gebhart/patrepeval huggingface dataset:
Antiphospholipid antibodies directed against a combination of phospholipids with prothrombin, protein C, or protein S: an explanation for their pathogenic mechanism? [see comments] (1993)

Despite many studies on the pathophysiology of antiphospholipid antibodies (aPL), the mechanism by which aPL causes thrombosis has not been established. We have tried to elucidate the paradox between the prolongation of the clotting time of phospholipid-dependent coagulation tests in vitro and the occurrence of thrombosis in vivo. The effect on endothelial cell-mediated prothrombinase activity of 30 IgG fractions, of which 22 prolong the aPTT of normal plasma, was investigated. Only 4 of 22 fractions (18%) inhibited prothrombinase activity when tested on this more physiologic phospholipid surface, indicating that in most patients with aPL the prolongation of clotting tests is predominantly as in vitro phenomenon. It was recently reported that in detection methods for aPL, two plasma proteins, beta 2-glycoprotein I and prothrombin, enhance the binding of aPL to phospholipids. We have studied the specificity of the 4 IgG fractions that inhibit the prothrombinase activity and found that they were directed against a combination of phospholipids and prothrombin. However, the involvement of prothrombin in binding of aPL leading to impaired thrombin generation could still result in both a bleeding and a thrombotic tendency. Therefore, we proposed a new thrombogenic mechanism for aPL in which aPL bind to complexes of phospholipids and coagulation proteins, thereby interfering in different coagulation reactions. We tested this new hypothesis by investigating the effect of IgG from the same 30 patients on the activated protein C (APC)-mediated factor Va inactivation in the absence and presence of protein S. Three IgGs that inhibited APC-mediated factor Va inactivation independent of protein S and 4 additional IgGs that inhibited in the presence of protein S were found. Furthermore, we could specifically adsorb the inhibitory IgG with cardiolipin vesicles to which APC with or without protein S was bound. In conclusion, these results suggest that subpopulations of aPL exist that are directed to complexes of phospholipids and different plasma proteins. The identity of the plasma proteins involved in the binding of aPL might determine which pathogenic mechanism causes thrombosis.
Constitutive episomal expression of polypeptide IX (pIX) in a 293-based cell line complements the deficiency of pIX mutant adenovirus type 5 (1995)

The human adenovirus type 5 capsid is composed of a number of distinct polypeptides. It has been shown previously that one of these, polypeptide IX (pIX), is not absolutely required for the production of viable virus. However, viruses lacking this polypeptide have a significantly reduced packaging limit and, in the one case studied, also show a thermolabile virion phenotype. This report describes the use of eukaryotic episomal vectors based on the Epstein-Barr virus replicon to generate cells which stably express pIX. These cells provide pIX that is efficiently incorporated into virions that are genetically pIX-; such enhanced thermostability. These cells have also been used to isolate a genetically pIX- virus having a genome of length some 2.3 kbp in excess of the previously defined packaging limit for pIX- virus; the resulting virions have wild-type thermostability. These cells expand the theoretical capacity of adenovirus vectors for foreign DNA to around 9.2 kbp and may therefore be useful in gene therapy applications in which vector capacity is limiting.
Gastrointestinal stem cells (2002)

Turnover of the epithelial cell lineages within the gastrointestinal tract is a constant process, occurring every 2-7 days under normal homeostasis and increasing after damage. This process is regulated by multipotent stem cells, which give rise to all gastrointestinal epithelial cell lineages and can regenerate whole intestinal crypts and gastric glands. The stem cells of the gastrointestinal tract are as yet undefined, although it is generally agreed that they are located within a 'niche' in the intestinal crypts and gastric glands. Studies of allophenic tetraparental chimeric mice and targeted stem cell mutations suggest that a single stem cell undergoes asymmetrical division to produce an identical daughter cell, and thus replicate itself, and a committed progenitor cell which further differentiates into an adult epithelial cell type. The discovery of stem cell plasticity in many tissues, including the ability of transplanted bone marrow to transdifferentiate into intestinal subepithelial myofibroblasts, provides a potential use of bone marrow cells to deliver therapeutic genes to damaged tissues, for example, in treatment of mesenchymal diseases in the gastrointestinal tract, such as fibrosis and Crohn's disease. Studies are beginning to identify the molecular pathways that regulate stem cell proliferation and differentiation into adult gastrointestinal cell lineages, such as the Wnt and Notch/Delta signalling pathways, and the importance of mesenchymal-epithelial interactions in normal gastrointestinal epithelium and in development and disease.
The Role of High-Density Lipoproteins in Reducing the Risk of Vascular Diseases, Neurogenerative Disorders, and Cancer (2010)

High-density lipoprotein (HDL) is one of the major carriers of cholesterol in the blood. It attracts particular attention because, in contrast with other lipoproteins, as many physiological functions of HDL influence the cardiovascular system in favourable ways unless HDL is modified pathologically. The functions of HDL that have recently attracted attention include anti-inflammatory and anti-oxidant activities. High anti-oxidant and anti-inflammatory activities of HDL are associated with protection from cardiovascular disease. Atheroprotective activities, as well as a functional deficiency of HDL, ultimately depend on the protein and lipid composition of HDL. Further, numerous epidemiological studies have shown a protective association between HDL-cholesterol and cognitive impairment. Oxidative stress, including lipid peroxidation, has been shown to be the mediator of the pathologic effects of numerous risk factors of Alzheimer's disease. Lifestyle interventions proven to increase HDL- cholesterol levels including "healthy" diet, regular exercise, weight control, and smoking cessation have also been shown to provide neuro-protective effects. This review will focus on current knowledge of the beneficial effects of HDL-cholesterol as it relates to cardiovascular diseases, breast and lung cancers, non-Hodgkin's lymphoma, as well as its neuroprotective potential in reducing the risk of Alzheimer's disease and dementia.
The Dynamic Two-Fluid Model OLGA: Theory and Application (1991)

Summary Dynamic two-fluid models have found a wide range of application in the simulation of two-phase-flow systems, particularly for the analysis of steam/water flow in the core of a nuclear reactor. Until quite recently, however, very few attempts have been made to use such models in the simulation of two-phase oil and gas flow in pipelines. This paper presents a dynamic two-fluid model, OLGA, in detail, stressing the basic equations and the two-fluid models applied. Predictions of steady-state pressure drop, liquid holdup, and flow-regime transitions are compared with data from the SINTEF Two-Phase Flow Laboratory and from the literature. Comparisons with evaluated field data are also presented.
The role of interleukin-2 receptor alpha in cancer (2005)

Interleukin-2 (IL-2) is the major growth factor for activated T-lymphocytes and stimulates clonal expansion and maturation of these lymphocytes. IL-2 binds to its receptor complex, IL-2Ralpha, beta, and gamma chains, and exerts its effect via second messengers, mainly tyrosine kinases, which ultimately stimulate gene expression. The heterotrimerization of the receptor chains leads to high affinity binding for IL-2. The functional importance of IL-2Ralpha in hematopoietic cell systems is well known. However, the potential role that IL-2Ralpha plays in tumorigenesis is still not fully elucidated. Il-2Ralpha expression has been found in many types of cancers, including leukemia, lymphoma, lung, breast, head-and-neck and prostate. Recent evidence shows that high expression of IL-2Ralpha in tumors correlates with a poor prognosis for the patient. This review details the current known functions of IL-2Ralpha in cancer cells and some of the therapies used to combat IL-2Ralpha-mediated cell signaling.
Extractive fermentation for butyric acid production from glucose by Clostridium tyrobutyricum (2003)

A novel extractive fermentation for butyric acid production from glucose, using immobilized cells of Clostridium tyrobutyricum in a fibrous bed bioreactor, was developed by using 10% (v/v) Alamine 336 in oleyl alcohol as the extractant contained in a hollow-fiber membrane extractor for selective removal of butyric acid from the fermentation broth. The extractant was simultaneously regenerated by stripping with NaOH in a second membrane extractor. The fermentation pH was self-regulated by a balance between acid production and removal by extraction, and was kept at approximately pH 5.5 throughout the study. Compared with conventional fermentation, extractive fermentation resulted in a much higher product concentration (>300 g/L) and product purity (91%). It also resulted in higher reactor productivity (7.37 g/L. h) and butyric acid yield (0.45 g/g). Without on-line extraction to remove the acid products, at the optimal pH of 6.0, the final butyric acid concentration was only approximately 43.4 g/L, butyric acid yield was 0.423 g/g, and reactor productivity was 6.77 g/L. h. These values were much lower at pH 5.5: 20.4 g/L, 0.38 g/g, and 5.11 g/L. h, respectively. The improved performance for extractive fermentation can be attributed to the reduced product inhibition by selective removal of butyric acid from the fermentation broth. The solvent was found to be toxic to free cells in suspension, but not harmful to cells immobilized in the fibrous bed. The process was stable and provided consistent long-term performance for the entire 2-week period of study.
Nonlinear dynamics of heart rate in epilepsy (2002)

The relationships between onset of ictal activity and changes in heart rate are examined using Poincare analysis based on R-to-R intervals from EKGs recorded simultaneously with multi-electrode EEGs. The R-to-R intervals are used to compute 2-D and 3-D Poincare plots, where 2-D plots are scatter diagrams of intervals against adjacent intervals, and 3-D plots include intervals as a function of time. Data was examined beginning several minutes prior to seizure. The Poincare technique was chosen due to its noted success in the study of heart failure and the existing relationship between epileptic seizure and syncopal attacks. The intention of this paper is to identify heart rate as a valid indicator of precursor activity in epileptic seizure occurrences. This is done through visual observation of rotated 3-D Poincare plots and the Student's t-test technique to identify recorded measurements of pre-ictal heart rate activity. Finding a relationship between heart rate variation using R-to-R intervals may be significant in distinguishing heart rate as a precursor agent of neurological seizure occurrences.
Flash Memory: Photochemical Imprinting of Neuronal Action Potentials onto a Microbial Rhodopsin (2014)

We developed a technique, "flash memory", to record a photochemical imprint of the activity state--firing or not firing--of a neuron at a user-selected moment in time. The key element is an engineered microbial rhodopsin protein with three states. Two nonfluorescent states, D1 and D2, exist in a voltage-dependent equilibrium. A stable fluorescent state, F, is reached by a photochemical conversion from D2. When exposed to light of a wavelength λ(write), population transfers from D2 to F, at a rate determined by the D1 ⇌ D2 equilibrium. The population of F maintains a record of membrane voltage which persists in the dark. Illumination at a later time at a wavelength λ(read) excites fluorescence of F, probing this record. An optional third flash at a wavelength λ(reset) converts F back to D2, for a subsequent write-read cycle. The flash memory method offers the promise to decouple the recording of neural activity from its readout. In principle, the technique may enable one to generate snapshots of neural activity in a large volume of neural tissue, e.g., a complete mouse brain, by circumventing the challenge of imaging a large volume with simultaneous high spatial and high temporal resolution. The proof-of-principle flash memory sensors presented here will need improvements in sensitivity, speed, brightness, and membrane trafficking before this goal can be realized.
Identification of the molecular attributes required for aminoglycoside activity against Leishmania (2013)

Leishmaniasis, a parasitic disease caused by protozoa of the genus Leishmania, affects millions of people worldwide. Aminoglycosides are mostly known as highly potent, broad-spectrum antibiotics that exert their antibacterial activity by selectively targeting the decoding A site of the bacterial ribosome, leading to aberrant protein synthesis. Recently, some aminoglycosides have been clinically approved and are currently used worldwide for the treatment of leishmaniasis; however the molecular details by which aminoglycosides induce their deleterious effect on Leishmaina is still rather obscure. Based on high conservation of the decoding site among all kingdoms, it is assumed that the putative binding site of these agents in Leishmania is the ribosomal A site. However, although recent X-ray crystal structures of the bacterial ribosome in complex with aminoglycosides shed light on the mechanism of aminoglycosides action as antibiotics, no such data are presently available regarding their binding site in Leishmania. We present crystal structures of two different aminoglycoside molecules bound to a model of the Leishmania ribosomal A site: Geneticin (G418), a potent aminoglycoside for the treatment of leishmaniasis at a 2.65-Å resolution, and Apramycin, shown to be a strong binder to the leishmanial ribosome lacking an antileishmanial activity at 1.4-Å resolution. The structural data, coupled with in vitro inhibition measurements on two strains of Leishmania, provide insight as to the source of the difference in inhibitory activity of different Aminoglycosides. The combined structural and physiological data sets the ground for rational design of new, and more specific, aminoglycoside derivatives as potential therapeutic agents against leishmaniasis.
High accuracy plasma density measurement using hybrid Langmuir probe and microwave interferometer method (2007)

High spatial resolution plasma density measurements have been taken as part of an investigation into magnetic nozzle physics at the NASA/MSFC Propulsion Research Center. These measurements utilized a Langmuir triple probe scanned across the measurement chord of either of two stationary rf interferometers. By normalizing the scanned profile to the microwave interferometer line-integrated density measurement for each electrostatic probe measurement, the effect of shot-to-shot variation of the line-integrated density can be removed. In addition, by summing the voltage readings at each radial position in a transverse scan, the line density can be reconstituted, allowing the absolute density to be determined, assuming that the shape of the profile is constant from shot to shot. The spatial and temporal resolutions of this measurement technique depend on the resolutions of the scanned electrostatic probe and the interferometer. The measurement accuracy is 9%-15%, which is on the order of the accuracy of the rf interferometer. The measurement technique was compared directly with both scanning rf interferometer and standard Langmuir probe theory. The hybrid technique compares favorably with the scanning rf interferometer, and appears more accurate than probe theory alone. Additionally, our measurement technique is generally applicable even for nonaxisymmetric plasmas.
SH2-B Is a Positive Regulator of Nerve Growth Factor-mediated Activation of the Akt/Forkhead Pathway in PC12 Cells (2003)

To gain insight into the mechanism by which the adapter protein SH2-B promotes nerve growth factor (NGF)-mediated neuronal differentiation and survival, the effect of SH2-B on the serine/threonine kinase Akt/protein kinase B and downstream effector proteins was examined. PC12 cells stably overexpressing SH2-Bbeta, which exhibit enhanced NGF-induced neuronal differentiation compared with control cells, showed enhanced and prolonged NGF-induced phosphorylation of Akt on Ser473 and Akt enzymatic activity. Surprisingly, NGF-induced phosphorylation of Akt on Ser473 and Akt activity were not altered in cells overexpressing SH2-Bbeta(R555E) with a defective SH2 domain, despite the ability of the overexpressed SH2-Bbeta(R555E) to block NGF-induced differentiation. Consistent with SH2-Bbeta enhancing the activity of Akt, cells overexpressing SH2-Bbeta but not SH2-Bbeta(R555E) exhibited increased and/or prolonged phosphorylation of the pro-apoptotic Akt effector proteins, glycogen synthase kinase-3, and forkhead transcription factors, FKHRL1/FOXO3 and FKHR/FOXO1. Immunolocalization studies indicated that, although ectopically expressed FKHR was primarily concentrated in the cytoplasm of control cells and cells transiently overexpressing SH2-Bbeta, it was concentrated in the nucleus of cells transiently overexpressing SH2-Bbeta(R555E). Similarly, SH2-Bbeta stimulated the accumulation of FKHR in the cytoplasm of 293T and COS-7 cells, whereas SH2-Bbeta(R555E) enhanced its accumulation in the nucleus. In PC12 cells stably expressing forms of SH2-Bbeta, SH2-Bbeta mimicked the ability of NGF to promote redistribution of FKHR to the cytoplasm whereas SH2-Bbeta(R555E) blocked this effect of NGF. Taken together, these data indicate that SH2-B is a positive regulator of NGF-mediated activation of the Akt/Forkhead pathway.
Engineering of a Genetically Encodable Fluorescent Voltage Sensor Exploiting Fast Ci-VSP Voltage-Sensing Movements (2008)

Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a genetically encodable fluorescent protein voltage sensor (VSFP) in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence read-outs.
New design for low-loss star couplers and arrayed waveguide grating devices (2002)

We propose a new loss reduction method in star couplers employing UV-written tapers that replace the free propagation region in the conventional star couplers and apply them to an arrayed waveguide grating (AWG) device. The insertion loss of the new AWG device can be reduced to 0.31 dB, which is about 0.7 dB lower than that of the AWG without UV-written tapered waveguides.
Biosynthesis and posttranslational processing of site-directed endoproteolytic cleavage mutants of pro-neuropeptide Y in mouse pituitary cells. (1990)

Although pairs of basic amino acids are common endoproteolytic sites in prohormones, the enzymes responsible for these cleavages have not yet been characterized. To investigate the specificity of these endoproteases, cDNAs encoding pro-neuropeptide Y (pro-NPY) containing all four pairs of basic amino acids were expressed in AtT-20 cells. Pro-NPY was selected as a model substrate because it undergoes a single cleavage at the sequence -Lys-Arg- during posttranslational processing. AtT-20 cells, a mouse anterior pituitary corticotrope line, were selected because they synthesize pro-adrenocorticotropic hormone (pro-ACTH)/endorphin and cleave a well characterized subset of the eight pairs of basic amino acids in the precursor. Altered cDNAs encoding pro-NPY with -Arg-Arg-, -Arg-Lys-, or Lys-Lys- at the cleavage site were used to generate stable cell lines. The production of NPY and the carboxyl-terminal peptide was studied using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gel filtration, reversed-phase high performance liquid chromatography, ion-exchange high performance liquid chromatography, tryptic peptide mapping, and microsequencing. Direct amino acid labeling confirmed the identity of the pair of basic amino acids at the cleavage site. Even when the four pairs of basic amino acids were presented in the same structural context, the rate, extent, and type of cleavage was substrate-specific. Pro-NPY(-Arg-Arg-) was cleaved at a rate similar to that observed for the wild-type pro-NPY(-Lys-Arg-). In contrast, pro-NPY(-Arg-Lys-) was cleaved at a much lower rate, and pro-NPY (-Lys-Lys-) was cleaved very poorly. Following endoproteolytic cleavage, the pair of basic amino acids present did not alter the production of mature NPY with a COOH-terminal Tyr-NH2. While two of the three mutant pro-NPY molecules were processed to wild-type carboxyl-terminal peptide, the carboxyl-terminal peptide derived from pro-NPY(-Arg-Lys-) contained an amino-terminal lysine residue, indicating that biosynthetic endoproteolysis occurred in the middle or at the amino terminus of the pair of basic amino acid residues at the cleavage site. Expression of wild-type or mutant pro-NPY inhibited cleavages within the endogenous pro-ACTH/endorphin; poorly cleaved pro-NPY mutants (Lys in the second position of the cleavage site) were the most potent inhibitors of pro-ACTH/endorphin cleavage.
Reconfigurable accelerators for combinatorial problems (2000)

Reconfigurable accelerators can improve process time on combinatorial problems with fine-grained parallelism. Such problems contain a huge number of logical operations (NOT, AND and OR) that can evaluate simultaneously, a characteristic that varies considerably from problem to problem. Because of this variability, such combinatorial problems are approached using instance-specific reconfiguration-hardware tailored to a specific algorithm and a specific set of input data. Boolean satisfiability (SAT for short) is a common combinatorial problem that exhibits fine-grained parallelism. SAT varies considerably based on the situation. Its solution is thus an ideal candidate for improvements based on instance-specific reconfiguration. In fact, simulation of an instance-specific accelerator show potential speed-ups by a factor of up to 140,000 in execution time over the solution by a software solver. The authors detail the results of their prototype that results an order-of-magnitude speed-up in the execution of difficult satisfiability problems.
A dynamic T cell–limited checkpoint regulates affinity-dependent B cell entry into the germinal center (2011)

The germinal center (GC) reaction is essential for the generation of the somatically hypermutated, high-affinity antibodies that mediate adaptive immunity. Entry into the GC is limited to a small number of B cell clones; however, the process by which this limited number of clones is selected is unclear. In this study, we demonstrate that low-affinity B cells intrinsically capable of seeding a GC reaction fail to expand and become activated in the presence of higher-affinity B cells even before GC coalescence. Live multiphoton imaging shows that selection is based on the amount of peptide-major histocompatibility complex (pMHC) presented to cognate T cells within clusters of responding B and T cells at the T-B border. We propose a model in which T cell help is restricted to the B cells with the highest amounts of pMHC, thus allowing for a dynamic affinity threshold to be imposed on antigen-binding B cells.