gebhart/patrepeval huggingface dataset:
Self-assembly and calcium-binding sites in laminin. A three-arm interaction model (1993)

Laminin, a four-arm glycoprotein, polymerizes in vitro into networks similar to those found in basement membranes. We have dissected this calcium-dependent assembly by analyzing proteolytic fragment binding using equilibrium gel filtration, ultracentrifugation, and electron microscopy. The cathepsin G fragment C1-4 (three short arms) was found to aggregate with a critical concentration similar to that for laminin. Like laminin polymerization, this assembly was inhibited by the smaller elastase short arm fragments E4 (B1 domains VI and V) and E1' (A-B2 short arm complex). Fragment E4 bound directly to E1' in a calcium-dependent manner (KD = 1.4 microM). In contrast, homologous self-interactions of short arm fragments and all interactions of long arm fragments were considerably weaker or nonexistent. While electron micrographs of E1' or E4 alone contained mostly monomers, those of E1'/E4 mixtures contained dimers and oligomers with E1' dimers connected to each other through their A and B2 arms, often with visible E4 molecules at their junctions. 45Ca2+ bound principally to fragment E1' with localization to the end of the B2 chain. These data support a model in which polymerization requires the interaction of all three ligands, one from each short arm, with calcium activating assembly by binding to the B2 short arm.
Rapid and Unambiguous Identification of Melamine in Contaminated Pet Food Based on Mass Spectrometry with Four Degrees of Confirmation (2007)

A method for analyzing pet food without sample processing is described for rapid identification of melamine based on mass spectrometry (MS) using soft ionization by direct analysis in real time (DART) to provide accurate measurement of mass and isotope-peak intensities, in-source collisionally activated dissociation (CAD) fragmentation, and determination of active hydrogens. Usually, MS analyses based on other than electron ionization (EI) spectra can be suspect because of the limited amount of information provided by a single mass spectral peak (or very few peaks). In such cases, additional degrees of confirmation are desirable to increase confidence in the experimental results. Chromatographic retention time can provide a degree of confidence; however, this requires time and, in some cases, detailed sample processing. Currently, the United States Food and Drug Administration uses a gas chromatography-EI-MS technique for the determination of melamine in pet food that involves sample extraction and derivatization prior to a lengthy chromatographic separation. In the method described here, identification is also confirmed through a determination of the number of active hydrogen atoms in the analyte molecule achieved by hydrogen/deuterium (H/D) exchange by treatment with deuterium oxide (D2O) at the initial stage of analysis. Cross-correlation of these four experimental data provides an unambiguous identification of melamine in contaminated pet food without the need for any sample preparation or chromatography. Limits of detection and the validity of the H/D exchange method as a confirmatory technique are also presented.
Improvement of erythropoiesis in β-thalassemic mice by continuous erythropoietin delivery from muscle (2000)

beta-Thalassemias are highly prevalent genetic disorders that can cause severe hemolytic anemia. The main pathophysiologic feature of beta-thalassemia is the accumulation of unpaired alpha-globin chains in erythrocyte precursors and red blood cells (RBCs). This accumulation alters cell membrane function and results in early cell destruction and ineffective erythropoiesis. Correction of globin chain imbalance through the induction of fetal hemoglobin (HbF) synthesis is a tentative therapeutic approach for this class of diseases. In short-term in vitro or in vivo assays, recombinant human erythropoietin increases the frequency of erythroid precursors programmed to HbF in humans and to beta-minor globin in mice. In contrast, long-term treatment of beta-thalassemic patients did not induce HbF significantly. We took advantage of highly efficient adeno-associated virus-mediated (AAV-mediated) gene transfer into mouse muscle to induce a robust and sustained secretion of mouse erythropoietin in beta-thalassemic mice, which represent a suitable model for human beta-thalassemia intermedia. A 1-year follow-up of 12 treated animals showed a stable correction of anemia associated with improved RBC morphology, increased beta-minor globin synthesis, and decreased amounts of alpha-globin chains bound to erythrocyte membranes. More effective erythropoiesis probably accounted for a reduction of erythroid cell proliferation, as shown by decreased proportions of circulating reticulocytes and by reduced iron 59 ((59)Fe) incorporation into erythroid tissues. This study indicates that the continuous delivery of high amounts of autologous erythropoietin induced a sustained stimulation of beta-minor globin synthesis and a stable improvement of erythropoiesis in the beta-thalassemic mouse model. (Blood. 2000;95:2793-2798)
Soluble surface proteins from Helicobacter pylori activate monocytes/macrophages by lipopolysaccharide-independent mechanism. (1991)

The inflammatory lesions associated with Helicobacter pylori gastritis and duodenitis contain large numbers of mononuclear cells. The close proximity of H. pylori to gastric mucosa suggests that the organism interacts with mononuclear cells, thereby modulating the inflammatory response. To investigate the role of monocytes/macrophages in this response, we examined the effect of whole H. pylori bacteria, H. pylori surface proteins, and H. pylori lipopolysaccharide (LPS) on purified human monocytes. Whole H. pylori and the extracted LPS induced expression of the monocyte surface antigen HLA-DR and interleukin-2 receptors, production of the inflammatory cytokines interleukin 1 and tumor necrosis factor (peptide and messenger RNA), and secretion of the reactive oxygen intermediate superoxide anion. Since H. pylori in vivo does not invade mucosal tissue, we determined whether soluble constituents of the bacteria could activate monocytes. Soluble H. pylori surface proteins, which are enriched for urease and do not contain LPS, stimulated phenotypic, transcriptional, and functional changes consistent with highly activated monocytes. These findings indicate that H. pylori is capable of activating human monocytes by an LPS-independent as well as an LPS-dependent mechanism. H. pylori activation of resident lamina propria macrophages and monocytes trafficking through the mucosa, leading to the secretion of increased amounts of inflammatory cytokines and reactive oxygen intermediates, could play an important role in mediating the inflammatory response associated with H. pylori gastritis and duodenitis.
Recent advances in the treatment of L-DOPA-induced dyskinesia. (2002)

Parkinson's disease (PD) is a degenerative movement disorder resulting from the loss of dopaminergic neurons in the substantia nigra pars compacta. The most widely used treatment for PD is administration of the dopamine precursor L-DOPA, although this eventually results in uncontrolled involuntary movements (dyskinesia) that can be more debilitating than the underlying disease itself. The causes of L-DOPA-induced dyskinesia are unclear, but probably involve non-physiological pulsatile stimulation of dopamine receptors or non-physiological dopamine release (eg, from serotonergic nerve terminals) in the striatum. In any case, this signaling leads to an imbalance in the activity of two basal ganglia pathways, the 'direct' and 'indirect' striatal output pathways, that are characterized by distinct neurochemical architectures. The wide range of neurotransmitter and neuromodulatory receptors present on these two striatal output pathways offers a huge range of potential therapeutic targets. Two main strategies for the treatment of dyskinesia exist: the use of drugs that can be given as an adjunct to L-DOPA, reducing the occurrence of dyskinesia without impairing its antiparkinsonian effect, or therapies with equal antiparkinsonian action as L-DOPA that do not elicit dyskinesia. Novel treatments for dyskinesia in clinical/preclinical development include A(2alpha) receptor antagonists, alpha(2) adrenoceptor antagonists, mu-opioid receptor antagonists and subtype-selective NMDA antagonists. Future research strategies are likely to focus on the molecular mechanisms underlying the emergence of dyskinesia and may lead to the development of agents that can prevent or reverse the cellular changes underlying this phenomenon.
The RAW benchmark suite: computation structures for general purpose computing (2002)

The RAW benchmark suite consists of twelve programs designed to facilitate comparing, validating, and improving reconfigurable computing systems. These benchmarks run the gamut of algorithms found in general purpose computing, including sorting, matrix operations, and graph algorithms. The suite includes an architecture-independent compilation framework, Raw Computation Structures (RawCS), to express each algorithm's dependencies and to support automatic synthesis, partitioning, and mapping to a reconfigurable computer. Within this framework, each benchmark is portably designed in both C and Behavioral Verilog and scalably parameterized to consume a range of hardware resource capacities. To establish initial benchmark ratings, we have targeted a commercial logic emulation system based on virtual wires technology to automatically generate designs up to millions of gates (14 to 379 FPGAs). Because the virtual wires techniques abstract away machine-level details like FPGA capacity and interconnect, our hardware target for this system is an abstract reconfigurable logic fabric with memory-mapped host I/O. We report initial speeds in the range of 2X to 1800X faster than a 2.82 SPECint95 SparcStation 20 and encourage others in the field to run these benchmarks on other systems to provide a standard comparison.
<title>Utility of quantitative ultrasound for tracking the progression of polycystic kidney disease</title> (2000)

We are combining techniques of quantitative ultrasonic imaging to study polycystic kidney disease (PKD) as the disease progresses to renal failure. Our goal is to use ultrasound noninvasively to detect morphological changes early in the disease process when interventions are most likely to be successful and prior to a significant loss in renal function. We are examining the kidneys of normal rats and those with PKD at various ages with several techniques to obtain comprehensive knowledge of the disease progression. The Han:SPRD rat inherits PKD as an autosomal dominant trait (ADPKD) that closely mimics ADPKD in humans. Changes in renal function are assessed using tracer kinetics (DTPA) and IOH clearance). Ultrasonic techniques, based on measurements of acoustic backscatter coefficients and parameters derived from these measurements, are sensitive to microscopic changes in the tissue morphology. Elasticity imaging is used to study the changes in the tissue macrostructure. All acoustic measurements are made using a state-of-the-art clinical imaging system (Siemens Elegra). Our results show that ultrasonic techniques are very sensitive to early changes in renal microstructure and macrostructure. Ultrasound can be used to detect changes in the renal cortex long before there is a measurable loss of renal function. These techniques are also useful for monitoring the progression of the disease. Most importantly, these techniques are noninvasive and directly applicable to humans.
Origin of acetylcholinesterase in the neuromuscular junction formed in the in vitro innervated human muscle (2004)

Synaptic basal lamina is interposed between the pre- and postsynaptic membrane of the neuromuscular junction (NMJ). This position permits deposition of basal lamina-bound NMJ components of both neuronal and muscle fibre origin. One such molecule is acetylcholinesterase (AChE). The origin of NMJ AChE has been investigated previously as the answer would elucidate the relative contributions of muscle fibers and motor neurons to NMJ formation. However, in the experimental models used in prior investigations either the neuronal or muscular components of the NMJs were removed, or the NMJs were poorly differentiated. Therefore, the question of AChE origin in the intact and functional NMJ remains open. Here, we have approached this question using an in vitro model in which motor neurons, growing from embryonic rat spinal cord explants, form well differentiated NMJs with cultured human myotubes. By immunocytochemical staining with species-specific anti-AChE antibodies, we are able to differentiate between human (muscular) and rat (neuronal) AChE at the NMJ. We observed strong signal at the NMJ after staining with human AChE antibodies, which suggests a significant muscular AChE contribution. However, a weaker, but still clearly recognizable signal is observed after staining with rat AChE antibodies, suggesting a smaller fraction of AChE was derived from motor neurons. This is the first report demonstrating that both motor neuron and myotube contribute synaptic AChE under conditions where they interact with each other in the formation of an intact and functional NMJ.
Electron microscopy of complexes of isolated acetylcholine receptor, biotinyl-toxin, and avidin. (1982)

The principal curarimimetic toxin of Naja naja siamensis derivatized with biotinyl groups binds specifically both to acetylcholine receptor, isolated from Torpedo californica electric tissue, and to avidin. Isolated complexes of receptor monomer or dimer, biotinyl-toxin, and avidin were negatively stained and examined in the scanning transmission electron microscope. We measured the angle made by the radius of each avidin bound at the periphery of a monomeric unit in dimer to the axis connecting the centers of the monomers, starting at the crosslink between the monomers. We infer from the distribution of these angles that one toxin binding site is located in the range of 45 degrees to 85 degrees and another at about 100 degrees further from the crosslink between the monomers. Because it is known that there are two toxin binding sites per monomer, associated with the two alpha chains, the bound avidins presumably point to portions of the alpha chains, indicating their positions relative to that portion of the delta chain located at the crosslink between monomers in dimer.
TMBETA-NET: discrimination and prediction of membrane spanning -strands in outer membrane proteins (2005)

We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning beta-strand segments. The amino acid compositions of globular and outer membrane proteins have been systematically analyzed and a statistical method has been proposed for discriminating outer membrane proteins. The prediction of membrane spanning segments is mainly based on feed forward neural network and refined with beta-strand length. Our program takes the amino acid sequence as input and displays the type of the protein along with membrane-spanning beta-strand segments as a stretch of highlighted amino acid residues. Further, the probability of residues to be in transmembrane beta-strand has been provided with a coloring scheme. We observed that outer membrane proteins were discriminated with an accuracy of 89% and their membrane spanning beta-strand segments at an accuracy of 73% just from amino acid sequence information. The prediction server is available at http://psfs.cbrc.jp/tmbeta-net/.
Cerebral glioma: evaluation with methionine PET. (1993)

The authors examined 50 patients with cerebral glioma with use of positron emission tomography (PET) and L-[methyl]-[11C]methionine to assess the grade of malignancy and the extent of cerebral glioma. Carbon-11 methionine was highly accumulated in the lesion in 31 of 32 patients with high-grade glioma and 11 of 18 patients with low-grade glioma. The rate of uptake of C-11 methionine in high-grade glioma was significantly higher than in low-grade glioma (P < .001). However, in individual cases it was difficult to evaluate the grade of malignancy only from the degree of C-11 methionine accumulation. In most cases, the area of increased accumulation of C-11 methionine did not correspond to the abnormalities seen at computed tomography (CT). Surgical intervention confirmed that methionine PET delineated the extent of cerebral glioma more clearly than did CT. The authors concluded that methionine PET has greater utility in assessing the extent rather than the grade of malignancy of cerebral glioma.
Intracellular compartmentation, structure and function of creatine kinase isoenzymes in tissues with high and fluctuating energy demands: the ‘phosphocreatine circuit’ for cellular energy homeostasis (1992)

Abstract not available.
Historical perspective on the physics of artificial lighting (2018)

We describe the evolution of lighting technologies used throughout the ages, and how the need for improvements was such that any new technology giving better and cheaper lighting was immediately implemented. Thus, every revolution in energy sources – gas, petrol electricity – was first put to large-scale use in lighting. We describe in some detail several “ancient” techniques of scientific interest, along with their physical limitations. Electroluminescence – the phenomenon by which LEDs directly convert electricity into light – was long thought to only be of use for indicators or flat panel displays supposed to replace the bulky cathode-ray tubes. The more recent uses of LEDs were mainly for street traffic lights, car indicators, small phone displays, followed by backlighting of TV screens. LED lamps for general lighting only emerged recently as the dominant application of LEDs thanks to dramatic decrease in cost, and continuous improvements of color quality and energy conversion efficiency.
Enhancement of KTP/532 laser disc decompression and arthroscopic microdiscectomy with a vital dye (1993)

Currently, the clinical indications and results of arthroscopic microdiscectomy and laser disc decompression come close to, but do not exceed, the results of classic discectomy or microdiscectomy for the whole spectrum of surgical disc herniations. However, as minimally invasive techniques continue to evolve, results can be expected to equal or be potentially superior to conventional surgery. This exhibit demonstrates how the use of a vital dye can enhance standard arthroscopic microdiscectomy techniques and, when used in conjunction with KTP/532 laser disc decompression, allows for better arthroscopic visualization, documentation, and extraction of nucleus pulposus, ultimately expanding the current limiting criteria for minimally invasive techniques. When proper patient selection is combined with good clinical indications, the surgical results are rather dramatic, often achieving immediate relief of sciatica in the operating room.
Resonant detection of subterahertz radiation by plasma waves in a submicron field-effect transistor (2002)

The resonant detection of subterahertz radiation by two-dimensional electron plasma confined in a submicron gate GaAs/AlGaAs field-effect transistor is demonstrated. The results show that the critical parameter that governs the sensitivity of the resonant detection is ωτ, where ω is the radiation frequency and τ is the momentum scattering time. By lowering the temperature and hence increasing τ and increasing the detection frequency ω, we reached ωτ∼1 and observed resonant detection of 600 GHz radiation in a 0.15 μm gate length GaAs field-effect transistor. The evolution of the observed photoresponse signal with temperature and frequency is reproduced well within the framework of a theoretical model.
Caspase inhibitors prevent cisplatin-induced apoptosis of auditory sensory cells (1998)

In vitro studies tested the efficacy of three caspase inhibitors, Ac-VAD-cmk (caspase-1 inhibitor), z-DEVD-fmk (caspase-3 inhibitor) and B-D-fmk (BOCDFK, a general inhibitor), for protecting auditory sensory cells from cisplatin-damage induced loss. Treatment of 3-day-old rat organ of Corti explants with these caspase inhibitors protected > 80% of the auditory hair cells from cisplatin-damage initiated apoptosis. Dissociated cell cultures of 3-day-old rat spinal ganglia treated with any of these three caspase inhibitors in addition to exogenous neurotrophin have highly significant increases in neuronal survival following cisplatin exposure. These results indicate that loss of auditory sensory cells as a result of cisplatin-induced damage involves apoptosis and that blocking of this cell death pathway at the caspase level effectively rescues both hair cells and neurons.
Characterization of proteoglycans from adult bovine tendon. (1985)

Proteoglycans were extracted in good yield from the proximal, fibrous portion of adult bovine tendon with 4 m guanidine HCl. They comprise less than 1% of the dry weight of the tissue. Using CsCl density gradient centrifugation, gel chromatography, and ion exchange chromatography, two populations of proteoglycans were separated and purified from other tissue proteins. One was a large, chondroitin sulfate proteoglycan with high buoyant density in CsCl. This component appeared to be composed of two or three subpopulations as detected by agarose/polyacrylamide electrophoresis, although they could not be effectively separated from one another for individual characterization. As a group, the large proteoglycans eluted from Sepharose CL-2B with Kav from 0.1-0.5 and their core protein had Mr greater than 200,000 with high contents of glutamic acid, serine, and glycine. The glycosaminoglycan chains had a weight average Mr of 17,000 and more than 98% of the uronic acid was glucuronic acid. This group comprised only 12% of the total proteoglycan of the tissue. The other 88% of the proteoglycans appeared to represent one group of small molecules that eluted from Sepharose CL-2B at Kav = 0.70. They demonstrated buoyant densities in a CsCl gradient ranging from greater than or equal to 1.51 to 1.30 g/ml. Their core protein had an apparent Mr = 48,000 following removal of the glycosaminoglycan chains by digestion with chondroitinase ABC. This core protein had a particularly high content of aspartic acid/asparagine and leucine. The glycosaminoglycan chains had a weight average Mr of 37,000 and were dermatan sulfate containing 73% iduronic acid. Those molecules found at highest buoyant density appeared to have additional glycosaminoglycan chains that were shorter. Proteoglycans were also extracted from the pressure-bearing distal region of this tendon, where contents of proteoglycan per wet weight of tissue were 3-fold higher and as much as 50% of this was as large as the large proteoglycans from the proximal tissue. Preparations of large proteoglycans from both tendon regions contained molecules capable of interacting with hyaluronic acid.
Investigations of the 'active' edge of plaque psoriasis: vascular proliferation precedes changes in epidermal keratin (1994)

We have investigated markers of epidermal proliferation and differentiation in terms of keratin expression, the morphology of the cutaneous vasculature, and numbers of cutaneous mast cells, in patients with chronic plaque psoriasis. Using the phenomenon of the 'active edge', we have studied these features in the psoriatic plaque itself, and in the clinically normal active and inactive edges of the same plaque. Our results confirm the anticipated changes in keratin profiles, mast cell numbers and psoriatic morphology of the vasculature within the plaque itself. They further indicate that the vascular changes precede the epidermal and mast cell features at the active edge, and that the inactive edge is inactive for all of these variables. Mediators responsible for the vascular proliferation and elongation must be present in increased amounts at the active edge when compared with the inactive, and include locally produced and circulating factors.