gebhart/patrepeval huggingface dataset:
Individual VH genes detected with oligonucleotide probes from the complementarity-determining regions. (1990)

The germ-line and expressed Ig repertoire was examined with three oligonucleotide probes from the CDR regions of VH18/2, a VH gene from the largest human VH gene family, VHIII. Each oligonucleotide probe detected small numbers of germ-line bands (1-5) under conditions in which single base differences can be detected; more than half of these bands were polymorphic. The combined results from pairs of oligonucleotides from CDR1 and CDR2 identified a single band on Southern blots, as did a probe from the 5' end of CDR2. This band contains the 18/2 germ-line gene. The nucleotide sequence of expressed VH genes that hybridized to both CDR probes or to the 5' CDR2 probe were greater than or equal to 97% homologous to 18/2 in both the framework and CDR regions. This group of closely related VH genes, the 18/2 CDR family, appears to be overexpressed. The role of polymorphisms and differential expression of individual V genes in multigenic autoimmune diseases, as well as the organization and expression of individual V genes, can be examined with pairs of oligonucleotides from CDR1 and the 3' end of CDR2, or with probes from the 5' end of CDR2.
Human Preproparathyroid Hormone Synthesized inEscherichia coliis Transported to the Surface of the Bacterial Inner Membrane but Not Processed to the Mature Hormone* (1987)

cDNA encoding human preproPTH (hpreproPTH) was expressed in Escherichia coli to study the processing of the precursor to hPTH and its secretion by the bacterial secretory apparatus. We first constructed hybrid genes that differed randomly in the distance between the E. coli lac promoter's ribosomal binding site and DNA encoding a fusion protein with beta-galactosidase activity and the prepro sequence of hpreproPTH on the aminoterminus. Starting with clones identified as efficient producers of beta-galactosidase on indicator agar plates, the coding sequence for hpreproPTH was reconstituted intact. In a different construction we placed the hpreproPTH coding sequence downstream from the lac promoter at a distance of 12 base pairs from the ribosomal binding site. PTH immunoreactive proteins from multiple clones were identified by protein gel electrophoresis and by protein microsequencing. PTH-related proteins encoded by different plasmids were shown to be hpreproPTH with amino-terminal extensions of either two or four amino acids and as authentic hpreproPTH. Two hPTH fragments, hPTH(3-84) and hPTH(8-84), were also observed. The trypsin accessibility of hpreproPTH and of the two hPTH fragments in pulse-chase, cell-fractionation experiments using intact and lysed spheroplasts lets us conclude that the mammalian signal sequence directs hpreproPTH to the surface of the spheroplast membrane but is not appropriately cleaved by the signal peptidase.
Bulk acoustic wave-coupled resonator filters: Concept, design, and application (2011)

Bulk-acoustic-wave-coupled resonator filters is an emerging technology that is capable of meeting increasingly ambitious demands of wireless applications by addressing performance, chip size, and die cost. This article outlines the fundamental design principles of these filters. A major consideration of filter design is the choice of the coupling structure between the two vertically stacked resonators. This can be either a multilayer Bragg coupler or a novel structure using a single layer of a very low acoustic impedance material. It is demonstrated how spurious modes are related to the dispersion diagram and how they affect the passband characteristics. For the suppression of these spurious modes suitable edge termination techniques are discussed. Based on optimized coupler performance and known parasitic effects, we analyze circuit design methods for microwave filters and duplexers with specific passband, roll-off, and wideband responses. We show as example a miniature 2.0 × 1.6 mm2 Universal Mobile Telecommunication System (UMTS) Band1 duplexer fabricated using the coupler resonator technology. © 2011 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2011.
DFT Modulated Filter Bank Design for Oversampled Subband Systems (1998)

Filter banks are widely used in digital signal processing, often integrated in a multirate scheme, to reduce the implementation cost and to improve algorithmic performance. DFT modulated filter banks are commonly used to design oversampled subband schemes. Oversampled subband schemes are attractive as they trade off between complexity gain and aliasing distortion. Ideally, the overall effect of a subband system is that of a pure delay, i.e. the subband system is perfectly reconstructing. In this paper we present design techniques for perfect and nearly perfect reconstruction oversampled DFT modulated filter banks. One of the disadvantages of a perfect reconstruction filter bank design is that the stopband attenuation of the filters is typically small, which could have a negative impact on intermediate subband operations such as subband adaptive filtering. Nearly perfect reconstruction filter banks can be designed to overcome this problem, leading to a better performance of the intermediate algorithms.
Intramural Delivery of Rapamycin With α v β 3 -Targeted Paramagnetic Nanoparticles Inhibits Stenosis After Balloon Injury (2008)

Local intramural delivery of alpha(v)beta(3)-targeted rapamycin nanoparticles inhibited stenosis without delaying endothelial healing after balloon injury.
Solutions for Lipophilic Drugs: A Biodegradable Polymer Acting as Solvent, Matrix, and Carrier to Solve Drug Delivery Issues (2011)

The purpose of this study was to investigate the polyester hexylsubstituted poly(lactide) (hexPLA) as a possible solvent for lipophilic substances and excipient for pharmaceutical formulations. HexPLA is a biodegradable and semi-solid polymer, which allows the incorporation of active substances by simple mixing and local or systemic application to the patient through injection. The solvent behavior of hexPLA was investigated by adding the lipophilic dye Sudan III to the polymer matrix and optical monitoring of the dissolution process over time by microscopy. As a drug, the antipsychotic compound haloperidol was analyzed for its solubility in hexPLA of different molecular weights by preparing saturated solutions, and measuring the amount of incorporated drug with UV spectroscopy. The influence of the rate of solubilized to suspended drug on the burst release behavior of haloperidol from hexPLA-formulations was investigated in release tests. It is demonstrated that hexPLA dissolves both lipophilic substances, Sudan III and Haloperidol. In the molecular weight range between 2,000 g/mol and 10,000 g/mol, a lower molecular weight hexPLA resulted in a higher incorporation capacity for haloperidol. By changing from a suspension formulation of haloperidol to a solution formulation, the initial burst release established for classical PLA and PLGA systems could be minimized. HexPLA is shown to be a potent solvent and excipient for lipophilic drugs, allowing the initial burst of drug release to be modified and controlled.
Efficiency analysis of multihypothesis motion-compensated prediction for video coding (2000)

Overlapped block motion compensation or B-frames are examples of multihypothesis motion compensation where several motion-compensated signals are superimposed to reduce the bit-rate of a video codec. This paper extends the wide-sense stationary theory of motion-compensated prediction (MCP) for hybrid video codecs to multihypothesis motion compensation. The power spectrum of the prediction error is related to the displacement error probability density functions (pdfs) of an arbitrary number of hypotheses in a closed-form expression. We then study the influence of motion compensation accuracy on the efficiency of multihypothesis motion compensation as well as the influence of the residual noise level and the gain from optimal combination of N hypotheses. For the noise-free limiting case, doubling the number of (equally good) hypotheses can yield a gain of up to 1/2 bits/sample, while doubling the accuracy of motion compensation can additionally reduce the bit-rate by up to 1 bit/sample independent of N. For realistic noise levels, it is shown that the introduction of B-frames or overlapped block motion compensation can provide larger gains than doubling motion compensation accuracy. Spatial filtering of the motion-compensated candidate signals becomes less important if more hypotheses are combined. The critical accuracy beyond which the gain due to more accurate motion compensation is small moves to larger displacement error variances with increasing noise and increasing number of hypotheses N. Hence, sub-pel accurate motion compensation becomes less important with multihypothesis MCP. The theoretical insights are confirmed by experimental results for overlapped block motion compensation, B-frames, and multiframe motion-compensated prediction with up to eight hypotheses from ten previous frames.
Identification of the innate human immune response to surface-exposed proteins of coagulase-negative staphylococci (1991)

The presumed host defense against coagulase-negative staphylococci (ConS), recognized pathogens in hosts with compromised immunity or indwelling medical devices, is opsonophagocytosis. Targets for opsonization remain unclear. Using radiolabeling techniques, we identified the surface-exposed proteins of ConS and determined the innate humoral immune responses to them among healthy adults. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of surface proteins extrinsically labeled with 125I demonstrated 20 to 30 proteins with molecular weights of 15,000 to greater than 130,000. Five to ten of these proteins were immunogenic and recognized by normal human sera, including predominant 18-, 41-, 48-, and 51-kDa proteins. We also evaluated the humoral response of cancer patients with ConS bacteremia. Patients' sera obtained before bacteremic episodes demonstrated a pattern of reactivity similar to that of normal human sera. When patients' sera obtained after bacteremic episodes were used to determine whether an expanded immune response followed infection, only one of seven showed reactivity with more proteins than seen with the innate response. Western blot (immunoblot) analysis and whole-cell enzyme-linked immunosorbent assays were also evaluated. This study identifies (i) the surface-exposed proteins available for host interaction, (ii) the innate human antibody response to these proteins, and (iii) the immune response of cancer patients with ConS bacteremia.
The Role of Collinear Photons In the Rare Decay B to X_s ell ell (2008)

We review the phenomenology of the rare decay {bar B} {yields} X{sub s}{ell}{sup +}{ell}{sup -}. We present the results of a detailed phenomenological analysis and discuss the role of the decay in the search for new physics at present and future colliders. Moreover, we extensively elaborate on the size of electromagnetic logarithms ln(m{sub b}{sup 2}/m{sub {ell}}{sup 2}) in view of experimental cuts. We point out the differences in the analyses of BaBar and Belle and give suggestions on how to treat collinear photons in the experimental analyses. These recommendations correspond precisely to theoretical prescriptions and can be combined with measurements performed at a Super-B factory.
Role of MT-MMPs and MMP-2 in pancreatic cancer progression (2000)

Activation of matrix metalloproteinase-2 (MMP-2) by the membrane-type matrix metalloproteinases (MT-MMPs) has been associated with tumor progression. In the present study, we examined the role of MMP-2 and its activators MT1-MMP, MT2-MMP and MT3-MMP in pancreatic tumor cell invasion and the development of the desmoplastic reaction characteristic of pancreatic cancer tissues. Northern blot analyses revealed that transcript levels of MT1-MMP and MT2-MMP, but not MT3-MMP, were enhanced in pancreatic cancer tissues (n = 18) compared with both chronic pancreatitis (n = 9) and healthy pancreas (n = 9). A good correlation was found between MT1-MMP and both MMP-2 expression (p < 0.01) and activity in pancreatic cancer tissues. In addition, expression and activation of MMP-2 were strongly associated with the extent of the desmoplastic reaction in pancreatic cancer tissues. Invasion assays showed a good correlation between MMP-2 expression and activity and the invasive potential of pancreatic cancer cell lines. In cell lines with high levels of MMP-2 expression and activity, the MMP inhibitor Batimastat led to significant reduction of the number of invading cells. Our results suggest that MT1-MMP is involved in the progression of pancreatic cancer via activation of MMP-2. MMP-2 itself plays an important role in tumor cell invasion and appears to be associated with the development of the characteristic desmoplastic reaction in pancreatic cancer.
Tonabersat (SB‐220453) a novel benzopyran with anticonvulsant properties attenuates trigeminal nerve‐induced neurovascular reflexes (2001)

1. The effects of tonabersat (SB-220453) were evaluated on trigeminal nerve ganglion stimulation-induced sensory-autonomic neurovascular reflexes in the anaesthetized cat. Comparisons were made to intravenous administration of carabersat (SB-204269), and to valproate, gabapentin and lamotrigine following intraduodenal administration. 2. There were no effects on resting blood pressure, heart rate, carotid blood flow or carotid vascular resistance for any compound evaluated. 3. Trigeminal nerve ganglion stimulation increased carotid blood flow by 65% and reduced vascular resistance by 41% with minimal effect on blood pressure (< 10%) and no effect on heart rate. Intravenous infusion of tonabersat or carabersat (both 3.4 micromol h(-1)) produced time related reductions in stimulation-induced responses with a maximal inhibition (relative to control) of 30 +/- 7% (n=4), at 240 min for tonabersat and 33+/-4% (n=3) at 180 min for carabersat. Tonabersat (11.5 micromol h(-1)) produced a similar inhibitory effect (32 +/- 9%, n=4) after 120 min of infusion. 4. Following intraduodenal administration of tonabersat, the maximal inhibition of nerve stimulation-induced responses was 55 +/- 4% at 120 min (n=4) for tonabersat 10 mg kg(-1), and 24+/-2% after 180 min for 1 mg kg(-1) (n=4). 5. Intraduodenal administration of sodium valproate (10 or 100 mg kg(-1) n=4/group) had no effect on neurovascular reflexes. Maximal inhibition of nerve ganglion-stimulated reductions in carotid vascular resistance were observed at 150 min for lamotrigine (50 mg kg(-1), 52+/-12%, n=4) and gabapentin (100 mg kg(-1), 17+/-13%, n=3). Lamotrigine 10 mg kg(-1) produced 22+/-11% (n=3) inhibition after 180 min. 6. These data demonstrate blockade of trigeminal parasympathetic reflexes with tonabersat, carabersat and other anticonvulsants. These agents may therefore have therapeutic benefit in conditions where this type of reflex is evident.
Peptide mapping by limited proteolysis in sodium dodecyl sulfate and analysis by gel electrophoresis. (1977)

A rapid and convenient method for peptide mapping of proteins has been developed. The technique, which is especially suitable for analysis of proteins that have been isolated from gels containg sodium dodecyl sulfate, involves partial enzymatic proteolysis in the presence of sodium dodecyl sulfate and analysis of the cleavage products by polyacrylamide gel electrophoresis. The pattern of peptide fragments produced is characteristic of the protein substrate and the proteolytic enzyme and is highly reproducible. Several common proteases have been used including chymotrypsin, Staphylococcus aureus protease, and papain.
Targeting the Hedgehog Pathway in Cancer: Can the Spines Be Smoothened? (2011)

Aberrant Hedgehog (Hh) pathway signaling has been suggested to play a role in the development of multiple solid tumors and hematologic malignancies. GDC-0449 is a novel first-in-human, first-in-class smoothened (SMO) inhibitor, which has completed its phase I evaluation and achieved proof of concept in tumors with Hh pathway mutations.
Scavenger receptor-like receptors for the binding of lipopolysaccharide and lipoteichoic acid to liver endothelial and Kupffer cells (2001)

This study was undertaken to identify the role of scavenger receptors in the catabolism of lipopolysaccharide (LPS) and lipoteichoic acid (LTA). LPS is mainly cleared from the blood by the liver. The Kupffer cells are primarily responsible for this clearance. Although several binding sites have been described for LPS and LTA, only CD14 is involved in LPS signalling. Scavenger receptor type A (SR-A) is expressed in the liver on endothelial cells and Kupffer cells, and macrosialin (class D scavenger receptor) is expressed on Kupffer cells. Fucoidin and poly-I are both good inhibitors of scavenger receptors. Fucoidin significantly reduced the serum clearance of [125I]-LPS and decreased liver uptake of [125I]-LPS by approximately 40%. Poly-I inhibited the binding of [125I]-LPS to isolated Kupffer and endothelial cells by 75%, while poly-A, a polyanionic substrate that does not block scavenger receptors, had no effect. LPS significantly inhibited the binding of acetylated LDL and oxidized LDL (two well-described scavenger receptor ligands) to isolated Kupffer and liver endothelial cells. OxLDL and acLDL did not affect the binding of LPS to these cells. We conclude that on both endothelial cells and Kupffer cells, LPS mainly binds to scavenger receptors, but SR-A and macrosialin contribute to a limited extent to the binding of LPS. Injection of LTA into C57Bl6 mice resulted in a maximal liver uptake of 20% of the injected dose. In the liver, 50% was bound by the Kupffer cells, 20% by parenchymal cells and 30% by liver endothelial cells. The contribution of SR-A to the plasma clearance of LTA was limited. A main component in the catabolism of LTA is the interaction of LTA with plasma lipoproteins, which limit the uptake of LTA by tissues and extend the plasma half-life of LTA.
Design, synthesis, and application of azabicyclo[X.Y.0]alkanone amino acids as constrained dipeptide surrogates and peptide mimics (2005)

Azabicyclo[X.Y.0]alkanone amino acids are challenging synthetic targets and useful tools for studying structure-activity relationships of native peptide ligands. They have been employed to increase potency and stability in conformationally rigid enzyme inhibitors and receptor ligands. Since last reviewed in 1997, activity in their synthesis and application has increased significantly and access is now available to a wider diversity of these peptide mimics. This review focuses on recent syntheses of these heterocyclic amino acids and their application in the investigation of biologically active peptides and peptide mimics.
Measurement Of Brain Microglial Proliferation Rates In Vivo: A Biomarker For Discovering Novel Anti‐Neuroinflammatory Agents (2006)

The objective of this study was to screen drugs in vivo for inhibition of neuroinflammation, using a recently developed stable isotope method. Microglia (MG), the resident immune cells of the brain, mediates neuroinflammation and contributes to the pathogenesis of many diseases, including Alzheimer’s, multiple sclerosis and stroke. MG proliferation was measured by incorporation of 2 H from heavy water ( 2 H 2 O) into the deoxyribose moiety of DNA, after administration of lipopolysaccharide (LPS, 1 mg/kg, i.p). Follow‐up studies were in the experimental autoimmune encephalomyelitis (EAE) model. MG were isolated from the brain, as CD11b + cells (LPS model) or as F4/80 + /CD45 low cells by flow cytometry (EAE model). Male mice were treated with drugs of different classes for 7 days while receiving 2 H 2 O (8% in drinking water). Minocycline (45 mg/kg, i.p.) and dexamethasone (5 mg/kg) inhibited MG proliferation. In the initial screen of drugs, treatment with 13‐cis‐retinoic acid (Accutane ® , 40 mg/kg) significantly decreased LPS‐induced MG proliferation. Follow‐up studies in EAE confirmed inhibition of MG proliferation. Etiocholanedione combined with low‐dose minocycline (30 mg/kg) inhibited MG proliferation. No effects were seen with aspirin, calcitriol, clofibrate, enalapril, ibuprofen, imipramine, ketoconazole or rosiglitazone. In summary, 2 H 2 O labeling of DNA is a high‐throughput, quantitative and highly reproducible method for measuring MG proliferation, and is useful for screening and discovering novel anti‐neuroinflammatory drugs. Support: KineMed, Inc.
SAVI: Synthetic apertures for long-range, subdiffraction-limited visible imaging using Fourier ptychography (2017)

Synthetic aperture radar is a well-known technique for improving resolution in radio imaging. Extending these synthetic aperture techniques to the visible light domain is not straightforward because optical receivers cannot measure phase information. We propose to use macroscopic Fourier ptychography (FP) as a practical means of creating a synthetic aperture for visible imaging to achieve subdiffraction-limited resolution. We demonstrate the first working prototype for macroscopic FP in a reflection imaging geometry that is capable of imaging optically rough objects. In addition, a novel image space denoising regularization is introduced during phase retrieval to reduce the effects of speckle and improve perceptual quality of the recovered high-resolution image. Our approach is validated experimentally where the resolution of various diffuse objects is improved sixfold.
Pyrosequencing™ : A one-step method for high resolution HLA typing (2003)

While the use of high-resolution molecular typing in routine matching of human leukocyte antigens (HLA) is expected to improve unrelated donor selection and transplant outcome, the genetic complexity of HLA still makes the current methodology limited and laborious. Pyrosequencing trade mark is a gel-free, sequencing-by-synthesis method. In a Pyrosequencing reaction, nucleotide incorporation proceeds sequentially along each DNA template at a given nucleotide dispensation order (NDO) that is programmed into a pyrosequencer. Here we describe the design of a NDO that generates a pyrogram unique for any given allele or combination of alleles. We present examples of unique pyrograms generated from each of two heterozygous HLA templates, which would otherwise remain cis/trans ambiguous using standard sequencing based typing (SBT) method. In addition, we display representative data that demonstrate long read and linear signal generation. These features are prerequisite of high-resolution typing and automated data analysis. In conclusion Pyrosequencing is a one-step method for high resolution DNA typing.
Lipoarabinomannan from Mycobacterium tuberculosis modulates the generation of reactive nitrogen intermediates by gamma interferon-activated macrophages (1994)

Lipoarabinomannan derived from the virulent Erdman strain and a rapidly growing, laboratory-attenuated strain of Mycobacterium tuberculosis were evaluated for their ability to modulate the production of nitric oxide (NO) by macrophages activated with IFN-γ or IFN-γ and LPS. It was observed that in macrophages pretreated with 100 µg ml−1 LAM, the NO induced by IFN-γ alone was augmented while the NO induced by IFN-γ and LPS was reduced. LAM was also shown to synergize with IFN-γ in the induction of NO, with AraLAM from the attenuated strain exhibiting greater potency than ManLAM from the Erdman strain. Despite the modulation of NO production, LAM did not affect the IFN-γ-induced macrophage growth inhibition of Francisella tularensis LVS, an organism whose growth inhibition in activated macrophages is dependent upon NO.