gebhart/patrepeval huggingface dataset:
Phosphoserine Aminotransferase, the Second Step‐Catalyzing Enzyme for Serine Biosynthesis (1999)

Abstract As a step toward analyzing the serine biosynthetic pathway in mammals, we have studied the properties of phosphoserine aminotransferase, the second step‐catalyzing enzyme. The Km values for 3‐phosphohydroxypyruvate and L‐phosphoserine are 5 and 35 mu M, respectively, and those for glutamate and alpha‐ketoglutarate are 1.2 and 0.8 mM, respectively. The product inhibition studies strengthened the support for a ping‐pong mechanism and allowed evaluation of Ki values for the four substrates. The equilibrium constant evaluated from the kinetic parameters is 40. Additionally, some physical properties relative to the bound coenzyme and the secondary structure were investigated. The results are consistent with a structural relationship between the Escherichia coli enzyme and the mammalian enzyme. The mammalian enzyme has specific kinetic parameters, the determination of which is a prerequisite to analyzing the serine biosynthetic pathway in mammals.
Smoothened as a new therapeutic target for human osteosarcoma (2010)

These findings suggest that inactivation of SMO may be a useful approach to the treatment of patients with osteosarcoma.
Control of magnetization dynamics in Ni/sub 81/Fe/sub 19/ thin films through the use of rare-earth dopants (2001)

We show that the magnetization dynamics of soft ferromagnetic thin films can be tuned using rare-earth (RE) dopants. Low concentrations (2 to 10%) of Tb in 50 nm Ni/sub 81/Fe/sub 19/ films are found to increase the Gilbert magnetic damping parameter /spl alpha/ over two orders of magnitude without great effect on easy axis coercivity or saturation magnetization. Comparison with Gd dopants indicates that the orbital character of the Tb moment is important for transferring magnetic energy to the lattice. Structural transformations from the crystalline to the amorphous state, observed over the first 2%-10% of RE doping, may play a contributing but not sufficient role in damping in these films. The approach demonstrated here shows promise for adjusting the dynamical response, from underdamped to critically damped, in thin film materials for magnetic devices.
Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors (2015)

In molecular evolutionary analyses, short DNA sequences are used to infer phylogenetic relationships among species. Here we apply this principle to the study of bacterial biosynthesis, enabling the targeted isolation of previously unidentified natural products directly from complex metagenomes. Our approach uses short natural product sequence tags derived from conserved biosynthetic motifs to profile biosynthetic diversity in the environment and then guide the recovery of gene clusters from metagenomic libraries. The methodology is conceptually simple, requires only a small investment in sequencing, and is not computationally demanding. To demonstrate the power of this approach to natural product discovery we conducted a computational search for epoxyketone proteasome inhibitors within 185 globally distributed soil metagenomes. This led to the identification of 99 unique epoxyketone sequence tags, falling into 6 phylogenetically distinct clades. Complete gene clusters associated with nine unique tags were recovered from four saturating soil metagenomic libraries. Using heterologous expression methodologies, seven potent epoxyketone proteasome inhibitors (clarepoxcins A-E and landepoxcins A and B) were produced from these pathways, including compounds with different warhead structures and a naturally occurring halohydrin prodrug. This study provides a template for the targeted expansion of bacterially derived natural products using the global metagenome.
Malware Classification Using Probability Scoring and Machine Learning (2019)

Malware classification plays an important role in tracing the attack sources of computer security. However, existing static analysis methods are fast in classification, but they are inefficient in some malware using packing and obfuscation techniques; the dynamic analysis methods have better universality for packing and obfuscation, but they will cause excessive classification cost. To overcome these shortcomings, in this paper, we propose a classification system Malscore based on the probability scoring and machine learning, which sets the probability threshold to concatenate static analysis (called Phase 1) and dynamic analysis (called Phase 2). The convolutional neural networks with spatial pyramid pooling were used to analyze the grayscale images (static features) in Phase 1, and the variable n-grams and machine learning were used to analyze the native API call sequences (dynamic features) in Phase 2. Malscore combined static analysis with dynamic analysis not only accelerated the static analysis process by taking advantage of the CNN in image recognition but also appeared to be more resilient to obfuscation by the dynamic analysis. Different from other static and dynamic analysis techniques, when malware is detected, due to the fact that malware will most likely be labeled only by static analysis, we could reduce the overheads by dynamically analyzing a few malware that has less obvious features or greater confusion in static analysis. We performed experiments on 174607 malware samples from 63 malware families. The result showed that Malscore achieved 98.82% accuracy for malware classification. Furthermore, Malscore was compared with the method of using static and dynamic analysis. The preprocessing and test time represented a reduction of 59.58% and 61.70%, respectively.
The streptokinase gene of group A streptococci: cloning, expression in <i>Escherichia coli</i>, and sequence analysis (1989)

The gene specifying the group A streptokinase (ska) gene was cloned from an M type 49 strain of Streptococcus pyogenes and shown to express in Escherichia coli. The nucleotide sequence of the DNA fragment carrying ska was determined and compared to that of the group C streptokinase gene (skc). There is 90% sequence identity between the two genes, with highly conserved transcription and translation control regions. The deduced amino acid sequence of the group A streptokinase (SKA) contains the same number of amino acids as that of group C streptokinase, with 85% sequence identity between the two proteins. Among 440 amino acid residues specified by the coding sequence, there are 62 non-identical residues with 45 conserved and 17 non-conserved residues. The non-identical residues are located in two major regions, spanning residues 174 to 244 and 270 to 290, with 40 and 10 amino acid changes, respectively. The sequence differences provide an explanation at the molecular level for the previous findings of immunological and chemical heterogeneity among streptokinase produced by pathogenic streptococci.
Cdc42Hs and Rac1 GTPases Induce the Collapse of the Vimentin Intermediate Filament Network (2000)

In this study we show that expression of active Cdc42Hs and Rac1 GTPases, two Rho family members, leads to the reorganization of the vimentin intermediate filament (IF) network, showing a perinuclear collapse. Cdc42Hs displays a stronger effect than Rac1 as 90% versus 75% of GTPase-expressing cells show vimentin collapse. Similar vimentin IF modifications were observed when endogenous Cdc42Hs was activated by bradykinin treatment, endogenous Rac1 by platelet-derived growth factor/epidermal growth factor, or both endogenous proteins upon expression of active RhoG. This reorganization of the vimentin IF network is not associated with any significant increase in soluble vimentin. Using effector loop mutants of Cdc42Hs and Rac1, we show that the vimentin collapse is mostly independent of CRIB (Cdc42Hs or Rac-interacting binding)-mediated pathways such as JNK or PAK activation but is associated with actin reorganization. This does not result from F-actin depolymerization, because cytochalasin D treatment or Scar-WA expression have merely no effect on vimentin organization. Finally, we show that genistein treatment of Cdc42 and Rac1-expressing cells strongly reduces vimentin collapse, whereas staurosporin, wortmannin, LY-294002, R(p)-cAMP, or RII, the regulatory subunit of protein kinase A, remain ineffective. Moreover, we detected an increase in cellular tyrosine phosphorylation content after Cdc42Hs and Rac1 expression without modification of the vimentin phosphorylation status. These data indicate that Cdc42Hs and Rac1 GTPases control vimentin IF organization involving tyrosine phosphorylation events.
A comparison of steady-state evoked potentials to modulated tones in awake and sleeping humans (1991)

Steady-state evoked potential responses were measured to binaural amplitude-modulated (AM) and combined amplitude- and frequency-modulated (AM/FM) tones. For awake subjects, AM/FM tones produced larger amplitude responses than did AM tones. Awake and sleeping responses to 30-dB HL AM/FM tones were compared. Response amplitudes were lower during sleep and the extent to which they differed from awake amplitudes was dependent on both carrier and modulation frequencies. Background EEG noise at the stimulus modulation frequency was also reduced during sleep and varied with modulation frequency. A detection efficiency function was used to indicate the modulation frequencies likely to be most suitable for electrical estimation of behavioral threshold. In awake subjects, for all carrier frequencies tested, detection efficiency was highest at a modulation frequency of 45 Hz. In sleeping subjects, the modulation frequency regions of highest efficiency varied with carrier frequency. For carrier frequencies of 250 Hz, 500 Hz, and 1 kHz, the highest efficiencies were found in two modulation frequency regions centered on 45 and 90 Hz. For 2 and 4 kHz, the highest efficiencies were at modulation frequencies above 70 Hz. Sleep stage affected both response amplitude and background EEG noise in a manner that depended on modulation frequency. The results of this study suggest that, for sleeping subjects, modulation frequencies above 70 Hz may be best when using steady-state potentials for hearing threshold estimation.
A Study of Write Margin of Spin Torque Transfer Magnetic Random Access Memory Technology (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Key design parameters of 64 Mb STT-MRAM at 90-nm technology node are discussed. A design point was developed with adequate TMR for fast read operation, enough energy barrier for data retention and against read disturbs, a write voltage satisfying the long term reliability against dielectric breakdown and a write bit error rate below <emphasis emphasistype="italic"><formula formulatype="inline"><tex Notation="TeX">$10^{-9}$</tex></formula></emphasis>. A direct experimental method was developed to determine the data retention lifetime that avoids the discrepancy in the energy barrier values obtained with spin current- and field-driven switching measurements. Other parameters detrimental to write margins such as backhopping and the existence of a low breakdown population are discussed. At low bit-error regime, new phenomenon emerges, suggestive of a bifurcation of switching modes. The dependence of the bifurcated switching threshold on write pulse width, operating temperature, junction dimensions and external field were studied. These show bifurcated switching to be strongly influenced by thermal fluctuation related to the spatially inhomogeneous free layer magnetization. An external field along easy axis direction assisting switching was shown to be effective for significantly reducing the percentage of MTJs showing bifurcated switching. </para>
InP/ZnSe/ZnS: A Novel Multishell System for InP Quantum Dots for Improved Luminescence Efficiency and Its application in a Light-Emitting Device (2012)

Indium phosphide (InP) quantum dots (QDs) are considered alternatives to Cd-containing QDs for application in light-emitting devices. The multishell coating with ZnSe/ZnS was shown to improve the photoluminescence quantum yield (QY) of InP QDs more strongly than the conventional ZnS shell coating. Structural proof for this system was provided by X-ray diffraction and transmission electron microscopy. QY values in the range of 50–70% along with peak widths of 45–50 nm can be routinely achieved, making the optical performance of InP/ZnSe/ZnS QDs comparable to that of Cd-based QDs. The fabrication of a working electroluminescent light-emitting device employing the reported material demonstrated the feasibility of the desired application.
National Stroke Association guidelines for the management of transient ischemic attacks (2006)

The final recommendations on the care of patients with transient ischemic attacks emphasize the importance of urgent evaluation and treatment. The novel approach used to develop these guidelines is feasible, allows for rapid updating, and may reduce bias.
Relationship between sugar chain structure and biological activity of recombinant human erythropoietin produced in Chinese hamster ovary cells. (1989)

Two forms of erythropoietin, EPO-bi and EPO-tetra, with different biological activities were isolated from the culture medium of a recombinant Chinese hamster ovary cell line, B8-300, into which the human erythropoietin gene had been introduced. EPO-bi, an unusual form, showed only one-seventh the in vivo activity and 3 times higher in vitro activity of the previously described recombinant human EPO (standard EPO). In contrast, EPO-tetra showed both in vivo and in vitro activities comparable to those of the standard EPO. EPO-bi, EPO-tetra, and the standard EPO had the same amino acid composition and immunoreactivity. However, structural analyses of their N-linked sugar chains revealed that EPO-bi contains the biantennary complex type as the major sugar chain, while EPO-tetra and the standard EPO contain the tetraantennary complex type as the major sugar chain. From examination of various preparations of recombinant human EPO, we found a positive correlation between the in vivo activity of EPO and the ratio of tetraantennary to biantennary oligosaccharides. These results suggest that higher branching of the N-linked sugar chains is essential for effective expression of in vivo biological activity of EPO.
Endothelial cell activation induced by tumor necrosis factor and lymphotoxin. (1989)

Alterations in the morphology and histochemistry of vascular endothelial cells (EC) have been repeatedly observed at sites of chronic inflammation and immune reactions. These changes, which are most prominent in the EC postcapillary venules present in areas with large lymphocytic infiltrates, include the acquisition of a columnar or cuboidal morphology, the development of ribonuclease-sensitive metachromasia, and an increase in intracellular organelles. Thus, EC at sites of inflammation appear to be activated and to demonstrate increased metabolic activity. This study reports that both tumor necrosis factor-alpha (TNF) and lymphotoxin (LT) can activate cultured human umbilical vein EC, as measured by: 1) increased adhesiveness for lymphocytes, 2) increased cell metabolism, as measured by RNA and protein synthesis, and 3) increased cell volume. Although gamma interferon (IFN-gamma) and interleukin-1 (IL-1) have been shown previously to stimulate EC adhesiveness for lymphocytes, these two cytokines had only marginal effects on EC RNA and protein synthesis, and both caused a decrease in EC volume. These findings suggest that TNF and LT play a role in the type of activation of EC in vivo that leads to the development of tall endothelium and increased lymphocyte emigration.
Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter (2014)

Lentiviral vectors almost universally use heterologous internal promoters to express transgenes. One of the most commonly used promoter fragments is a 1.2-kb sequence from the human ubiquitin C (UBC) gene, encompassing the promoter, some enhancers, first exon, first intron and a small part of the second exon of UBC. Because splicing can occur after transcription of the vector genome during vector production, we investigated whether the intron within the UBC promoter fragment is faithfully transmitted to target cells. Genetic analysis revealed that more than 80% of proviral forms lack the intron of the UBC promoter. The human elongation factor 1 alpha (EEF1A1) promoter fragment intron was not lost during lentiviral packaging, and this difference between the UBC and EEF1A1 promoter introns was conferred by promoter exonic sequences. UBC promoter intron loss caused a 4-fold reduction in transgene expression. Movement of the expression cassette to the opposite strand prevented intron loss and restored full expression. This increase in expression was mostly due to non-classical enhancer activity within the intron, and movement of putative intronic enhancer sequences to multiple promoter-proximal sites actually repressed expression. Reversal of the UBC promoter also prevented intron loss and restored full expression in bidirectional lentiviral vectors.
Recovering Signals From Lowpass Data (2010)

The problem of recovering a signal from its low frequency components occurs often in practical applications due to the lowpass behavior of many physical systems. Here, we study in detail conditions under which a signal can be determined from its low-frequency content. We focus on signals in shift-invariant spaces generated by multiple generators. For these signals, we derive necessary conditions on the cutoff frequency of the lowpass filter as well as necessary and sufficient conditions on the generators such that signal recovery is possible. When the lowpass content is not sufficient to determine the signal, we propose appropriate pre-processing that can improve the reconstruction ability. In particular, we show that modulating the signal with one or more mixing functions prior to lowpass filtering, can ensure the recovery of the signal in many cases, and reduces the necessary bandwidth of the filter.
Near-Infrared Surface-Enhanced Raman Spectroscopy. Part II: Copper and Gold Colloids (1989)

Near-infrared (NIR) surface-enhanced Raman spectra (SERS) on copper and gold metal colloids were obtained with a Fourier transform Raman spectrometer using a Nd:YAG laser (1.064 μm) for excitation. Enhanced spectra were observed for pyridine and 3-chloropyridine (CP) on copper colloids and for tris(orthophenanthroline)ruthenium(II), Ru(o-phen) 3 2+ , on copper and gold colloids. The copper-colloid surface-enhanced Raman spectra of pyridine and CP were compared with spectra measured for these molecules on copper electrodes. NIR-SERS enhancements on the metal colloids were at least as large as for visible-wavelength excited SERS. Good-quality spectra of Ru(o-phen) 3 2+ were obtained at solution concentrations as low as 0.025 mM.
Effects of free fatty acids on glucose transport and IRS-1–associated phosphatidylinositol 3-kinase activity (1999)

To examine the mechanism by which free fatty acids (FFA) induce insulin resistance in human skeletal muscle, glycogen, glucose-6-phosphate, and intracellular glucose concentrations were measured using carbon-13 and phosphorous-31 nuclear magnetic resonance spectroscopy in seven healthy subjects before and after a hyperinsulinemic-euglycemic clamp following a five-hour infusion of either lipid/heparin or glycerol/heparin. IRS-1-associated phosphatidylinositol 3-kinase (PI 3-kinase) activity was also measured in muscle biopsy samples obtained from seven additional subjects before and after an identical protocol. Rates of insulin stimulated whole-body glucose uptake. Glucose oxidation and muscle glycogen synthesis were 50%-60% lower following the lipid infusion compared with the glycerol infusion and were associated with a approximately 90% decrease in the increment in intramuscular glucose-6-phosphate concentration, implying diminished glucose transport or phosphorylation activity. To distinguish between these two possibilities, intracellular glucose concentration was measured and found to be significantly lower in the lipid infusion studies, implying that glucose transport is the rate-controlling step. Insulin stimulation, during the glycerol infusion, resulted in a fourfold increase in PI 3-kinase activity over basal that was abolished during the lipid infusion. Taken together, these data suggest that increased concentrations of plasma FFA induce insulin resistance in humans through inhibition of glucose transport activity; this may be a consequence of decreased IRS-1-associated PI 3-kinase activity.
Evaluation of Fluid Resuscitation Control Algorithms via a Hardware-in-the-Loop Test Bed (2019)

This type of testing enables relatively fast evaluation of physiologic closed-loop control systems to aid in iterative design processes and offers complementary means to existing techniques (e.g., in silico, in vivo, and clinical studies) for testing of such systems against a wide range of disturbances and scenarios.
Endoscope lens with dual fields of view and resolutions for multiphoton imaging (2010)

We report the development of a miniaturized dual-optical-zone endoscope objective lens. The lens has two foci, with 0.18 and 0.50 NAs. We demonstrate multiphoton imaging with dual fields of view and resolutions using the new lens. A combination of multiphoton and single-photon microscopic imaging is also demonstrated.
Temporal continuity of levels of detail in Delaunay triangulated terrain (1996)

The representation of a scene at different levels of detail is necessary to achieve real-time rendering. In aerial views, only the part of the scene that is close to the viewing point needs to be displayed with a high level of detail, while more distant parts can be displayed with a low level of detail. However, when a sequence of images is generated and displayed in real-time, the transition between different levels of detail causes noticeable temporal aliasing. In this paper, we propose a method, based on object blending, that visually softens the transition between two levels of Delaunay triangulation. We present an algorithm that establishes, in an off-line process, a correspondence between two given polygonal objects. The correspondence enables on-line blending between two representations of an object, so that one representation (level of detail) progressively evolves into the other.
Restart trail for stackless BVH traversal (2010)

A ray cast algorithm utilizing a hierarchical acceleration structure needs to perform a tree traversal in the hierarchy. In its basic form, executing the traversal requires a stack that holds the nodes that are still to be processed. In some cases, such a stack can be prohibitively expensive to maintain or access, due to storage or memory bandwidth limitations. The stack can, however, be eliminated or replaced with a fixed-size buffer using so-called stackless or short stack algorithms. These require that the traversal can be restarted from root so that the already processed part of the tree is not entered again. For kd-tree ray casts, this is accomplished easily by ray shortening, but the approach does not extend to other kinds of hierarchies such as BVHs.In this paper, we introduce restart trail, a simple algorithmic method that makes restarts possible regardless of the type of hierarchy by storing one bit of data per level. This enables stackless and short stack traversal for BVH ray casts, where using a full stack or constraining the traversal order have so far been the only options.