT Genes, WNT14 and WNT15, One of Which (WNT15) Is Closely Linked to WNT3 on Human Chromosome 17q21 (1997)

The Wnt gene family consists of at least 15 structurally related genes that encode secreted extracellular signaling factors. Wnt proteins function in a range of critical developmental processes in both vertebrates and invertebrates and are implicated in regulation of cell growth and differentiation in certain adult mammalian tissues, including the mammary gland. We have isolated a number of WNT sequences from human genomic DNA, two of which, designated WNT14 and WNT15, represent novel members of the Wnt gene family. We also isolated WNT sequences from human mammary cDNA and present evidence that WNT13 is expressed in human breast tissue, in addition to those previously described. WNT14 and WNT15 appear to have originated from an ancestral branch of the Wnt gene family that also includes the Wnt9 sequences found in jawless and cartilaginous fishes. A Wnt14 cDNA was also isolated from chicken and a partial Wnt15 sequence from mouse. We show that human WNT14 maps to chromosome 1 and that WNT15 maps distal to BRCA1 on chromosome 17q21, where it lies within 125 kb of another WNT family member, WNT3.
Effect of tension and placement of a prosthetic anterior cruciate ligament on the anteroposterior laxity of the knee (1992)

We wished to determine the optimal tension required to restore normal joint laxity to anterior cruciate ligament (ACL)-deficient knees using a braided polyethylene ACL prosthesis (PACL). In 10 cadaveric specimens, we measured the anteroposterior (AP) laxity of the intact knee at 10 degrees, 30 degrees, 60 degrees, and 90 degrees of flexion. The ACL was then removed and replaced with the PACL using tunnel-tunnel (T-T) and "over-the-top" (OTT) placement techniques. In both positions, the PACL was initially tensioned to 0, 9, 18, and 27 N with the knee flexed to 30 degrees. AP joint laxity was then measured at each flexion angle. With an increase in initial tension, there was a corresponding decrease in AP laxity. At 30 degrees and 90 degrees of flexion, AP laxity was not significantly different from normal using T-T placement and an initial tension of 0 N. At 90 degrees of flexion, AP laxity was not significantly different from normal using OTT placement at 0 or 9 N of initial tension. For both positions, all other tension levels and flexion angles constrained AP laxity. No laxity differences were detected between the OTT and T-T positions at any flexion angle. The variability in AP laxity of the T-T position was significantly greater than OTT. With a 150-N anterior shear force applied to the proximal tibia, the maximum tensions developed in the PACL were not significantly different between the two positions except at 90 degrees. The results suggest that implantation of the PACL is best performed using OTT positioning with an initial tension of 0 N applied at 30 degrees of knee flexion.
Novel Glycodendrimers Self-Assemble to Nanoparticles which Function as Polyvalent Ligands In Vitro and In Vivo (2002)

Size is important: Noncovalent nanoparticles are formed by the self-assembly of glycodendrimers containing both a ligand and a self-assembling moiety. Particle size reaches an optimum at the second and third generation, larger dendritic species show less efficient self-assembly. It is the nanoparticles, not the individual molecules, that governs their potency as polyvalent receptor blockers (see scheme), both in vitro and in vivo.
Asymptotic Performance of Linear Receivers in MIMO Fading Channels (2009)

Linear receivers are an attractive low-complexity alternative to optimal processing for multiple-antenna multiple-input multiple-output (MIMO) communications. In this paper, we characterize the information-theoretic performance of MIMO linear receivers in two different asymptotic regimes. For fixed number of antennas, we investigate the limit of error probability in the high-signal-to noise-ratio (SNR) regime in terms of the diversity-multiplexing tradeoff (DMT). Following this, we characterize the error probability for fixed SNR in the regime of large (but finite) number of antennas.As far as the DMT is concerned, we report a negative result: we show that both linear zero-forcing (ZF) and linear minimum mean- square error (MMSE) receivers achieve the same DMT, which is largely suboptimal even in the case where outer coding and deAcircnot coding is performed across the antennas. We also provide an apAcircnot proximate quantitative analysis of the markedly different behavior of the MMSE and ZF receivers at finite rate and nonasymptotic SNR, and show that while the ZF receiver achieves poor diversity at any finite rate, the MMSE receiver error curve slope flattens out progressively, as the coding rate increases. When SNR is fixed and the number of antennas becomes large, we show that the mutual information at the output of an MMSE or ZF linear receiver has fluctuations that converge in distribution to a Gaussian random variable, whose mean and variance can be characterized in closed form. This analysis extends to the linear reAcircnot ceiver case a well-known result previously obtained for the optimal receiver. Simulations reveal that the asymptotic analysis captures accurately the outage behavior of systems even with a moderate number of antennas.
Patterns of Axillary Lymph Node Metastasis in Breast Cancer (1995)

The pattern of axillary lymph node involvement was analyzed in a review of 377 cases of T1-4 breast cancers. Clinical judgment of the axillary status proved to be wrong in approximately one-third of the cases. In univariate analysis, a strong correlation (P < .01) between the number of involved nodes, tumor size, and blood vessel invasion was found. Other features of the primary tumor (lymphatic invasion, degree of differentiation, presence of necrotic areas) were related to a lesser degree (P < .05). While others (age, site) were not at all significant. However, the number of nodes resected proved to be the most important determinant of all (P = .003). Also, the simple distinction between node-negative and node-positive cases is strongly dependent on the extent of axillary dissection (P = .009). In multivariate analysis, only the number of resected nodes and T stage showed a good relationship with the number of positive nodes. Skip metastases above levels 1 and 2 were seen in only 2% of the cases. A clear influence of the number of invaded nodes on survival could be demonstrated. These findings are discussed, especially as concerns the technique, prognostic significance, and therapeutic usefulness of axillary dissection.
A Novel Dual Specificity Phosphatase SKRP1 Interacts with the MAPK Kinase MKK7 and Inactivates the JNK MAPK Pathway (2002)

Mitogen-activated protein kinases (MAPKs) are activated in response to various extracellular stimuli, and their activities are regulated by upstream activating kinases and protein phosphatases such as MAPK phosphatases (MKPs). We report the identification and characterization of a novel MKP termed SKRP1 (SAPK pathway-regulating phosphatase 1). It contains an extended active site sequence motif conserved in all MKPs but lacks a Cdc25 homology domain. Immunoblotting analysis revealed that SKRP1 is constitutively expressed, and its transcripts of 4.0 and 1.0 kb were detected in almost tissues examined. SKRP1 was highly specific for c-Jun N-terminal kinase (JNK) in vitro and effectively suppressed the JNK activation in response to tumor necrosis factor alpha or thapsigargin. Endogenous SKRP1 was present predominantly in the cytoplasm and co-localized with JNK. However, SKRP1 does not bind directly to its target JNK, but co-precipitation of SKRP1 with the MAPK kinase MKK7, a JNK activator, was found in vitro and in vivo. Furthermore, we found that SKRP1 did not interfere with the co-precipitation of MKK7 with JNK. Together, our findings indicate that SKRP1 interacts with its physiological substrate JNK through MKK7, thereby leading to the precise regulation of JNK activity in vivo.