gebhart/patrepeval huggingface dataset:
Role of glucose carrier in human erythrocyte water permeability (1992)

Although the transport properties of human erythrocyte water channels have been well characterized, the identity of the protein(s) mediating water flow remains unclear. Recent evidence that glucose carriers can conduct water raised the possibility that the glucose carrier, which is abundant in human erythrocytes, is the water channel. To test this possibility, water permeabilities and glucose fluxes were measured in large unilamellar vesicles (LUV) containing human erythrocyte lipid alone (lipid LUV), reconstituted purified human erythrocyte glucose carrier (Glut1 LUV), or reconstituted glucose carrier in the presence of other human erythrocyte ghost proteins (ghost LUV). In glucose and ghost LUV, glucose carriers were present at 25% of the density of native erythrocytes, were oriented randomly in the bilayer, and exhibited characteristic inhibition of glucose flux when exposed to cytochalasin B. Osmotic water permeability (Pf, in centimeters per second; n = 4) averaged 0.0012 +/- 0.00033 in lipid LUV, 0.0032 +/- 0.0015 in Glut1 LUV, and 0.006 +/- 0.0014 in ghost LUV. Activation energies of water flow for the three preparations ranged between 10 and 13 kcal/mol; p-(chloromercuri)benzenesulfonate (pCMBS), an organic mercurial inhibitor of erythrocyte water channels, and cytochalasin B did not alter Pf. These results indicate that reconstitution of glucose carriers at high density increases water permeability but does not result in water channel activity. However, because the turnover number of reconstituted carriers is reduced from that of native carriers, experiments were also performed on erythrocyte ghosts with intact water channel function. In ghosts, Pf averaged 0.038 +/- 0.013 (n = 9), while the activation energy for water flow averaged 3.0 +/- 0.3 kcal/mol.(ABSTRACT TRUNCATED AT 250 WORDS)
Cutaneous innervation in sensory neuropathies (1995)

Skin biopsies stained with the sensitive panaxonal marker anti-PGP9.5 demonstrated significant reduction in intraepidermal fibers in sensory neuropathies. This simple and repeatable technique is a reliable method for quantitation of small cutaneous sensory fibers. In addition, skin biopsies may be useful in assessing the course and spatial distribution of involvement in peripheral nerve disease.
High power electrostatic motor with micropatterned electret on shrouded turbine (2005)

The paper describes the fabrication process of a shrouded turbine and surface modification using fluorinated silane coupling agents to stabilize the charges of a silicon-dioxide electret. The shrouded turbine was fabricated by cavity-through etching, which is deep reactive ion etching (DRIE) through a wafer having cavities made by DRIE and fusion bonding. By using this process, a shrouded turbine with little eccentricity was obtained without damaging the inner structures such as blades and flow ways. Charge stability of electrets was deteriorated by miniaturizing the size. The charge deterioration was caused by leakage current through the surface. To decrease the surface conduction, the surface was terminated by fluorine with silane coupling agents. As a result, the charge stability of a silicon-dioxide electret was improved 100 times compared with HMDS (hexamethyldisilazane) treatment.
Mapping Sonic Hedgehog-Receptor Interactions by Steric Interference (2000)

We have defined regions in the Sonic hedgehog (Shh) molecule that are important for Patched (Ptc) receptor binding by targeting selected surface amino acid residues with probes of diverse sizes and shapes and assessing the effects of these modifications on function. Eleven amino acid residues that surround the surface of the protein were chosen for these studies and mutated to cysteine residues. These cysteines were then selectively modified with thiol-specific probes, and the modified proteins were tested for hedgehog receptor binding activity and their ability to induce differentiation of C3H10T1/2 cells into osteoblasts. Based on these analyses, approximately one-third of the Shh surface can be modified without effect on function regardless of the size of the attachment. These sites are located near to where the C terminus protrudes from the surface of the protein. All other sites were sensitive to modification, indicating that the interaction of Shh with its primary receptor Ptc is mediated over a large surface of the Shh protein. For sites Asn-50 and Ser-156, function was lost with the smallest of the probes tested, indicating that these residues are in close proximity to the Ptc-binding site. The epitope for the neutralizing mAb 5E1 mapped to a close but distinct region of the structure. The structure-activity data provide a unique view of the interactions between Shh and Ptc that is not readily attainable by conventional mapping strategies.
Structural requirements for C3d,g/Epstein-Barr virus receptor (CR2/CD21) ligand binding, internalization, and viral infection. (1990)

The structure of CR2, the human C3d,g/EBV receptor (CR2/CD21) consists of 15 or 16 60-70 amino acid repeats called short consensus repeats (SCRs) followed by a transmembrane and a 34-amino acid intracytoplasmic domain. Functions of CR2 include binding the human complement component C3d,g when it is covalently attached to targets or cross-linked in the fluid phase. In addition, CR2 binds the Epstein-Barr virus (EBV) and mediates internalization of EBV and subsequent infection of cells. In order to explore functional roles of the repetitive extracytoplasmic SCR structure and the intracytoplasmic domain of CR2, we have created truncated CR2 (rCR2) mutants bearing serial deletions of extracytoplasmic SCRs and also the intracytoplasmic tail. We then stably transfected these rCR2 mutants into two cell lines, murine fibroblast L cells and human erythroleukemic K562 cells. Phenotypic analysis of these expressed mutants revealed that 1) The C3d,g- and EBV-binding sites are found in the two amino-terminal SCRs of CR2, 2) expression of SCRs 3 and 4 is further required for high affinity binding to soluble cross-linked C3d,g, 3) the intracytoplasmic domain of CR2 is not required for binding C3d,g or EBV but is necessary for internalization of cross-linked C3d,g as well as for EBV infection of cells, 4) monoclonal anti-CR2 antibodies with similar activities react with single widely separated epitopes, and 5) no functional roles can yet be clearly assigned to SCRs 5-15, as rCR2 mutants not containing these SCRs show no major differences from wild-type rCR2 in binding or internalizing cross-linked C3d,g or mediating EBV binding and infection.
Physical chemistry of macromolecules: basic principles and issues (1995)

Preface to the Second Edition. Preface to the First Edition. 1. Introduction. 2. Syntheses of Macromolecular Compounds. 3. Distribution of Molecular Weight. 4. Macromolecular Thermodynamics. 5. Chain Configuration. 6. Liquid Crystals. 7. Rubber Elasticity. 8. Viscosity and Viscoelasticity. 9. Osmotic Pressure. 10. Diffusion. 11. Sedimentation. 12. Optical Rotatory Dispersion and Circular Dichroism. 13. High-Performance Liquid Chromatography and Electrophoresis. 14. Light Scattering. 15. Fourier Series. 16. Small-Angle X-Ray Scattering, Neutron Scattering, and Laser Light Scattering. 17. Electronic and Infrared Spectroscopy. 18. Protein Molecules. 19. Nuclear Magnetic Resonance. 20. X-Ray Crystallography. Author Index. Subject Index.
QDPSK signal transmission performance with postdetection selection diversity reception in land mobile radio (1991)

The bit error rate (BER) performance of 16-128 kb/s Nyquist raised-cosine filtered quaternary differential phase-shift keying (RC-QDPSK) signal transmission was experimentally investigated. Two-branch postdetection selection diversity reception was employed. Measured results are presented for the BER performance due to additive white Gaussian noise (AWGN), cochannel interference, and multipath channel delay spread. Field BER measurements were also conducted at a carrier frequency of 1.45 GHz in an area characterized by high-rise buildings and in an area surrounded by mountains. The results show that postdetection selection diversity is a simple yet powerful technique to improve the BER performance in fading mobile radio channels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Small Molecule–Gold Nanorod Conjugates Selectively Target and Induce Macrophage Cytotoxicity towards Breast Cancer Cells (2012)

Gold nanoparticles are known to activate anti-tumor potential in macrophage immune cells; however, the subsequent effects of these cells on others nearby are poorly understood. A novel gold-nanoparticle conjugate that selectively targets and induces cytotoxic activity of tumor-associated macrophages towards breast cancer cells in co-culture is synthesized. These constructs are promising new tools for studying fundamental biological interactions with nanoscale materials and candidates for emerging macrophage-mediated delivery applications.
Probing protein unfolding through monitoring cysteine alkylation by matrix-assisted laser desorption/ionisation mass spectrometry (2000)

Matrix-assisted laser desorption/ionisation mass spectrometry was used to monitor interaction between three proteins and two basic Immobiline chemicals (pK 10.3 and pK >12) commonly used in immobilised pH gradients (IPG). For two of the investigated proteins, the observed alkylation channels of the cysteine residues exhibited unmistakable response to their gradual denaturation following treatment with different concentrations (0-8 M) of two commonly used denaturants, urea and guanidine hydrochloride. Our assessment for protein unfolding is based on the number and relative intensity of the alkylation channels, yet the present mass spectrometry data are in good agreement with data based on optical rotatory dispersion, in which another approach was used to assess protein unfolding. Whether the present simple, fast and specific mass spectrometry method can be developed as a probe for monitoring folding/unfolding of cysteine-containing proteins can only be demonstrated by generating similar data for a larger number of proteins.
Evaluating security products with clinical trials (2009)

One of the largest challenges faced by purchasers of security products is evaluating their relative merits. While customers can get reliable information on characteristics such as runtime overhead, user interface, and support quality, the actual level of protection provided by different security products is mostly unranked—or, worse yet, ranked using criteria that do not generally reflect their performance in practice. Even though researchers have been working on improving testing methodologies, given the complex interactions of users, uses, evolving threats, and different deployment environments, there are fundamental limitations on the ability of lab-based measurements to determine real world performance. To address these issues, we propose an alternative evaluation method, computer security clinical trials. In this method, security products are deployed in randomly selected subsets of targeted populations and are monitored to determine their performance in normal use. We believe that clinical trials can provide solid evidence of the efficacy of security products, much as they have in the field of medicine. 1
High power, high efficiency antiguide laser arrays (1991)

An antiguide laser diode array has been fabricated which radiates a predominantly single lobe far field with a full-width at half-maximum of 1.5 times the diffraction limit at a continuous wave output power of 500 mW with a differential quantum efficiency of 50%. By spectrally resolving the far field of the device at high operating powers it is shown that the two longitudinal modes correspond to adjacent lateral modes of the array. The operation of the second lateral mode is the result of spatial hole-burning of the first optical mode.
Hepatocyte culture on biodegradable polymeric substrates (1991)

The interactions of primary rat liver cells with biodegradable polymeric substrates were investigated in vitro to assess the suitability of the polymer materials for use in cell transplantation devices. The kinetics of cell adhesion to, and the growth and biochemical function of cells maintained on, films formed from poly (D,L-lactic-co-glycolic acid, 88: 12) (PLGA) or from a 50/50 (w/w) blend of PLGA and poly (L-lactic acid) (PLLA) were evaluated in comparison to two control substrates, matrigel coated or collagen-coated polystyrene petri dishes. The rate of cell adhesion to both types of polymeric substrates was similar to the rate of adhesion to the collagen control substrate, but of the two polymers, only the blend was suitable for extended culture. Hepatocytes maintained on the polymer blend films showed retention of differentiated cell function as measured by the rate of albumin secretion-the rate of albumin secretion by cells on the films was the same as the rate for cells on matrigel and reached a level in the range of reported in vivo levels (140-160 microg/10(6) cells/24 h). In contrast, albumin secretion by hepatocytes maintained on collagen-coated polystyrene culture dishes declined over five days to a level one third that of the initial level and one fifth that of cells maintained on the polymer blend films on day five. Such retention of differentiated cell function by hepatocytes in culture has previously been observed only when hepatocytes were cultured in the presence of exogenous extracellular matrix proteins or were cocultured with another cell type. In addition to retention of differentiated function, the cells maintained on the polymer blend films also displayed rates of DNA synthesis similar to controls maintained on collagen-coated polystyrene, a substrate optimal for DNA synthesis.
Sparse Neural Networks With Large Learning Diversity (2011)

Coded recurrent neural networks with three levels of sparsity are introduced. The first level is related to the size of messages that are much smaller than the number of available neurons. The second one is provided by a particular coding rule, acting as a local constraint in the neural activity. The third one is a characteristic of the low final connection density of the network after the learning phase. Though the proposed network is very simple since it is based on binary neurons and binary connections, it is able to learn a large number of messages and recall them, even in presence of strong erasures. The performance of the network is assessed as a classifier and as an associative memory.
Single-chain MHC class II molecules induce T cell activation and apoptosis (1996)

MHC class II/peptide complexes displayed on the surface of APCs play a pivotal role in initiating specific T cell responses. Evidence is presented here that components of this heterotrimeric complex can be genetically linked into a single polypeptide chain. Soluble single-chain (sc) murine class II IA(d) molecules with and without covalently attached peptides were produced in a recombinant baculovirus-insect cell expression system. Correct conformation of these molecules was verified based on 1) reactivity to Abs directed against conformational epitopes in IA(d) and 2) peptide-specific recognition of the IA(d)/peptide complexes by T cells. Both sc class II molecules loaded the appropriate peptides and sc class II/peptide fusions were effective in stimulating T cell responses, including cytokine release and apoptosis. Mammalian cells were also found to be capable of expressing functional sc class II molecules on their cell surfaces. The findings reported here open up the possibility of producing large amounts of stable sc class II/peptide fusion molecules for structural characterization and immunotherapeutic applications.
Progestational agents for the prevention of preterm birth (2008)

Abstract In a risk/benefit analysis, currently the use of PAs used in women with a previous history of PTB appears to be worthwhile though the impact on the PTB rate may be minor since 80-90% of women who deliver preterm have no past history. PTB is a heterogeneous condition. With the exception of extremes of gestational age, PTB is due in equal parts to SPTL, preterm prelabour rupture of the membranes (PPROM) and elective PTB for fetomaternal indications. The assessment of the use of PAs to prevent PTB should only relate to previous and subsequent SPTL and not to PTB due to fetomaternal indications.
A Generalized Solution of the Orthogonal Procrustes Problem (1966)

A solution T of the least-squares problem AT = B + E , given A and B so that trace ( E′E )= minimum and T′T = I is presented. It is compared with a less general solution of the same problem which was given by Green [5]. The present solution, in contrast to Green's, is applicable to matrices A and B which are of less than full column rank. Some technical suggestions for the numerical computation of T and an illustrative example are given.
Compiling for EDGE Architectures (2006)

Explicit data graph execution (EDGE) architectures offer the possibility of high instruction-level parallelism with energy efficiency. In EDGE architectures, the compiler breaks a program into a sequence of structured blocks that the hardware executes atomically. The instructions within each block communicate directly, instead of communicating through shared registers. The TRIPS EDGE architecture imposes restrictions on its blocks to simplify the microarchitecture: each TRIPS block has at most 128 instructions, issues at most 32 loads and/or stores, and executes at most 32 register bank reads and 32 writes. To detect block completion, each TRIPS block must produce a constant number of outputs (stores and register writes) and a branch decision. The goal of the TRIPS compiler is to produce TRIPS blocks full of useful instructions while enforcing these constraints. This paper describes a set of compiler algorithms that meet these sometimes conflicting goals, including an algorithm that assigns load and store identifiers to maximize the number of loads and stores within a block. We demonstrate the correctness of these algorithms in simulation on SPEC2000, EEMBC, and microbenchmarks extracted from SPEC2000 and others. We measure speedup in cycles over an Alpha 21264 on microbenchmarks.
Gene Sequence and Properties of an s -Triazine Ring-Cleavage Enzyme from Pseudomonas sp. Strain NRRLB-12227 (1999)

Pesticides based on the s-triazine ring structure are widely used in cultivation of food crops. Cleavage of the s-triazine ring is an important step in the mineralization of s-triazine compounds and hence in their complete removal from the environment. Cyanuric acid amidohydrolase cleaves cyanuric acid (2,4,6-trihydroxy-s-triazine), which yields carbon dioxide and biuret; the biuret is subject to further metabolism, which yields CO(2) and ammonia. The trzD gene encoding cyanuric acid amidohydrolase was cloned into pMMB277 from Pseudomonas sp. strain NRRLB-12227, a strain that is capable of utilizing s-triazines as nitrogen sources. Hydrolysis of cyanuric acid was detected in crude extracts of Escherichia coli containing the cloned gene by monitoring the disappearance of cyanuric acid and the appearance of biuret by high-performance liquid chromatography (HPLC). DEAE and hydrophobic interaction HPLC were used to purify cyanuric acid amidohydrolase to homogeneity, and a spectrophotometric assay for the purified enzyme was developed. The purified enzyme had an apparent K(m) of 0.05 mM for cyanuric acid at pH 8.0. The enzyme did not cleave any other s-triazine or hydroxypyrimidine compound, although barbituric acid (2,4, 6-trihydroxypyrimidine) was found to be a strong competitive inhibitor. Neither the nucleotide sequence of trzD nor the amino acid sequence of the gene product exhibited a significant level of similarity to any known gene or protein.
Novel splice‐site mutation in ATP8B1 results in atypical Progressive Familial Intrahepatic Cholestasis Type 1 (2012)

This work expands the phenotypic spectrum of PFIC1, and highlights the overlap in clinical phenotype between Alagille syndrome and PFIC1. Knowledge of the causative mutation allows for carrier testing and prenatal diagnosis in this community.
Pharmacokinetic analysis of immunotoxin uptake in solid tumors: role of plasma kinetics, capillary permeability, and binding. (1990)

The delivery of cell-specific protein toxins to the interstitium of solid tumors was examined in athymic mice bearing s.c. human rhabdomyosarcoma (TE671) tumors. The toxins are diphtheria toxin (DT), Mr = 60,000, and an immunotoxin, Mr = 210,000. The immunotoxin is a chemical conjugate of a mutant DT defective in binding and a monoclonal antibody specific for the human transferrin receptor. The plasma, tumor, and muscle concentrations of DT, immunotoxin, and closely related nonbinding controls were measured 2, 6, and 24 h after i.v. injection into tumor-bearing mice. Both DT and immunotoxin are specific for the human xenograft in the mouse because DT is very toxic to human cells but not to murine cells and immunotoxin is directed against a human cell receptor. A compartmental pharmacokinetic model was developed for the analysis of the in vivo data to provide plasma-to-tissue transport constants (capillary permeability-area products), binding parameters (products of the association constant and the initial binding site concentration), and the interstitial fluid flow rate. The model also provides a simple mathematical framework for understanding the effect of these variables on the localization of macromolecules in tumors. The plasma-to-tissue transport constant of immunotoxin in TE671 tumor was 0.13 microliters/min/g, compared to 0.29 microliters/min/g for DT. However, despite the lower capillary permeability of the larger molecular weight toxin, the cumulative tumor exposure to immunotoxin was 80% higher than that to DT after 24 h. A longer plasma half-life and higher apparent in vivo binding parameter of immunotoxin compared to DT contributed to the higher tumor exposure. Plasma-to-tissue transport constants for tumor were 60 to 100% higher than those for muscle. This finding is consistent with observations by others that tumor vasculature is more permeable than are normal muscle capillaries. Also, the interstitial fluid flow of the tumor, 0.80 microliters/min/g, was higher than that of muscle, 0.58 microliters/min/g. The product of the binding affinity and binding site concentration for immunotoxin in vivo was 530 times lower than that predicted based on in vitro measurements. Lower expression of antigen binding sites, inaccessibility of binding sites in vivo, and degradation of the toxin are several possible factors that may account for the in vitro-in vivo differences in binding. This study illustrates the interrelationship of plasma kinetics, capillary permeability, and binding and their effects on toxin concentrations that are achieved in the tissue interstitium.
Development of defined and minimal media for the growth of the hyperthermophilic archaeon Pyrococcus furiosus Vc1 (1997)

The nutritional requirements of Pyrococcus furiosus were determined using extended continuous culture in the absence of elemental sulfur in an anaerobic gaslift bioreactor. Replacement of complex nutrients by maltose, amino acids and vitamins alone supported growth. When the organic components of this defined medium were optimised, equilibrium cell densities of 10 10 ml 31 were achieved. Selective feeding and withdrawal revealed requirements for L-proline, L-cysteine and D-biotin. Replacement of maltose by dextrin allowed growth in closed bottles on both the defined and minimal media, again in the absence of elemental sulfur. A simple procedure for the efficient plating of P. furiosus on solid media was also developed.
Glycemic Effect of a Single High Oral Dose of the Novel Sweetener Sucralose in Patients With Diabetes (1996)

The present results support the conclusion that sucralose consumption does not adversely affect short-term blood glucose control in patients with diabetes.