gebhart/patrepeval huggingface dataset:
Identification of immunoglobulin lambda isotype gene rearrangements by Southern blot analysis. (1996)

The human immunoglobulin lambda (Ig(lambda)) gene locus contains seven homologous C(lambda) exons which are organized in a tandem array, each of which is preceded by a single J(lambda) gene segment. The J-C(lambda)1, J-C(lambda)2, J-C(lambda)3, and J-C(lambda)7 are functional gene regions and encode for the four Ig(lambda) isotypes, whereas J-C(lambda)4, J-C(lambda)5, and J-C(lambda)6 are non-functional (pseudo) Ig(lambda) gene regions. Recently, we demonstrated that Southern blot analysis with the IGLC3 probe in combined EcoRI/HindIII digests allows detection of approximately 95% of all clonal Ig(lambda) gene rearrangements in B cell malignancies. Although this single probe/enzyme combination is quite effective in detecting Ig(lambda) gene rearrangements, it should be noted that it results in a complex pattern of multiple germline bands of different density, which needs experience for correct interpretation. To improve further the reliable detection and identification of clonal Ig(lambda) gene rearrangements, we developed a new set of seven 'isotype-specific' DNA probes: the IGLC1D probe for the J-C(lambda)1 gene region, the IGLC2D probe for the J-C(lambda)2 gene region, the IGLJ2 probe for the highly homologous J-C(lambda)2 and J-C(lambda)3 gene regions, and the IGLC4D, IGLJ5, IGLJ6, and IGLJ7 probes for the last four J-C(lambda) gene regions, respectively. In combination with optimally chosen digests (ie HindIII, BglII, BamHI, and/or EcoRI) the seven probes indeed allow easy detection and identification of all rearrangements in the seven J-C(lambda) gene regions. The applicability of the probe/enzyme combinations was confirmed upon analysis of clonal 'Ig(lambda)-isotype' gene rearrangements in 40 B lineage malignancies.
Molecular Characterization of Membrane Type and Ganglioside-specific Sialidase (Neu3) Expressed in E. coli (2004)

Endogenous expression of human membrane type ganglioside sialidase (Neu3) was examined in various cell lines including NB-1, U87MG, SK-MEL-2, SK-N-MC, HepG2, Hep3B, Jurkat, HL-60, K562, ECV304, Hela and MCF-7. Expression was detected in the neuroblastoma cell lines NB-1 and SK-N-MC, and also in erythroleukemia K562 cells, but not in any other cells. We isolated a Neu3 cDNA from K562 cells and expressed a His-tagged derivative in a bacterial expression system. The purified recombinant product of approximately 48 kDa had sialidase activity toward 4-methyl-umbelliferyl-alpha-D-N-acetylneuraminic acid (4MU-NeuAc). The optimal pH of the purified Neu3 protein for GD3 ganglioside was 4.5. The enzyme also efficiently hydrolyzed GD3, GD1a, GD1b and GM3 whereas sialyllactose, 4MU-NeuAc, GM1 and GM2 were poor substrates, and it had no activity against sialylated glycoproteins such as fetuin, transferrin and orosomucoid. We conclude that the sialidase activity of Neu3 is specific for gangliosides.
The GTPase-activating Protein RGS4 Stabilizes the Transition State for Nucleotide Hydrolysis (1996)

RGS proteins constitute a newly appreciated group of negative regulators of G protein signaling. Discovered by genetic screens in yeast, worms, and other organisms, two mammalian RGS proteins, RGS4 and GAIP, act as GTPase-activating proteins for members of the Gi family of G protein alpha subunits. We have purified recombinant RGS4 to homogeneity and demonstrate that it acts catalytically to stimulate GTP hydrolysis by Gi proteins. Furthermore, RGS4 stabilizes the transition state for GTP hydrolysis, as evidenced by its high affinity for the GDP-AlF4--bound forms of Goalpha and Gialpha and its relatively low affinity for the GTPgammaS- and GDP-bound forms of these proteins. Consequently, RGS4 is most likely not a downstream effector for activated Galpha subunits. All members of the Gi subfamily of proteins tested are substrates for RGS4 (including Gtalpha and Gzalpha); the protein has lower affinity for Gqalpha, and it does not stimulate the GTPase activity of Gsalpha or G12alpha.
Gene Therapy Vectors Based on Adeno-Associated Virus Type 1 (1999)

The complete sequence of adeno-associated virus type 1 (AAV-1) was defined. Its genome of 4,718 nucleotides demonstrates high homology with those of other AAV serotypes, including AAV-6, which appears to have arisen from homologous recombination between AAV-1 and AAV-2. Analysis of sera from nonhuman and human primates for neutralizing antibodies (NAB) against AAV-1 and AAV-2 revealed the following. (i) NAB to AAV-1 are more common than NAB to AAV-2 in nonhuman primates, while the reverse is true in humans; and (ii) sera from 36% of nonhuman primates neutralized AAV-1 but not AAV-2, while sera from 8% of humans neutralized AAV-2 but not AAV-1. An infectious clone of AAV-1 was isolated from a replicated monomer form, and vectors were created with AAV-2 inverted terminal repeats and AAV-1 Rep and Cap functions. Both AAV-1- and AAV-2-based vectors transduced murine liver and muscle in vivo; AAV-1 was more efficient for muscle, while AAV-2 transduced liver more efficiently. Strong NAB responses were detected for each vector administered to murine skeletal muscle; these responses prevented readministration of the same serotype but did not substantially cross-neutralize the other serotype. Similar results were observed in the context of liver-directed gene transfer, except for a significant, but incomplete, neutralization of AAV-1 from a previous treatment with AAV-2. Vectors based on AAV-1 may be preferred in some applications of human gene therapy.
SHORT COMMUNICATION EXTENSION OF FINITE LENGTH SIGNALS FOR SUB-BAND CODING (1989)

Some problems associated with sub-band coding of images are investigated. The filtering operations needed for splitting an input into different frequency bands, as well as their reconstruction, require an extension beyond the length of the finite signal. If not properly made, the necessary signal extension can yield distortion of the reconstructed signal, and it may complicate the compression of high-pass frequency bands. Five different methods of signal extensions have been investigated for sub-band coding. It turns out that extending the signal so that continuity is maintained may be a sufficient remedy, as shown in an image coding example. Zusammenfassung. In diesem Artikel besch~iftigen wir uns mit einigen Teilproblemen bei der Subbandcodierung von Bildern. Die Filteroperationen, die fiir die Aufspaltung des Bildes in mehrere Frequenzb~inder wie auch fiir die zugeh6rige Rekonstruk- tion gebraucht werden, ben6tigen Signalwerte jenseits der Grenzen des finiten Bildsignales. Die notwendige Erg~inzung des Signals kann Nebeneffekte zur Folge haben, wie z.B. die Verzerrung des rekonstruierten Signals, und sie kann die Kom- primierung der h/Sheren Frequenzb~inder erschweren. Wir haben insgesamt ffinf verschiedene Methoden der Erweiterung des Signals fiber die Bildgrenzen hinaus unter dem Gesichtspunkt der Subbandcodierung untersucht und die zwei genannten Nebenwirkungen in Betracht gezogen. Wie sich zeigt, genfigt es, bei der Erweiterung des Bildsignals die Kontinuit~it sicherzustellen; dies wird an einem praktischen Beispiel zur Bildcodierung demonstriert.
Novel CT-based Three-dimensional Software Improves the Characterization of Cam Morphology (2013)

Software-based three-dimensional (3-D) imaging generated alpha angles larger than those found by plain radiograph and CT, and these differences were the result of location of measurement. An automated 3-D assessment that accurately describes the location and topography of FAI may be needed to adequately characterize preoperative deformity.
<title>Image-guided noninvasive surgery with ultrasound phased arrays</title> (1998)

The current status and the future needs of image-guided ultrasound phased array systems for noninvasive surgery are addressed. Preliminary results from an integrated image- guided therapeutic phased array system for noninvasive surgical applications currently being developed at our laboratory are shown. The therapeutic array utilizes piezo- composite transducer technology and operates (therapeutically) at 1 and 2 MHz. It consists of 64 elements on a spherical shell with a geometric center at 100 mm from its apex. The array was shown to be capable of producing well defined thermal lesions in tissue media at depths from 40 to 60 mm and to scan therapeutic foci up to +/- 15 mm from its geometric center. Image guidance is provided by a modified diagnostic ultrasound scanner which, in addition to providing standard B-scan images of the target region, provides real-time images of the temperature rise due to the therapeutic beam. The temperature information is obtained using a correlation based algorithm for echo displacement estimation, which can be directly related to local variation in tissue temperature due to the therapeutic beam. A complete description of the combined imaging/therapy system is given. Furthermore, illustrative examples of noninvasive real-time image-guided tissue ablation, temperature estimation, and temperature control are presented and discussed.
Improving joint stereo audio coding by adaptive inter-channel prediction (2002)

A method for exploiting inter-channel redundancies of stereophonic or multichannel audio signals is presented. In contrast to known stereo redundancy reduction techniques used in joint stereo audio coding. Where only the statistical dependencies between two concurrent samples of the left and right channel signals are considered, the adaptive inter-channel prediction also takes into account possible phase or time delay between the channels and exploits more than only one value of the cross-correlation function. The analysis of subjective listening test results has shown that this technique is especially effective for a class of test sequences which has proven to be most critical for the ISO MPEG Layer II and Layer III codecs at bit rates of 2/spl times/64 kbit/s. For these signals the gain due to the stereo redundancy reduction technique used in Layer III joint stereo coding is less than 5-10 dB, while in Layer II joint stereo coding no specific stereo redundancy reduction technique is used. In a first step, the adaptive inter-channel prediction has been applied to an ISO MPEG Layer II codec. The simulation results show that a prediction gain up to 30-40 dB can be achieved for large parts of the above mentioned signals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interaction of iC3b with recombinant isotypic and chimeric forms of CR2 (1991)

CR2 is a component of a signal transduction complex on B lymphocytes that augments B cell responses to Ag. We have quantitatively assessed binding by the two isotypic forms of CR2 for two of its ligands, the polymerized iC3b (p(iC3b)) fragment of C3, and gp350/220, the EBV membrane protein. The recombinant 15-SCR or 16-SCR forms of CR2 bound p(iC3b) with identical affinities. Full binding activity of CR2 for p(iC3b) was observed with a chimera comprised of SCR-1 and -2 of CR2 fused to SCR-17 through -30 of CR1. Therefore, the alternatively spliced SCR-10a has no role in binding p(iC3b), and the binding activity of wild type receptor for iC3b can be reconstituted with SCR-1 and -2 of CR2. The binding affinities of the two isoforms of CR2 for soluble gp350/220 were also similar. Additional sites in the C3c region of C3 have been postulated also to interact with CR2. However, monomeric iC3b and C3d were equally effective in inhibiting the binding of p(iC3b) to CR2, indicating that the C3c region of iC3b does not contribute to the interaction of iC3b with CR2. Finally, the relative abilities of C3b and iC3b to bind to CR1 and CR2 were compared. The conversion of C3b to iC3b generated a ligand with an approximate 100-fold decrease in affinity for CR1 and a 10-fold increased affinity for CR2, resulting in a 1000-fold greater likelihood for binding to the latter receptor that may then promote B cell activation.
A Generalized Wellbore and Surface Facility Model, Fully Coupled to a Reservoir Simulator (2004)

Summary The formulation of a black-oil or compositional fully coupled surface and subsurface simulator is described. It is based on replacing the well model in a conventional reservoir simulator with a generalized network model of the wells and facilities. This allows for representation of complex wellbore geometry and downhole equipment. The method avoids the inefficiencies and/or inaccuracies of other coupled models, in which wells and facilities are treated as separate domains or in which the global system is not solved simultaneously. Example cases demonstrate the performance of the model for cases with simple and segmented wellbores (with and without facilities).
Differential Binding of Histidine-rich Glycoprotein (HRG) to Human IgG Subclasses and IgG Molecules Containing κ and λ Light Chains (1999)

In previous studies we showed that the plasma protein histidine-rich glycoprotein (HRG) binds strongly to pooled human IgG. In the present work myeloma proteins consisting of different human IgG subclasses were examined for their ability to interact with human HRG. Using an IAsys optical biosensor we found initially that IgG subclasses differ substantially in their affinity of interaction with HRG. However, the most striking finding was the observation that the kinetics of the HRG interaction was dramatically affected by whether the IgG subclasses contained the kappa or lambda light (L)-chains. Thus, the on-rate for the binding of HRG to the kappa L-chain containing IgG1 and IgG2 (IgG1kappa and IgG2kappa) was approximately 4- and approximately 10-fold faster than that for the binding of HRG to lambda L-chain containing IgG1 and IgG2 (IgG1lambda and IgG2lambda), respectively, with the dissociation constants (K(d)) in the range 3-5 nM and 112-189 nM for the kappa and lambda isoforms, respectively. In contrast, the on-rate for the binding of HRG to IgG3kappa and IgG4kappa was found to be 9- and 20-fold slower than that for the binding of HRG to IgG3lambda and IgG4lambda, respectively, with the K(d) in the range 147-268 nM and 96-109 nM for the kappa and lambda isoforms, respectively. The binding of HRG to immunoglobulins containing the kappa L-chain (particularly IgG1kappa) was generally potentiated in the presence of a physiological concentration (20 microM) of Zn(2+) (K(d) decreased to 0.60 +/- 0.01 for IgG1kappa), but Zn(2+) had no effect or slightly inhibited the binding of HRG to immobilized IgG subclasses possessing the lambda L-chain. Interestingly, HRG also bound differentially to Bence Jones (BJ) proteins containing kappa and lambda L-chains, with HRG having a 14-fold lower K(d) for BJkappa than for BJlambda when 20 microM Zn(2+) was present. HRG also bound to IgM (IgMkappa), but the affinity of this interaction (K(d) approximately 1.99 +/- 0.05 microM) was markedly lower than the interaction with IgG, and the affinity was actually decreased 4-fold in the presence of Zn(2+). The results demonstrate that both the heavy (H)- and L-chain type have a profound effect on the binding of HRG to different IgG subclasses and provide the first evidence of a functional difference between the kappa and lambda L-chains of immunoglobulins.
Hypersensitive substrate for ribonucleases (1999)

A substrate for a hypersensitive assay of ribonucleo-lytic activity was developed in a systematic manner. This substrate is based on the fluorescence quenching of fluorescein held in proximity to rhodamine by a single ribonucleotide embedded within a series of deoxynucleotides. When the substrate is cleaved, the fluorescence of fluorescein is manifested. The optimal substrate is a tetranucleotide with a 5′,6-carboxyf luorescein label (6-FAM) and a 3′,6-carboxy-tetramethylrhodamine (6-TAMRA) label: 6-FAM-dArUdAdA-6-TAMRA. The fluorescence of this substrate increases 180-fold upon cleavage. Bovine pancreatic ribonuclease A (RNase A) cleaves this substrate with a kcat/Km of 3.6 × 107 M-1 s-1. Human angiogenin, which is a homolog of RNase A that promotes neovascularization, cleaves this substrate with a kcat/Km of 3.3 × 107 M-1 s-1. This value is >10-fold larger than that for other known substrates of angiogenin. With these attributes, 6-FAM dArUdAdA-6-TAMRA is the most sensitive known substrate for detecting ribo-nucleolytic activity. This high sensitivity enables a simple protocol for the rapid determination of the inhibition constant (Ki) for competitive inhibitors such as uridine 3′-phosphate and adenosine 5′-diphosphate.
Self-Assembly of CdSe−ZnS Quantum Dot Bioconjugates Using an Engineered Recombinant Protein (2000)

A novel and direct method is described for conjugating protein molecules to luminescent CdSe−ZnS core−shell nanocrystals (Quantum Dots) for use as bioactive fluorescent probes in sensing, imaging, immunoassay, and other diagnostics applications. The approach makes use of a chimeric fusion protein designed to electrostatically bind to the oppositely charged surface of capped colloidal quantum dots (QDs). Preparation of protein-modified QD dispersions with high quantum yield, little or no particle aggregation, and retention of biological activity was achieved. Combining the advantages of lipoic acid capped CdSe−ZnS quantum dots (photochemical stability, a wide range of size-dependent emission wavelengths, and aqueous compatibility) with facile electrostatic conjugation of bioactive proteins, this type of hybrid bioinorganic conjugate represents a powerful fluorescent tracking tool for diverse applications. The design and preparation of a model QD/protein conjugate based on E. coli Maltose Binding Protein is described, together with functional characterization of this new type of nanoassembly using luminescence, laser scanning microscopy, and bioassay.
Novel light diffusing fiber for use in medical applications (2016)

Fiber-based cylindrical light diffusers are often used in photodynamic therapy to illuminate a luminal organ, such as the esophagus. The diffusers are often made of plastic and suffer from short diffusion lengths and low transmission efficiencies over a broad spectrum. We have developed Fibrance<sup>TM</sup>, a glass-based fiber optic cylindrical diffuser which can illuminate a fiber from 0.5 cm to 10 meters over a broad wavelength range. With these longer illumination lengths, a variety of other medical applications are possible beyond photodynamic therapy. We present a number of applications for Fibrance ranging from in situ controllable illumination for Photodynamic Therapy to light guided anatomy highlighting for minimally invasive surgery to mitigating hospital acquired infections and more.
Relationship Between Adiponectin and Glycemic Control, Blood Lipids, and Inflammatory Markers in Men With Type 2 Diabetes (2004)

Our study supports the hypothesis that increased adiponectin levels might be associated with better glycemic control, better lipid profile, and reduced inflammation in diabetic subjects. Measures that increase adiponectin levels might be valuable targets for decreasing the atherosclerotic risk present in diabetes.
A high-yielding, generic fed-batch cell culture process for production of recombinant antibodies (2000)

A fed-batch cell culture process was developed that has general applicability to all evaluated Sp2/0 (n = 8) and NS0 (n = 1) antibody-producing cell lines. The two key elements of this generic process were a protein-free concentrated feed medium, and a robust, metabolically responsive feeding strategy based on the off-line measurement of glucose. The fed-batch process was shown to perform equivalently at the 15 L development scale and 750 L manufacturing scale. Compared to batch cultures, the fed-batch process yielded a 4. 3 fold increase in the average integral of viable cell concentration and a 1.7 fold increase in average specific antibody production rate, equivalent to a 7.6 fold increase in average final antibody concentration. The highest producing cell line reached a peak viable cell concentration of 1.0 x 10(7) cell mL(-1) and a final antibody concentration of 750 mg L(-1) in a 10 day process. For all lines evaluated, reducing bioreactor pH set point from 7.2 to 7.0 resulted in an additional 2.4 fold increase in average final antibody concentration. The optimized fed-batch process consistently yielded a volumetric productivity exceeding 50 mg L(-1) day(-1). This generic, high-yielding fed-batch process significantly decreased development time, and increased manufacturing efficiency, thereby facilitating the clinical evaluation of numerous recombinant antibodies.
Energy conservation in heterogeneous server clusters (2005)

The previous research on cluster-based servers has focused on homogeneous systems. However, real-life clusters are almost invariably heterogeneous in terms of the performance, capacity, and power consumption of their hardware components. In this paper, we argue that designing efficient servers for heterogeneous clusters requires defining an efficiency metric, modeling the different types of nodes with respect to the metric, and searching for request distributions that optimize the metric. To concretely illustrate this process, we design a cooperative Web server for a heterogeneous cluster that uses modeling and optimization to minimize the energy consumed per request. Our experimental results for a cluster comprised of traditional and blade nodes show that our server can consume 42% less energy than an energy-oblivious server, with only a negligible loss in throughput. The results also show that our server conserves 45% more energy than an energy-conscious server that was previously proposed for homogeneous clusters.
Glucagon-like Peptide-1 (GLP-1) Analogs: Recent Advances, New Possibilities, and Therapeutic Implications (2014)

Glucagon-like peptide-1 (GLP-1) is an incretin that plays important physiological roles in glucose homeostasis. Produced from intestine upon food intake, it stimulates insulin secretion and keeps pancreatic β-cells healthy and proliferating. Because of these beneficial effects, it has attracted a great deal of attention in the past decade, and an entirely new line of diabetic therapeutics has emerged based on the peptide. In addition to the therapeutic applications, GLP-1 analogs have demonstrated a potential in molecular imaging of pancreatic β-cells; this may be useful in early detection of the disease and evaluation of therapeutic interventions, including islet transplantation. In this Perspective, we focus on GLP-1 analogs for their studies on improvement of biological activities, enhancement of metabolic stability, investigation of receptor interaction, and visualization of the pancreatic islets.
Self-assembly of polystyrene nano particles into patterns of random-close-packed monolayers via chemically induced adsorption (2002)

We have found that addition of 1-ethyl 3-(3-(dimethylamino)propyl)carbodiimide (EDC) to a suspension of sulfated polystyrene (PS) nanoparticles leads to formation of an irregular, dense-packed monolayer of self-assembled particles on homogeneous as well as chemically patterned surfaces. The adsorption process depends sensitively on the EDC concentration with a critical concentration of 13 mM. At higher concentrations above this critical value, random-close-packed (rcp) monolayers form irrespective of whether the substrate is native gold, a gold surface modified by either hydrophobic or hydrophilic alkanethiols, or chromium/chromium oxide. On the other hand, at lower concentrations particle adsorption is observed only on carboxy-terminated surfaces. We will describe how this phenomenon can be utilized to form 2-dimensional patterns of PS nanoparticles. First, a pattern consisting of carboxy and methyl-terminated thiols is formed on native gold by means of microcontact printing (µCP). Subsequent exposure of the pattern to a suspension of sulfated PS particles with an appropriate EDC concentration in the range 1.3 to 5.2 mM leads to a patterned rcp monolayer. In the second half of the paper we discuss various adsorption mechanisms based on observations with UV–vis spectroscopy and scanning electron microscopy (SEM). Two adsorption mechanisms governing the observed phenomena are proposed.