gebhart/patrepeval huggingface dataset:
Autoantibody-associated cross-reactive idiotype-bearing human B lymphocytes: distribution and characterization, including Ig VH gene and CD5 antigen expression (1991)

Monoclonal antibodies (MoAbs) specific for autoantibody associated cross-reactive idiotypes (CRIs) frequently recognize the Igs of neoplastic B cells in patients with chronic lymphocytic leukemia (CLL) and/or Waldenstrom's macroglobulinemia. Very little is known regarding the normal B cells expressing CRIs (CRI-positive B cells). Using a variety of MoAbs against CRIs we investigated the distribution and topographic localization of CRI-positive B cells in normal adult human lymphoid tissues. We found that CRI-positive B cells represent a significant B-cell subpopulation expressing surface IgM (greater than 90%), IgG (approximately 5%), or IgA (approximately 2%). CRI-positive B cells are homogeneously distributed throughout all lymphoid tissues, accounting for 10% to 15% of all B lymphocytes, with the exception of the thymus, in which they represent the predominant B cell population. Immunophenotypic studies showed (1) that a small subpopulation (3.7% +/- 0.8%) of CRI-positive B cells are activated in vivo, based on CD25 and CD38 antigen expression; and (2) that approximately 50% of CRI-positive B cells express the 67-Kd pan-T-lymphocyte CD5 antigen, suggesting that the CRI-positive B-cell subset and the recently described CD5-positive B-cell subset are closely related. This hypothesis is supported by the fact that CRI-positive B cells produce oligo or polyreactive Igs, which are a characteristic feature of CD5-positive B cells, and also by the fact that both B-cell subpopulations appear to use similar and restricted Ig VH gene family members.
Epitope-Specific Human Influenza Antibody Repertoires Diversify by B Cell Intraclonal Sequence Divergence and Interclonal Convergence (2011)

We generated from a single blood sample five independent human mAbs that recognized the Sa antigenic site on the head of influenza hemagglutinin and exhibited inhibitory activity against a broad panel of H1N1 strains. All five Abs used the V(H)3-7 and J(H)6 gene segments, but at least four independent clones were identified by junctional analysis. High-throughput sequence analysis of circulating B cells revealed that each of the independent clones were members of complex phylogenetic lineages that had diversified widely using a pattern of progressive diversification through somatic mutation. Unexpectedly, B cells encoding multiple diverging lineages of these clones, including many containing very few mutations in the Ab genes, persisted in the circulation. Conversely, we noted frequent instances of amino acid sequence convergence in the Ag combining sites exhibited by members of independent clones, suggesting a strong selection for optimal binding sites. We suggest that maintenance in circulation of a wide diversity of somatic variants of dominant clones may facilitate recognition of drift variant virus epitopes that occur in rapidly mutating virus Ags, such as influenza hemagglutinin. In fact, these Ab clones recognize an epitope that acquired three glycosylation sites mediating escape from previously isolated human Abs.
Power-aware resource allocation in high-end systems via online simulation (2005)

Traditionally, scheduling in high-end parallel systems focuses on how to minimize the average job waiting time and on how to maximize the overall system utilization. Despite the development of scheduling strategies that aim at maximizing system utilization, parallel supercomputing traces that span long time periods indicate that such systems are mostly underutilized. Much of the time there is simply not enough load to keep the system fully utilized, although time periods do exist where system utilization levels peak at nearly 95%. In this paper, we propose a new family of scheduling policies that aims at minimizing power consumption and cooling costs by selectively choosing to power down (or put in "sleep" mode) parts of the system during periods of low load. Our goal is the development of a scheduling mechanism that adaptively adjusts the number of processors to the offered load while meeting predefined service-level agreements (SLAs). This scheduling mechanism uses online simulation, i.e., lightweight simulation modules that can execute while the system and its scheduler are in operation, and can guide resource provisioning in parallel systems. Detailed experimentation using traces from the Parallel Workloads Archive indicates that the proposed online mechanism is a viable alternative to conserve energy while meeting performance-based SLAs.
Therapeutic Implications of Mesenchymal Stem Cells in Liver Injury (2011)

Mesenchymal stem cells (MSCs), represent an attractive tool for the establishment of a successful stem-cell-based therapy of liver diseases. A number of different mechanisms contribute to the therapeutic effects exerted by MSCs, since these cells can differentiate into functional hepatic cells and can also produce a series of growth factors and cytokines able to suppress inflammatory responses, reduce hepatocyte apoptosis, regress liver fibrosis, and enhance hepatocyte functionality. To date, the infusion of MSCs or MSC-conditioned medium has shown encouraging results in the treatment of fulminant hepatic failure and in end-stage liver disease in experimental settings. However, some issues under debate hamper the use of MSCs in clinical trials. This paper summarizes the biological relevance of MSCs and the potential benefits and risks that can result from translating the MSC research to the treatment of liver diseases.
Multiple Independent Defective Suppressor-mutator Transposon Insertions in Arabidopsis: A Tool for Functional Genomics (1999)

A new system for insertional mutagenesis based on the maize Enhancer/Suppressor-mutator (En/Spm) element was introduced into Arabidopsis. A single T-DNA construct carried a nonautonomous defective Spm (dSpm) element with a phosphinothricin herbicide resistance (BAR) gene, a transposase expression cassette, and a counterselectable gene. This construct was used to select for stable dSpm transpositions. Treatments for both positive (BAR) and negative selection markers were applicable to soil-grown plants, allowing the recovery of new transpositions on a large scale. To date, a total of 48,000 lines in pools of 50 have been recovered, of which approximately 80% result from independent insertion events. DNA extracted from these pools was used in reverse genetic screens, either by polymerase chain reaction (PCR) using primers from the transposon and the targeted gene or by the display of insertions whereby inverse PCR products of insertions from the DNA pools are spotted on a membrane that is then hybridized with the probe of interest. By sequencing PCR-amplified fragments adjacent to insertion sites, we established a sequenced insertion-site database of 1200 sequences. This database permitted a comparison of the chromosomal distribution of transpositions from various T-DNA locations.
GE132+Natural: Novel promising dietetic supplement with antiproliferative influence on prostate, colon, and breast cancer cells. (2013)

The data obtained demonstrated that GE132+Natural is effective in inhibiting cancer cell proliferation, indicating its potential beneficial health effects. In addition, the results pointed that adult mesenchymal stem cells might be valuable as a test system for evaluating the toxicity and efficacy of new medicines or chemicals.
Self Tuning Texture Optimization (2015)

Abstract The goal of example‐based texture synthesis methods is to generate arbitrarily large textures from limited exemplars in order to fit the exact dimensions and resolution required for a specific modeling task. The challenge is to faithfully capture all of the visual characteristics of the exemplar texture, without introducing obvious repetitions or unnatural looking visual elements. While existing non‐parametric synthesis methods have made remarkable progress towards this goal, most such methods have been demonstrated only on relatively low‐resolution exemplars. Real‐world high resolution textures often contain texture details at multiple scales, which these methods have difficulty reproducing faithfully. In this work, we present a new general‐purpose and fully automatic self‐tuning non‐parametric texture synthesis method that extends Texture Optimization by introducing several key improvements that result in superior synthesis ability. Our method is able to self‐tune its various parameters and weights and focuses on addressing three challenging aspects of texture synthesis: (i) irregular large scale structures are faithfully reproduced through the use of automatically generated and weighted guidance channels; (ii) repetition and smoothing of texture patches is avoided by new spatial uniformity constraints ; (iii) a smart initialization strategy is used in order to improve the synthesis of regular and near‐regular textures, without affecting textures that do not exhibit regularities. We demonstrate the versatility and robustness of our completely automatic approach on a variety of challenging high‐resolution texture exemplars.
Phosphorylation by cellular casein kinase II is essential for transcriptional activity of vesicular stomatitis virus phosphoprotein P. (1992)

We have previously shown that phosphorylation of vesicular stomatitis virus (VSV) phosphoprotein P by cellular protein kinase activity is an essential prerequisite for its transcriptional function. We have now purified this protein kinase by monitoring its ability to phosphorylate bacterially expressed, unphosphorylated P protein. Biochemical studies showed that the kinase is indistinguishable from casein kinase II, a ubiquitous cyclic AMP-independent protein kinase present in a wide variety of eukaryotic cells and tissues. Functional VSV transcription could be reconstituted with viral L protein, N-RNA template, and P protein phosphorylated by either purified cellular protein kinase or purified casein kinase II. The unusual role of casein kinase II in the transcription process of a nonsegmented negative-strand RNA virus would have important implications in host-virus interactions and antiviral therapy.
Site-Directed Mutagenesis and Oxygen Isotope Incorporation Studies of the Nucleophilic Aspartate of Haloalkane Dehalogenase (1994)

Haloalkane dehalogenase catalyzes the hydrolytic cleavage of carbon-halogen bonds in a broad range of halogenated aliphatic compounds. The X-ray structure suggests that Asp124, which is located close to an internal cavity, carries out a nucleophilic attack on the C alpha of the substrate, releasing the halogen. To study the mechanism of hydrolysis, this aspartate residue was mutated to alanine, glycine, or glutamate. The mutant enzymes showed no activity toward 1,2-dichloroethane and 1,2-dibromoethane. Incubation of purified wild-type dehalogenase with 1,2-dichloroethane in the presence of H2(18)O resulted in the incorporation of 18O in 2-chloroethanol and in the carboxylate group of Asp124. This shows that the reaction proceeds by covalent catalysis with the formation of an alkyl-enzyme intermediate that is hydrolyzed by attack of solvent water on the carbonyl carbon of Asp124. On the basis of amino acid sequence similarity between haloalkane dehalogenase and epoxide hydrolases, it is proposed that a conserved aspartate residue is also involved in covalent catalysis by the latter enzymes.
Rapid measurement of protein kinase and phosphatase activities by slot-filtration. (1992)

A slot-filtration method has been developed for the detection and quantitation of protein kinase and phosphatase activities. In this technique, after kinase-dependent phosphorylation or phosphatase-dependent dephosphorylation of different substrates, samples are transferred under vacuum onto nitrocellulose using a slot-blotting apparatus. Non-incorporated or released radioactivity is then removed by filtration and washing under vacuum. Quantitation is performed by scintillation or Cerenkov counting of the excised membrane slots. Application of the method to the assay of four different protein kinases (protein kinase N, cyclic AMP-dependent protein kinase and calcium/calmodulin-dependent protein kinases type I and type III) and one phosphatase is presented. A number of protein substrates with varying molecular masses and isoelectric points were found suitable for the slot-filtration technique. The method is applicable to impure as well as purified kinase and phosphatase preparations, can be used over a wide range of concentrations of substrates, has a very low background of nonspecific ATP binding and provides highly reproducible data. The slot-filtration method can also be adapted for use with ion-exchange paper, particularly for assays using peptides as substrates. The technique, with either nitrocellulose or ion-exchange paper, can be used to rapidly process large numbers of samples and can be simultaneously applied to direct comparison of different kinases, phosphatases and/or substrates in the same experiment.
Direction of arrival estimation based on information geometry (2016)

In this paper, a new direction of arrival (DOA) estimation approach is devised using concepts from information geometry (IG). The proposed method uses geodesic distances in the statistical manifold of probability distributions parametrized by their covariance matrix to estimate the direction of arrival of several sources. In order to obtain a practical method, the DOA estimation is treated as a single-variable optimization problem, for which the DOA solutions are found by means of a line search. The relation between the proposed method and MVDR beamformer is elucidated. An evaluation of its performance is carried out by means of Monte Carlo simulations and it is shown that the proposed method provides improved resolution capabilities at low SNR with respect to MUSIC and MVDR.
Ribonuclease inhibitors (2006)

RNases are important enzymes of cell metabolism, influencing gene expression, affecting cell growth and differentiation, and participating in cell defense against pathogens and induction of apoptosis. Since RNases mostly occur in complex with their inhibitors in the cell, the inhibitors also play a role in the above processes. The review considers natural protein RNase inhibitors of animals, plants, and bacteria, as well as synthetic low-molecular-weight inhibitors. Special emphasis is placed on the prospective use of RNase inhibitors in the therapy of cancer and allergy. While RNases are widespread, the number of the available natural and synthetic inhibitors is limited. A pressing problem is to design highly effective low-molecular-weight inhibitors of the RNase activity of angiogenin and eosinophil-associated RNases for anticancer and antiallergy therapy.
Glucagon-Like Peptide-I and the Control of Insulin Secretion in the Normal State and in NIDDM (1993)

Potentiation of glucose-induced insulin secretion by intestinal factors has been described for many years. Today, two major peptides with potent insulinotropic action have been recognized: gastric inhibitory peptide and truncated forms of glucagon-like peptide I, GLP-I(7-37) or the related GLP-I(7-36)amide. These hormones have specific beta-cell receptors that are coupled to production of cAMP and activation of cAMP-dependent protein kinase. Elevation in intracellular cAMP levels is required to mediate the glucoincretin effect of these hormones: the potentiation of insulin secretion in the presence of stimulatory concentrations of glucose. In addition, circulating glucoincretins maintain basal levels of cAMP, which are necessary to keep beta-cells in a glucose-competent state. Interactions between glucoincretin signaling and glucose-induced insulin secretion may result from the phosphorylation of key elements of the glucose signaling pathway by cAMP-dependent protein kinase. These include the ATP-dependent K+ channel, the Ca++ channel, or elements of the secretory machinery itself. In NIDDM, the glucoincretin effect is reduced. However, basal or stimulated gastric inhibitory peptide and glucagon-like peptide I levels are normal or even elevated, suggesting that signals induced by these hormones on the beta-cells are probably altered. At pharmacological doses, infusion of glucagon-like peptide I but not gastric inhibitory peptide, can ameliorate postprandial insulin secretory response in NIDDM patients. Agonists of the glucagon-like peptide I receptor have been proposed as new therapeutic agents in NIDDM.
LYMPHANGIOGENESIS IN TISSUE-ENGINEERED SMALL INTESTINE (2004)

Lymphangiogenesis occurs in tissue-engineered small intestine. This is the first demonstration of lymphatic vessels in an engineered tissue.
Multiple vs. wide shared bus multiprocessors (1989)

In this paper we compare the simulated performance of a family of multiprocessor architectures based on a global shared memory. The processors are connected to the memory through caches that snoop one or more shared buses in crossbar arrangement.
THE GENETICS OF SUSCEPTIBILITY TO MULTIPLE SCLEROSIS1 (1982)

Journal Article THE GENETICS OF SUSCEPTIBILITY TO MULTIPLE SCLEROSIS Get access RICHARD S. SPIELMAN, RICHARD S. SPIELMAN Search for other works by this author on: Oxford Academic PubMed Google Scholar NEAL NATHANSON NEAL NATHANSON Search for other works by this author on: Oxford Academic PubMed Google Scholar Epidemiologic Reviews, Volume 4, Issue 1, 1982, Pages 45–65, https://doi.org/10.1093/oxfordjournals.epirev.a036251 Published: 01 March 1982
The chemokine receptor CCR7 mediates corneal antigen-presenting cell trafficking. (2007)

These data suggest that in inflammation, APC expressing CCR7 on their cell surface interact with CCL21 to facilitate their migration from the cornea to draining LN via afferent lymphatics.
A three-part system for refining intraocular lens power calculations (1988)

A three-part system that determines the correct power for an intraocular lens (IOL) to achieve a desired postoperative refraction is presented. The three components are (1) data screening criteria to identify improbable axial length and keratometry measurements, (2) a new IOL calculation formula that exceeds the current accuracy of other formulas for short, medium, and long eyes, and (3) a personalized "surgeon factor" that adjusts for any consistent bias in the surgeon's results, from any source, based on a reverse solution of the new formula; the reverse solution uses the postoperative stabilized refraction, the dioptric power of the implanted IOL, and the preoperative corneal and axial length measurements to calculate the personalized surgeon factor. The improved accuracy of the new formula was proven by performing IOL power calculations on 2,000 eyes from 12 surgeons and comparing the results to seven other currently used formulas.
Targeting of retroviral vectors through protease-substrate interactions. (1996)

Targetable, injectable vectors would greatly facilitate the development of in vivo therapy strategies. Viral and nonviral vectors can be targeted through ligand-receptor interactions, but protease-substrate interactions have not previously been exploited for vector targeting. Epidermal growth factor (EGF) was fused to a retroviral envelope glycoprotein via a cleavable linker comprising a factor Xa protease recognition signal. Vector particles displaying the cleavable EGF domain could bind to EGF receptors on human cells but did not transfer their genes until they were cleaved by factor Xa protease, whereupon gene delivery proceeded normally. Proteolytic activation of receptor-targeted vectors can therefore provide the basis for a novel two-step targeting strategy that may facilitate efficient targeted in vivo delivery of therapeutic genes.
Effect of Treatment with Biosynthetic Human Growth Hormone (GH) on Peripheral Blood Lymphocyte Populations and Function in Growth Hormone-Deficient Children (1990)

GH influences the immune response. The mechanism is not known; however, the presence of receptors for GH on human lymphocytes as well as its ability to influence and modulate immune responses in animals suggest an association between GH and immune function in man. We evaluated the effect of recombinantly derived natural sequence human GH (hGH) on lymphocyte surface antigen expression, response to mitogenic stimulation, expression of interleukin-1 receptors, and production of anti-hGH antibodies in GH-deficient children. The only observed changes were a decrease in the percentage of B-cells and a transient increased reactivity to phytohemagglutinin stimulation. It appears from the results of our studies that the administration of hGH has a selective effect on lymphocyte immune function; however, we cannot eliminate a role for hGH in the initiation or regulation of antigen-mediated immune responses.
[Treatment of chronic wounds with cultured autologous keratinocytes as suspension in fibrin glue]. (2000)

Cultivated keratinocytes have been used for treatment of chronic wounds. Our group developed a new application form, using a suspension of subconfluently cultivated keratinocytes in fibrin glue (keratinocyte-fibrin-glue-suspension = KFGS), which has successfully been used in burn patients. Altogether 8 patients (average: 57 yrs.) with complex chronic wounds of different origin were treated with KFGS. All wounds, which had been existing from 4 months to 14 years, showed good reepithelization. Up to now there has been observed stable wound closure for 4 years after grafting. This study demonstrates the wound healing potency of a keratinocyte-fibrin-glue-suspension also for chronic wounds. Fibrin glue seems to be both an ideal application vehicle as a biological matrix for the cultivated keratinocytes. The transplantation of cultivated autologous keratinocytes as suspension in fibrin glue is a promising way in the treatment of chronic wounds.
Highly reliable 45-nm-half-pitch Cu interconnects incorporating a Ti/TaN multilayer barrier (2010)

A Ti/TaN multi-layer can achieve a highly reliable Cu interconnect with a porous SiOC (ELK; k <; 2.5) structure. Ti shows good wettability with Cu and unique properties with extreme low-k (ELK)-structured interconnects. On the other hand, Ta is known to be an effective barrier to Cu diffusion. We confirmed that the Ti barrier is different from the Ta barrier from the viewpoint of metal-oxide behavior and improved electromigration (EM) and stress migration (SM). In addition, the time-dependent dielectric breakdown (TDDB) characteristic can be improved by using a Ti barrier combined with a TaN barrier.
Cardiac Ultrarapid Delayed Rectifiers (1999)

Classical cardiac delayed rectifier currents activate at least two orders of magnitude slower than delayed rectifier currents in nerve and skeletal muscle tissue. It has recently become evident that many cardiac tissues express delayed rectifier currents with kinetics similar to those of nerve and muscle. These currents have been designated I(Kur) (for 'ultrarapid' delayed rectifier), in contrast to the classical cardiac rapid (I(Kr)) and slow (I(Ks)) delayed rectifier components. Although the kinetics of I(Kur) in different species and tissues are similar, their pharmacological properties vary greatly. It now appears that the differences among various I(Kur)s are due to differences in the molecular basis. A variety of Shaker-related clones (Kv1.2, 1.5, 2.1 and 3.1) that form I(Kur) channels upon heterologous expression have been identified with specific I(Kur)s (e.g. Kv1.2, rat atrium; Kv1.5, mouse ventricle and human atrium; Kv3.1, dog atrium). The present article reviews the distribution, biophysical and pharmacological properties, molecular basis and functional role of I(Kur), as well as the potential value of I(Kur) as a target for new antiarrhythmic drug development.