gebhart/patrepeval huggingface dataset:
Folding and interaction of subunits at the antibody combining site (1976)

The Fv fragment derived from mouse myeloma protein 315 possessing anti-dinitrophenyl (DNP) activity, is composed of two subunits, the peptide chain VL and VH. In 8 M urea there is a complete dissociation of VL and VH and an approximately twofold increase in the fluorescence emission of Fv with a characteristic red shift of 11 nm. Upon dilution of Fv from 8 M urea into neutral buffer full regain of activity was observed, concomitant with regain of native fluorescence spectrum. The decrease in fluorescence upon dilution from 8 M urea was used to follow the renaturation process of Fv. At relatively high protein concentration (2.5 x 10(-6) M) two steps were observed during renaturation: a fast one, which is completed in less than 30 s, and a slower step, which proceeds for approximately 20 min. The fast process represents the refolding and association of VL and VH to form an active FV, whereas the slow step is attributed to the formation of "incorrect" associates between VL and VH which slowly reshuffle to the thermodynamically stable active FV. Indeed, at low protein concentration (1.5 x 10(-8 M) only the fast step is observed and renaturation is completed in less than 30s. The presence of hapten does not affect the rate of renaturation of FV. Reoxidation of FV completely reduced in 8 M urea was also found to yield a fully active Fv. Since either VL or VH have only one intrachain disulfide bond, reoxidation was performed at high protein concentration (3 mg/ml) in 8 M urea followed by dilution into neutral buffer. This demonstrates that variable domains not only exist in immunoglobulin structure but can also fold correctly independent of the rest of the peptide chains.
Growth of rhizosphere-competent mutants of Trichoderma harzianum on carbon substrates (1988)

When the strains of Trichoderma harzianum were grown in Czapek-Dox broth without saccharose with cotton linters, microcrystalline cellulose, wood cellulose, or xylan as a sole source of carbon, the rhizosphere-competent mutants produced significantly higher biomass than the rhizosphere-incompetent wild types. Both mutants and wild types did not readily grow on glucose, galactose, cellobiose, or xylose as sole source of carbon. The mutants, T-95 and T-12B, produced significantly higher biomass when grown on complex carbohydrates with added simple sugars. The wild types did not produce significantly greater biomass when both simple and complex sugars were the carbon sources than when either substrate was used alone. The ability of the mutants to grow more rapidly on complex carbon substrates (typical of those found on root surfaces) than their wild-type parents, and to increase biomass when simple sugars were added along with the cellulose substrate could be of ecological significance and a characteristic of rhizosphere competence.
Effect of predicted protein-truncating genetic variants on the human transcriptome (2015)

Accurate prediction of the functional effect of genetic variation is critical for clinical genome interpretation. We systematically characterized the transcriptome effects of protein-truncating variants, a class of variants expected to have profound effects on gene function, using data from the Genotype-Tissue Expression (GTEx) and Geuvadis projects. We quantitated tissue-specific and positional effects on nonsense-mediated transcript decay and present an improved predictive model for this decay. We directly measured the effect of variants both proximal and distal to splice junctions. Furthermore, we found that robustness to heterozygous gene inactivation is not due to dosage compensation. Our results illustrate the value of transcriptome data in the functional interpretation of genetic variants.
Collagen-specific T-cell repertoire in blood and synovial fluid varies with disease activity in early rheumatoid arthritis (2008)

The collagen-specific T-cell receptor repertoire in peripheral blood and synovial fluid is restricted to a limited number of rearrangements in rheumatoid arthritis. The majority of the repertoire is shared between patients with early rheumatoid arthritis and it is modulated by therapy.
Comparison of the Kubo formula, the microscopic response method, and the Greenwood formula (2011)

For a mechanical perturbation, the microscopic response method is equivalent to and more convenient to use than the Kubo formula. When the gradient of the carrier density is small, the current density reduces to that used by Greenwood.
Assurance Escherichia coli 0157:H7: A Comparative Validation Study (1997)

A wide variety of food products, with emphasis on raw meat products, were analyzed simultaneously by 3 methods: the Assurance Escherichia coli O157:H7 (EHEC) enzyme immunosorbent assay (EIA), the EHEC visual immunoprecipitate assay (VIP), and a modified Bacteriological Analytical Manual (BAM) culture method. This paper reports results of a comparative study of the Assurance and modified BAM methods. In this comparative study, 1050 samples and controls gave false-negative rates of 1.0 and 0%, respectively, for the Assurance EIA and the modified BAM culture methods. The overall agreement between the 2 methods was 99.4%. Cultural confirmation of presumptive positive samples was problematic because competitive flora were present in higher levels than EHEC in the enrichment broth after incubation and the target organism had nondescript characteristics on the primary selective agar, hemorrhagic coli agar, which necessitated picking of additional colonies in many instances.
Matching 3-D smooth surfaces with their 2-D projections using 3-D distance maps (1991)

The matching of 3-D anatomical surfaces to 2-D x-ray projections is an important problem in computer and robot assisted surgery. This paper presents a new method for determining the rigid body transformation that describes this match. The method performs a least squares minimization of the distance between the camera-contour projection lines and the surface. To correctly deal with projection lines that penetrate the surface, the square of the minimum signed distance along each line (distances inside the object are negative) is minimized. To quick and accurately compute distances to the surface, the precomputed distance map is represented using an octree spline whose resolution increases near the surface. The octree allows for quickly finding the minimum distance along each line using best-first search. This paper presents experimental results of 3-D surface to 2-D projection matching, and also shows how our method works for 3-D to 3-D surface matching.
Acyl-Protein Thioesterase 2 Catalizes the Deacylation of Peripheral Membrane-Associated GAP-43 (2010)

An acylation/deacylation cycle is necessary to maintain the steady-state subcellular distribution and biological activity of S-acylated peripheral proteins. Despite the progress that has been made in identifying and characterizing palmitoyltransferases (PATs), much less is known about the thioesterases involved in protein deacylation. In this work, we investigated the deacylation of growth-associated protein-43 (GAP-43), a dually acylated protein at cysteine residues 3 and 4. Using fluorescent fusion constructs, we measured in vivo the rate of deacylation of GAP-43 and its single acylated mutants in Chinese hamster ovary (CHO)-K1 and human HeLa cells. Biochemical and live cell imaging experiments demonstrated that single acylated mutants were completely deacylated with similar kinetic in both cell types. By RT-PCR we observed that acyl-protein thioesterase 1 (APT-1), the only bona fide thioesterase shown to mediate deacylation in vivo, is expressed in HeLa cells, but not in CHO-K1 cells. However, APT-1 overexpression neither increased the deacylation rate of single acylated GAP-43 nor affected the steady-state subcellular distribution of dually acylated GAP-43 both in CHO-K1 and HeLa cells, indicating that GAP-43 deacylation is not mediated by APT-1. Accordingly, we performed a bioinformatic search to identify putative candidates with acyl-protein thioesterase activity. Among several candidates, we found that APT-2 is expressed both in CHO-K1 and HeLa cells and its overexpression increased the deacylation rate of single acylated GAP-43 and affected the steady-state localization of diacylated GAP-43 and H-Ras. Thus, the results demonstrate that APT-2 is the protein thioesterase involved in the acylation/deacylation cycle operating in GAP-43 subcellular distribution.
CD63 associates with CD11/CD18 in large detergent‐resistant complexes after translocation to the cell surface in human neutrophils1 (2000)

CD63 antibody binding to the neutrophil surface triggers a transient activation signal that regulates the adhesive activity and surface expression of CD11/CD18. Gel permeation chromatography demonstrated that all of the cell surface CD11/CD18 associated with CD63 eluted in the void volume, indicating that they were present in large detergent-resistant complexes. In contrast, the majority of the total cellular CD63, CD11 and CD18, which are largely intracellular, was not present in complexes. The data suggest that intracellular CD11, CD18 and CD63 are not in detergent-resistant complexes, but enter such complexes following translocation to the cell surface.
Stat3 Dimerization Regulated by Reversible Acetylation of a Single Lysine Residue (2005)

Upon cytokine treatment, members of the signal transducers and activators of transcription (STAT) family of proteins are phosphorylated on tyrosine and serine sites within the carboxyl-terminal region in cells. We show that in response to cytokine treatment, Stat3 is also acetylated on a single lysine residue, Lys685. Histone acetyltransferase p300-mediated Stat3 acetylation on Lys685 was reversible by type I histone deacetylase (HDAC). Use of a prostate cancer cell line (PC3) that lacks Stat3 and PC3 cells expressing wild-type Stat3 or a Stat3 mutant containing a Lys685-to-Arg substitution revealed that Lys685 acetylation was critical for Stat3 to form stable dimers required for cytokine-stimulated DNA binding and transcriptional regulation, to enhance transcription of cell growth-related genes, and to promote cell cycle progression in response to treatment with oncostatin M.
From carbon nanotube crystals to carbon nanotube flowers (2005)

We have investigated the very initial deposition stages of chemical vapor deposition (CVD) with ferrocene (Fe(C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> ) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) and xylene (C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</inf> H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</inf> ) for growing carbon nanotubes, and made clear that the mechanism for the self-organization behaviors of nanotubes at different growth stages by this approach. For instance, the organization of nanotubes into flower-like structures at prolonged deposition is developed from the crystal-like structures formed at early growth stages, both of which are closely related to and determined by the very initial deposition stages of this CVD approach. Based on this approach, ways have been established to build up different architectures of carbon nanotubes, by controlling the initial deposition stages of the CVD process, with which we have realized the selective growth of self-organized carbon nanotube structures. This study provides a new idea for growing carbon nanotube architectures by CVD.
The limits of instruction level parallelism in SPEC95 applications (1999)

No abstract available.
CXC chemokines located in the 4q21 region are up-regulated in breast cancer (2007)

Recent data suggest that chemokines could be essential players in breast carcinogenesis. We previously showed that the CXC chemokine CXCL8 (interleukin-8) was overexpressed in estrogen receptor alpha (ERalpha)-negative breast cell lines. Analysis of CXCL8 chromosomal location showed that several CXC chemokines (CXCL1, CXCL2, CXCL3, CXCL4, CXCL4V1, CXCL5, CXCL6, CXCL7, and CXCL8) were localized in the same narrow region (360 kb in size) of chromosome 4. We thus hypothesized that they could belong to the same cluster. Quantification of these chemokines in breast tumors showed that samples expressing high CXCL8 also produced elevated levels of CXCL1, CXCL3, and CXCL5, and displayed low content of ERalpha. CXCL1, CXCL2, CXCL3, CXCL5, and CXCL8 were co-regulated both in tumors and in breast cancer cell lines. CXCL5 and CXCL8 were mainly produced by epithelial cells, whereas CXCL1, CXCL2, and CXCL3 had a high expression in blood cells. The overexpression of these chemokines in tumor cells was not the result of gene amplification, but rather of an enhanced gene transcription. Our data suggest that high CXCL8 expression in tumors is mainly correlated to activating protein-1 (AP-1) pathway and to a minor extent to NF-kappaB pathway. Interestingly, CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, and CXCL8 chemokines were present at higher levels in metastases when compared with grade I and III biopsies. High levels of CXCL8, CXCL1, and CXCL3 accounted for a shorter relapse-free survival of ERalpha-positive patients treated with tamoxifen. In summary, we present evidences that multiple CXC chemokines are co-expressed in CXCL8-positive breast tumors. In addition, these chemokines could account for the higher aggressiveness of these types of tumors.
Metabolic Imaging by Hyperpolarized 13C Magnetic Resonance Imaging for In vivo Tumor Diagnosis (2006)

The "Warburg effect," an elevation in aerobic glycolysis, may be a fundamental property of cancer cells. For cancer diagnosis and treatment, it would be valuable if elevated glycolytic metabolism could be quantified in an image in animals and humans. The pyruvate molecule is at the metabolic crossroad for energy delivery inside the cell, and with a noninvasive measurement of the relative transformation of pyruvate into lactate and alanine within a biologically relevant time frame (seconds), it may be possible to quantify the glycolytic status of the cells. We have examined the metabolism after i.v. injection of hyperpolarized (13)C-pyruvate in rats with implanted P22 tumors. The strongly enhanced nuclear magnetic resonance signal generated by the hyperpolarization techniques allows mapping of pyruvate, lactate, and alanine in a 5 x 5 x 10 mm(3) imaging voxel using a 1.5 T magnetic resonance scanner. The magnetic resonance scanning (chemical shift imaging) was initiated 24 seconds after the pyruvate injection and had a duration of 14 seconds. All implanted tumors showed significantly higher lactate content than the normal tissue. The results indicate that noninvasive quantification of localized Warburg effect may be possible.
The Primary Structure of a Basic Leucine-rich Repeat Protein, PRELP, Found in Connective Tissues (1995)

We have determined the primary structure of a connective tissue matrix protein from the nucleotide sequence of a clone isolated from a human articular chondrocyte cDNA library. The major part of the amino acid sequence has also been determined by direct protein sequencing. The translated primary sequence corresponds to 382 amino acid residues, including a 20-residue signal peptide. The molecular mass of the mature protein is 41,646 Da. The main part of the protein consists of 10 leucine-rich repeats ranging in length from 20 to 26 residues, with asparagine at position 10 (B-type). The N-terminal part is unusual in that it is basic and rich in arginine and proline. There are four potential N-linked glycosylation sites present. In three of these sites, post-translational modifications are likely to be present since Asn was not found by direct protein sequencing. The amino- and carboxyl-terminal parts contain four and two cysteine residues, respectively, probably forming disulfide bonds by analogy with the other members of this family. The protein shows highest identity (36%) to fibromodulin and 33% to bovine lumican, two other leucine-rich repeat connective tissue proteins. Northern blot analysis showed the presence of an approximately 3.8-kilobase mRNA in different types of bovine cartilage and cultured osteoblasts, whereas RNAs isolated from bovine kidney, skin, spleen, thymus, and trabecular bone and rat calvaria were negative. Human articular chondrocyte and rat chondrosarcoma cell RNAs contained an additional mRNA of approximately 1.6 and 1.8 kilobases, respectively.
Millijoule femtosecond all-fiber system (2001)

Summary form only given. We have demonstrated the first all-fiber chirped pulse amplification (CPA) system producing millijoule-range ultrashort-pulses. Peak powers achieved of /spl sim/3 MW in a fiber amplifier are approximately two orders of magnitude higher compared to the previously reported case of mJ energies and > 100 ns long pulses from a Q-switched multimode fiber laser. Note that 400 ps stretching does not constitute a limit and /spl sim/1 ns stretched pulse durations are achievable with standard /spl sim/10 cm wide diffraction gratings. This indicates the straightforward possibility of further energy scaling with this fiber system. Also, the use of 1800 l/mm gratings will allow stretcher and compressor sizes to be significantly reduced. Furthermore, the robust fundamental-mode excitation and propagation properties of 50 /spl mu/m core fiber indicate that further core-size scaling is possible with potential for even higher pulse energies.
Behavior of Expanding Laser Produced Plasma in a MagneticField (1998)

Characteristics of a laser produced plasma expanding across an externally applied magnetic field (0.6 T) have been reported. Two to three times enhancement in x-ray emission from copper plasma has been observed for the laser intensity range ∼5 × 1011–5 × 1012 W/cm2. The x-ray yield has been found to increase with an increase in the magnetic field intensity. Enhancement in x-ray emission is correlated with confinement of an expanding plasma in an external magnetic field. Generation of fluid instability has been found at the expanding plasma surfaces where the kinetic pressure of the plasma equals the magnetic pressure.
Fluorine-19 nuclear magnetic resonance studies of aromatic compounds. Part 5. Transmission of substituent effects across two aromatic rings connected by C–C and –C– linkages (1977)

The 19F n.m.r. spectra of compounds of the type p-FC6H4·Z·C6H4X-p[Z = C⋮C, cis or trans CH:CH, CH2·CH2, threo or erythro CHBr·CHBr, CH, CH(OH), CHCl, or CHBr] have been used to examine the transmission of substituent effects of X across the group Z. When Z is unsaturated, the magnitude of the transmitted effect is not solely dependent upon the extent of conjugation between the rings; when Z is a saturated C–C bond the magnitude of the transmitted effect is sensitive to the conformational properties of the system. When Z is a single substituent carbon atom (CHY; Y = H, OH, Cl, or Br) the transmission is greater when Y = OH than for all the other substituents, which all show the same behaviour.
Recent advances in chronic lymphocytic leukemia therapy (2020)

Chronic lymphocytic leukemia is a genetically heterogeneous disease, and a complex set of genetic alterations is associated with its pathogenesis. CLL is the most common leukemia in the western countries, whereas it is rare in Asia, including Korea. The prognostic models integrate the traditional staging systems developed by Rai <i>et al</i>. and Binet <i>et al</i>. with biochemical and genetic markers. With the advent of molecular biology, a variety of targeted agents, including anti-CD20 antibodies, inhibitors of BCR signaling pathway, and BCL-2 inhibitors, have been introduced, which has changed the landscape of CLL treatment greatly. This review will focus on the risk stratification and the management of CLL in the era of novel small molecules.
New Support Vector Algorithms (2000)

We propose a new class of support vector algorithms for regression and classification. In these algorithms, a parameter nu lets one effectively control the number of support vectors. While this can be useful in its own right, the parameterization has the additional benefit of enabling us to eliminate one of the other free parameters of the algorithm: the accuracy parameter epsilon in the regression case, and the regularization constant C in the classification case. We describe the algorithms, give some theoretical results concerning the meaning and the choice of nu, and report experimental results.
Chimeric papillomavirus virus‐like particles induce a murine self‐antigen‐specific protective and therapeutic antitumor immune response (1999)

The use of chimeric virus-like particles represents a new strategy for delivering tumor antigens to the immune system for the initiation of antitumor immune responses. Immunization of DBA/2 mice with the P1A peptide derived from the P815 tumor-associated antigen P1A induced specific T-cell tolerance, resulting in progression of a regressor P815 cell line in all animals. However, immunization with a human papillomavirus type 16 L1 virus-like particle containing the P1A peptide in the absence of adjuvant induced a protective immune response in mice against a lethal tumor challenge with a progressor P815 tumor cell line. Additionally, we demonstrated that these chimeric virus-like particles could be used therapeutically to suppress the growth of established tumors, resulting in a significant survival advantage for chimeric virus-like particle-treated mice compared with untreated control mice. Chimeric virus-like particles can thus be used as a universal delivery vehicle for both tolerizing and antigenic peptides to induce a strong protective and therapeutic antigen-specific antitumor immune response. J. Cell. Biochem. 73:145–152, 1999. © 1999 Wiley-Liss, Inc.
Circularly Polarized Implantable Antenna for 915 MHz ISM-Band Far-Field Wireless Power Transmission (2018)

A wireless power link with circular polarization is studied in this letter for far-field wireless power transmission. First, a miniaturized circularly polarized (CP) implantable antenna is designed at 915 ISM band. The proposed antenna features a good miniaturization with the dimensions of 11 × 11 × 1.27 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> by employing the stub loading and capacitive coupling among the stubs. It has the smallest size and maintains good radiation performance, compared with previous CP implantable antennas. The simulated impedance bandwidth covers from 889 to 924 MHz for |S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> | less than -10 dB, and the axial-ratio (AR) bandwidth (AR <; 3 dB) is from 901 to 912 MHz. The results show that the antenna is suitable for far-field wireless power transmission. The proposed wireless power link achieves higher converted dc power compared to previous similar letter.
Light-field video coding using geometry-based disparity compensation (2014)

One of the main challenges in 3D light-field imaging approaches lies in the massive amount of visual information involved in providing 3D content with sufficient resolution. Consequently, adequate coding tools are essential for efficient transmission and storage of this type of content. In this context, this paper presents and evaluates two coding solutions based on the High Efficiency Video Coding (HEVC) scheme and for efficient compression of the 3D light-field content. These two coding schemes aim to exploit the 3D geometry-based disparity information in the 3D light field content and replace the block-based disparity estimation. In the first scheme, the disparity map of each view is used to directly derive the vectors for compensation, and in the second scheme these disparity vectors (for all views) are calculated (for non-occluded areas) from the disparity map of the base view. A comparative study of these proposed coding schemes is performed and future research directions are also discussed.