gebhart/patrepeval huggingface dataset:
Mutagenesis of human acetylcholinesterase. Identification of residues involved in catalytic activity and in polypeptide folding. (1992)

Evidence for the involvement of Ser-203, His-447, and Glu-334 in the catalytic triad of human acetylcholinesterase was provided by substitution of these amino acids by alanine residues. Of 20 amino acid positions mutated so far in human acetylcholinesterase (AChE), these three were unique in abolishing detectable enzymatic activity (less than 0.0003 of wild type), yet allowing proper production, folding, and secretion. This is the first biochemical evidence for the involvement of a glutamate in a hydrolase triad (Schrag, J.D., Li, Y., Wu, M., and Cygler, M. (1991) Nature 351, 761-764), supporting the x-ray crystal structure data of the Torpedo californica acetylcholinesterase (Sussman, J.L., Harel, M., Frolow, F., Oefner, C., Goldman, A., Toker, L. and Silman, I. (1991) Science 253, 872-879). Attempts to convert the AChE triad into a Cys-His-Glu or Ser-His-Asp configuration by site-directed mutagenesis did not yield effective AChE activity. Another type of substitution, that of Asp-74 by Gly or Asn, generated an active enzyme with increased resistance to succinylcholine and dibucaine; thus mimicking in an AChE molecule the phenotype of the atypical butyrylcholinesterase natural variant (D70G mutation). Mutations of other carboxylic residues Glu-84, Asp-95, Asp-333, and Asp-349, all conserved among cholinesterases, did not result in detectable alteration in the recombinant AChE, although polypeptide productivity of the D95N mutant was considerably lower. In contrast, complete absence of secreted human AChE polypeptide was observed when Asp-175 or Asp-404 were substituted by Asn. These two aspartates are conserved in the entire cholinesterase/thyroglobulin family and appear to play a role in generating and/or maintaining the folded state of the polypeptide. The x-ray structure of the Torpedo acetylcholinesterase supports this assumption by revealing the participation of these residues in salt bridges between neighboring secondary structure elements.
Novel Synthesis of Fosphenytoin: Anti-Convulsant Prodrug (2008)

Abstract A simple, new synthesis of fosphenytoin sodium 1, a prodrug, via imidate ester and employing mild reaction conditions is described.
Fundamental Dynamics of Reaction-Powered Space Vehicles (1951)

This paper is an attempt to place in correct perspective the current considerable speculation regarding the problem of interplanetary travel. The concept and importance of “escape velocity” is dealt with first, and then the elementary mass-ratio equations for the motion of a space vehicle under various conditions are derived. Available energy sources are considered next, the operational parameter being jet velocity. It is indicated that the maximum jet velocity conceivably attainable with chemical fuels is of the order of 20,000 ft. per sec. Nuclear fuels are dealt with and it is shown that, while energy potentials are very high, the problem of practical utilization is formidable. A thermodynamic type of atomic rocket motor employing an inert reaction mass to absorb the fission energy is postulated, and it is demonstrated that the heat transfer and materials requirements present a problem of the first magnitude. The influence of propellent density on the performance characteristics of both chemical and atomic rockets is discussed, and it is shown that propellents giving high jet velocities may not necessarily be the best to use. Orders of magnitude for the mass ratios required for various interplanetary flights are established, and it is indicated that only an atomic drive will render them small enough to be attainable in practice. It is concluded that, unless nuclear energy can be suitably harnessed, economical space-travel will not be feasible.
Model-based despeckling and information extraction from SAR images (2000)

Basic textures as they appear, especially in high resolution SAR images, are affected by multiplicative speckle noise and should be preserved by despeckling algorithms. Sharp edges between different regions and strong scatterers also must be preserved. To despeckle images, the authors use a maximum aposteriori (MAP) estimation of the cross section, choosing between different prior models. The proposed approach uses a Gauss Markov random field (GMRF) model for textured areas and allows an adaptive neighborhood system for edge preservation between uniform areas. In order to obtain the best possible texture reconstruction, an expectation maximization algorithm is used to estimate the texture parameters that provide the highest evidence. Borders between homogeneous areas are detected with a stochastic region-growing algorithm, locally determining the neighborhood system of the Gauss Markov prior. Smoothed strong scatterers are found in the ratio image of the data and the filtering result and are replaced in the image. In this way, texture, edges between homogeneous regions, and strong scatterers are well reconstructed and preserved. Additionally, the estimated model parameters can be used for further image interpretation methods.
Highly Enantioseletive Biginelli Reaction Using a New Chiral Ytterbium Catalyst:  Asymmetric Synthesis of Dihydropyrimidines (2005)

The highly enantioselective three-component Biginelli condensation catalyzed by a recyclable chiral ytterbium triflate with a novel hexadentate amine phenol ligand containing a pyridyl group has been developed. A wide range of optically active dihydropyrimidines with remarkable pharmacological interest was obtained in high yields with good to excellent enantioselectivities under mild conditions.
Breast epithelial antigens : molecular biology to clinical applications (1991)

Reporting on the clinical procedures that have now been developed from the initial research on using monoclonal antibodies to diagnose and treat breast cancer, the 21 papers also review promising research still in the pipeline. The various descriptions of breast epithelial antigens consider their mo
A Temporal Motif Mining Approach to Unsupervised Energy Disaggregation: Applications to Residential and Commercial Buildings (2013)

Non-intrusive appliance load monitoring has emerged as an attractive approach to study energy consumption patterns without instrumenting every device in a building. The ensuing computational problem is to disaggregate total energy usage into usage by specific devices, to gain insight into consumption patterns. We exploit the temporal ordering implicit in on/off events of devices to uncover motifs (episodes) corresponding to the operation of individual devices. Extracted motifs are then subjected to a sequence of constraint checks to ensure that the resulting episodes are interpretable. Our results reveal that motif mining is adept at distinguishing devices with multiple power levels and at disentangling the combinatorial operation of devices. With suitably configured processing steps, we demonstrate the applicability of our method to both residential and commercial buildings.
Circuit Recognition and Verification Based on Layout Information (1981)

The mathematical and technical background information for our highly efficient procedure of circuit recognition and verification from layout information is presented. Complete verification and extremely short computing times are the main goals. This procedure can be performed for bipolar as well as for MOS technologies and is part of the whole layout-control system LOCATE.
Progress of Phase-Change Single-Beam Overwrite Technology (1989)

Studies on relationships between single beam overwrite characteristics and physical and chemical properties of the phase change recording media and their mechanisms are reviewed. Improvements in overwrite characteristics based on these studies, especially improvements in carrier to noise ratio(C/N) and the life of recorded dots by the addition of one of the transition metal elements or Tt are also reported. The maximum C/N was 61dB and the estimated life of the recorded dots is longer than 100 years at 60°C.
Thermodynamic aspects of molecular beam epitaxy: High temperature growth in the GaAs/Ga1−<i>x</i>Al<i>x</i>As system (1985)

The thermodynamic framework is established for growth of GaAs and Ga1−xAlxAs by molecular beam epitaxy MBE, for the region where loss of gallium is significant. It is shown that the temperature dependence of gallium loss from GaAs is a function of the experimental beam pressures and not a basic property of the system. At a given temperature, gallium loss (and hence the growth rate for GaAs) is a function of arsenic pressure and in the alloys it is also a linear function of Al content. As2 is the equilibrium species used in the calculations. Comparison with experimental data is therefore limited, but it is clear that As4 dissociation is kinetically hindered when used in practice. Use of a closely controlled pressure of As2 is indicated to achieve good control of both layer thickness and alloy composition. The approach is likely to be more important in other alloy systems where lattice matching to the substrate is more critical.
Shared workload optimization (2014)

As a result of increases in both the query load and the data managed, as well as changes in hardware architecture (multicore), the last years have seen a shift from query-at-a-time approaches towards shared work (SW) systems where queries are executed in groups. Such groups share operators like scans and joins, leading to systems that process hundreds to thousands of queries in one go. SW systems range from storage engines that use in-memory co-operative scans to more complex query processing engines that share joins over analytical and star schema queries. In all cases, they rely on either single query optimizers, predicate sharing, or on manually generated plans. In this paper we explore the problem of shared workload optimization (SWO) for SW systems. The challenge in doing so is that the optimization has to be done for the entire workload and that results in a class of stochastic knapsack with uncertain weights optimization, which can only be addressed with heuristics to achieve a reasonable runtime. In this paper we focus on hash joins and shared scans and present a first algorithm capable of optimizing the execution of entire workloads by deriving a global executing plan for all the queries in the system. We evaluate the optimizer over the TPC-W and the TPC-H benchmarks. The results prove the feasibility of this approach and demonstrate the performance gains that can be obtained from SW systems.
Scanning of the internal structure part with laser ultrasonic in aviation industry (2011)

The detection of internal defects is a major production and safety issue for the newest generations of aircraft. New materials and manufacturing processes in the aircraft industry demand efficient quality assurance in manufacturing and inspection in maintenance. Advanced metallic material processes (titanium) are used or developed for the production of heavily loaded flying components (in fan blade construction). The inspection of these parts mainly made out of titanium (or CFRP) requires the determination of the percentage of bonded grain sizes around 10-30 µm. This is primarily due to the advantages of a high signal-to-noise ratio and good detection sensitivity. In this article, a diagnosing method of the blade interior by means of the laser ultrasonic is presented. Identification of small fatigue cracks presents a challenging problem during nondestructive testing of fatigue-damaged structures. Laser ultrasonic is a technique that uses two laser beams; one with a short pulse for the generation of ultrasound and another with a long pulse or continuous coupled to an optical interferometer for detection. The results of research of the internal blade structure are presented.
Changes in Aortic Stiffness and Augmentation Index After Acute Converting Enzyme or Vasopeptidase Inhibition (2005)

Augmentation index (AI), a measure of enhanced wave reflection, has been proposed as a bedside measure of aortic stiffness. However, because AI is potentially sensitive to various factors other than vessel wall stiffness, the utility of AI as a stiffness indicator may be limited. To assess relations between AI and vascular properties, we used arterial tonometry and aortic Doppler flow to evaluate trough (24 hours) and peak (4 hours) pulsatile hemodynamics and pulse wave velocity in 159 individuals with systolic hypertension at the completion of a 12-week period of monotherapy with the vasopeptidase inhibitor omapatrilat (80 mg; n=75) or the converting enzyme inhibitor enalapril (40 mg; n=84). Characteristic impedance (Zc) was calculated from the ratio of change in carotid pressure and aortic flow in early systole. Systolic ejection period (SEP), timing of wave reflection, and AI were assessed from the carotid waveform. Comparable acute reductions in mean pressure were associated with greater reductions in peripheral resistance with enalapril, whereas neither drug had an acute effect on Zc. Both drugs reduced AI, but neither drug altered the timing of wave reflection. Both drugs increased heart rate and shortened SEP. Multiple regression analysis demonstrated that the acute reduction in AI was most affected by reductions in SEP and peripheral resistance. Change in AI was inversely related to change in Zc and pulse wave velocity did not enter the model. Our findings indicate that AI is a complex surrogate marker that is inversely related to changes in proximal aortic stiffness in systolic hypertension.
Color coding cancer cells with fluorescent proteins to visualize in vivo cellular interaction in metastatic colonies. (2005)

We report here in vivo visualization of cancer cell interaction using stable sublines of green fluorescent protein (GFP)- and red fluorescent protein (RFP)-expressing HT-1080 human fibrosarcoma cells. These color-coded fibrosarcoma cell lines show similar cell proliferation and lung metastasis potential. The color-coded cells were mixed at a ratio of 1:1 and were injected into the tail vein of severe combined immunodeficient (SCID) mice. The resulting experimental lung metastases were simultaneously imaged and their ratio was determined by color-pixel analysis. Fluorescence color coding of cancer cells enables visualization of the interaction of cancer cells and can be used to distinguish cancer cells of any genotype or phenotype.
Miniaturized Broadband Ferrite T-DMB Antenna for Mobile-Phone Applications (2010)

Miniaturized 0.026 ¿ Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Z hexaferrite and Ni-Mn-Co spinel ferrite T-DMB antennas were fabricated and characterized for antenna performance. The Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Z hexaferrites were prepared with two different processes that are water quenching and air cooling. The water quenched Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Z hexaferrite antenna shows -6.5 dB of 3-D average gain at 190 MHz and 37 MHz of bandwidth at -10 dB. A magnetic tangent loss of water-quenched Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Z hexaferrite was lower than that of air-cooled Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Z hexaferrite. Compared to the hexaferrite antennas, the Ni-Mn-Co ferrite antenna shows higher frequency performance. Its gain and bandwidth were measured to be -5.83 dB at 215 MHz and 41 MHz, respectively. Omnidirectional gain pattern was observed from all fabricated ferrite antennas.
Risk of Non-Hodgkin Lymphoma and Lymphoproliferative Precursor Diseases in US Veterans With Hepatitis C Virus (2007)

Hepatitis C virus infection confers a 20% to 30% increased risk of non-Hodgkin lymphoma overall, and a 3-fold higher risk of Waldenström macroglobulinemia, a low-grade lymphoma. Risks were also increased for cryoglobulinemia. These results support an etiological role for HCV in causing lymphoproliferation and causing non-Hodgkin lymphoma.
Ultrafast T-Jump in Water:  Studies of Conformation and Reaction Dynamics at the Thermal Limit (2006)

We report the development of ultrafast T-jump with time resolution reaching the fundamental time scale of water thermalization time ( approximately 5 ps). The T-jump heats the bulk water up to 20 degrees C via the overtone absorption of the OH- stretch at 1.5 mum. The example given here shows the application of the methodology, for the first time, and the results demonstrate distinct time scales for solvation, conformational change, and thermal reaction.
Robustness and modularity properties of a non-covalent DNA catalytic reaction (2010)

The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks.
HLA-restricted epitope identification and detection of functional T cell responses by using MHC–peptide and costimulatory microarrays (2005)

Identification of T cell epitopes is a vital but often slow and difficult step in studying the immune response to infectious agents and autoantigens. We report a spatially addressable technique for screening large numbers of T cell epitopes for both specific antigen recognition and functional activity induced. This system uses microarrays of immobilized, recombinant MHC-peptide complexes, costimulatory molecules, and cytokine-capture antibodies. The array elements act as synthetic antigen-presenting cells and specifically elicit T cell responses, including adhesion, secretion of cytokines, and modulation of surface markers. The method allows facile identification of pertinent T cell epitopes in a large number of candidates and simultaneous determination of the functional outcome of the interaction. Using this method, we have characterized the activation of human CD4(+) and CD8(+) T cells responding to vaccinia, influenza, HIV-1, and Epstein-Barr viruses.
Transduction of the cytoplasmic domain of CTLA-4 inhibits TcR-specific activation signals and prevents collagen-induced arthritis (2008)

CTLA-4 (CD152) negatively regulates T cell activation signaling, and the cytoplasmic domain of CTLA-4 (ctCTLA-4) itself has the capacity to inhibit T cell activation in vitro and in vivo. In this study, the inhibitory mechanisms of the cell-permeable recombinant protein Hph-1-ctCTLA-4 on T cell activation and its ability to prevent collagen-induced arthritis were analyzed. Hph-1-ctCTLA-4 prevented human and mouse T cell activation and proliferation by inhibition of T cell receptor-proximal signaling and the arrest of the cell cycle. Furthermore, Hph-1-ctCTLA-4 protected human umbilical vein endothelial cells (HUVEC) from the human CTL allo-response. The incidence and severity of collagen-induced arthritis were significantly reduced and the erosion of cartilage and bone was effectively prevented by i.v. injection and transdermal administration of Hph-1-ctCTLA-4. Inflammatory cytokine production (IL-1beta, IL-6, TNF-alpha, IL-17A) and collagen-specific antibody levels were significantly reduced, and the numbers of activated T cells and infiltrating granulocytes were substantially decreased. These results demonstrate that systemic or transdermal application of a cell-permeable form of the cytoplasmic domain of CTLA-4 offers an effective therapeutic approach for autoimmune diseases such as rheumatoid arthritis.
Configurable Unitary Transformations and Linear Logic Gates Using Quantum Memories (2014)

We show that a set of optical memories can act as a configurable linear optical network operating on frequency-multiplexed optical states. Our protocol is applicable to any quantum memories that employ off-resonant Raman transitions to store optical information in atomic spins. In addition to the configurability, the protocol also offers favorable scaling with an increasing number of modes where N memories can be configured to implement arbitrary N-mode unitary operations during storage and readout. We demonstrate the versatility of this protocol by showing an example where cascaded memories are used to implement a conditional cz gate.
RESISTANCE OF THE SCRAPIE AGENT TO INACTIVATION BY PSORALENS (1983)

Abstract –In searching for a nucleic acid within the scrapie agent, we employed psoralens which penetrate the coats of most conventional viruses, form photoadducts with their genomes, and block replication of the viruses. Five psoralens, at concentrations up to 500 times greater than those required to inactivate conventional viruses, did not influence scrapie agent titers in partially purified preparations from murine spleen and hamster brain. 3 H‐psoralens were used to monitor the formation of photoadducts within nucleic acid standards added to preparations of the scrapie agent. Since no inhibition of psoralen photoadduct formation was observed in these preparations, one of three possibilities seems likely: the scrapie agent is devoid of nucleic acid, the psoralens failed to penetrate the protein coat of the agent, or its nucleic acid is unreactive with psoralens.
Phenotypic and genotypic characterization of commonly used human prostatic cell lines (2000)

The cell lines studied fell into three broad groups according to their phenotypic characteristics: (i) prostatic marker positive (LNCaP and LNCaP-r); (ii) high expression of most antigens (DU-145, PC-3 and BPH-1); and (iii) low or absent expression of most antigens (PNT1 A and 1B). Each of the cell lines derived from PC could be identified on the basis of exon 1 and 8 AR sequence variability. DU145 and BPH-1 had identical profiles of the three areas studied, but these cell lines are easily distinguished by their different phenotypic characteristics. PNT1A and 1B had identical genetic and similar phenotypic profiles, which is unsurprising given that they are subclones derived from the same parental line. Even so, these were separable on the basis of CK-19 immunostaining. Using a combination of geno- and phenotypic markers it was possible to derive a 'fingerprint' for each of the cell lines assessed, which will allow meaningful comparison between similar cell lines held in other laboratories.
50 Years Ago (1980)

Biochemistry 50 years ago was an exciting adventure, because of the large number of new findings that were 'waiting to be made'. I shall recount my experience of working in two different places where vitamin K deficiency was encountered independently in two unrelated sets of experi