gebhart/patrepeval huggingface dataset:
Characterization of Escherichia coli EutD: a phosphotransacetylase of the ethanolamine operon (2010)

The Escherichia coli genes pta and eutD encode proteins containing the phosphate-acetyltransferase domain. EutD is composed only by this domain and belongs to the ethanolamine operon. This enzyme has not been characterized yet, and its relationship to the multimodular E. coli phosphotransacetylase (Pta) remains unclear. In the present work, a detailed characterization of EutD from E. coli (EcEutD) was performed. The enzyme is a more efficient phosphotransacetylase than E. coli Pta (EcPta) in catalyzing its reaction in either direction and assembles as a dimer, being differentially modulated by EcPta effectors. When comparing EutD and Pta, both from E. coli, certain divergent regions of the primary structure responsible for their unique properties can be found. The growth on acetate of the E. coli pta acs double-mutant strain, was complemented by either introducing EcEutD or by inducing the eut operon with ethanolamine. In this case, the expression of a phosphotransacetylase different from Pta was confirmed by activity assays. Overall, the results indicate that EcEutD and Pta, although able to catalyse the same reaction, display differential efficiency and regulation, and also differ in the induction of their expression. However, under certain growth conditions, they can fulfil equal roles in E. coli metabolism.
Hole mobility enhancements in strained Si/Si1−yGey p-type metal-oxide-semiconductor field-effect transistors grown on relaxed Si1−xGex (x&lt;y) virtual substrates (2001)

We have achieved peak hole mobility enhancement factors of 5.15 over bulk Si in metal-oxide-semiconductor field-effect transistors (MOSFETs) by combining tensile strained Si surface channels and compressively strained 80% Ge buried channels grown on relaxed 50% Ge virtual substrates. To further investigate hole transport in these dual channel structures, we study the effects of strain, alloy scattering, and layer thickness on hole mobility enhancements in MOSFETs based upon these layers. We show that significant performance boosts can be obtained despite the effects of alloy scattering and that the best hole mobility enhancements are obtained for structures with thin Si surface layers.
Lookup Table Optimization for Sensor Linearization in Small Embedded Systems (2012)

This paper treats the problem of designing an optimal size for a lookup table used for sensor linearization. In small embedded systems the lookup table must be reduced to a minimum in order to reduce the memory footprint and intermediate table values are estimated by linear interpolation. Since interpolation introduces an estimation uncertainty that increases with the sparseness of the lookup table there is a trade-off between lookup table size and estimation precision. This work will present a theory for finding the minimum allowed size of a lookup table that does not affect the overall precision, i.e. the overall precision is determined by the lookup table entries' precision, not by the interpolation error.
Gangliosides as Targets for Monoclonal Antibody Therapy of Cancer (1990)

Certain classes of antibodies are capable of lysing tumor cells by either activating complement (complement-dependent cytotoxicity, or CDC) or by mediating immune effector cells (antibody-dependent cellular cytotoxicity, or ADCC). Non-cytotoxic antibodies are also capable of cell lysis after coupling with toxins, chemotherapeutic drugs, or radioisotopes. In addition, there are antibodies capable of blocking cell surface receptors, thereby inhibiting growth, metastasis, and invasion of the tumor cells. In view of these anti-tumor capabilities, a number of clinical trials involving monoclonal antibodies (Mab) targeted against human cancer have been performed. With the technical feasibility to produce large quantities of purified monoclonal antibodies with defined specificity, isotype, and function, monoclonal antibodies have generated much hope for the immunotherapy of human cancer.
Development and application of neural network algorithms for process diagnostics (1990)

The following three problems are addressed: (1) multiple-input single-output heteroassociative networks for signal validation for distributed sensor arrays; (2) multiple-input multiple-output autoassociative networks for plant-wide monitoring of a set of process variables for diagnostics; and (3) artificial neural networks for online estimation of chemical composition from spectroscopy data. Both static and dynamic forms of the backpropagation network (BPN) have been developed and applied to the solution of these problems. Chemometric data from Raman FT (Fourier transform) spectroscopy was used to estimate chemical sample composition. Several features of network training and implementations are presented, including adaptive updating of the sigmoidal threshold function during training, an optimal choice of hidden layer nodes using Shannon's information theory approach, and automatic scaling of network inputs and outputs for data encoding and decoding. The details of the development and implementation of the multilayer perceptrons and applications to industrial problems are highlighted.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lipoxins and Related Eicosanoids: Biosynthesis, Biological Properties, and Chemical Synthesis (1991)

Abstract Among the various enzymes found in human tissues that act on arachidonic acid, there are three major types of lipoxygenases (LO), operating at the 5‐, 12‐, and 15‐positions. The 5‐LO is a key enzyme and plays a central role in the biosynthesis of leukotrienes, which are potent arachidonate‐derived mediators of allergy and inflammation. Because of the importance of the 5‐LO‐derived products in human pathophysiology, studies were initiated to examine the consequences of initial lipoxygenation at C15 of arachidonic acid as well as to probe interactions between the major LO pathways. These studies led to the identification of a new series of biologically active tetraene‐containing eicosanoids termed lipoxins. This article summarizes the isolation, biosynthesis, and chemical synthesis of lipoxins and related systems, and reviews recent results concerning their formation and biological activities. The total synthesis of these molecules based on a new and general synthetic strategy involving palladium catalysis is reviewed. This synthetic approach has allowed the preparation of several types of acyclic eicosanoids in their naturally occurring forms which, in turn, allowed comparisons with naturally derived materials and enabled detailed studies of the biological actions of these biomolecules. Structure–activity relationships were also derived by combining chemical synthesis and biological investigations.
Exercise therapy in patients with myopathy (2000)

Common impairments experienced by patients with myopathy include muscle weakness, reduced endurance and cardiovascular fitness. Strength-training programmes, incorporating isometric, isotonic or isokinetic exercise, have been shown to improve muscle strength in the short term, without evidence of increased muscle damage using biochemical markers. However, there is some evidence that eccentric exercise may have adverse effects in patients with myopathy. Aerobic training programmes using cycle ergometers or treadmills have demonstrated an improvement in cardiovascular fitness, muscle strength and endurance, again without evidence of increased muscle damage. Further research is needed to determine the optimum training protocols for patients with various types of myopathy, and in particular to improve the ability of patients to be active and independent in daily life.
Molecular Basis of Calmodulin Binding to Cardiac Muscle Ca2+ Release Channel (Ryanodine Receptor) (2003)

Calmodulin (CaM) is a ubiquitous Ca2+-binding protein that regulates the ryanodine receptors (RyRs) by direct binding. CaM inhibits the skeletal muscle ryanodine receptor (RyR1) and cardiac muscle receptor (RyR2) at >1 microm Ca2+ but activates RyR1 and inhibits RyR2 at <1 microm Ca2+. Here we tested whether CaM regulates RyR2 by binding to a highly conserved site identified previously in RyR1. Deletion of RyR2 amino acid residues 3583-3603 resulted in background [35S]CaM binding levels. In single channel measurements, deletion of the putative CaM binding site eliminated CaM inhibition of RyR2 at Ca2+ concentrations below and above 1 microm. Five RyR2 single or double mutants in the CaM binding region (W3587A, L3591D, F3603A, W3587A/L3591D, L3591D/F3603A) eliminated or greatly reduced [35S]CaM binding and inhibition of single channel activities by CaM depending on the Ca2+ concentration. An RyR2 mutant, which assessed the effects of 4 amino acid residues that differ between RyR1 and RyR2 in or flanking the CaM binding domain, bound [35S]CaM and was inhibited by CaM, essentially identical to wild type (WT)-RyR2. Three RyR1 mutants (W3620A, L3624D, F3636A) showed responses to CaM that differed from corresponding mutations in RyR2. The results indicate that CaM regulates RyR1 and RyR2 by binding to a single, highly conserved CaM binding site and that other RyR type-specific sites are likely responsible for the differential functional regulation of RyR1 and RyR2 by CaM.
IL-15 modulates the effect of retinoic acid, promoting inflammation rather than oral tolerance to dietary antigens (2011)

The physiological immune response in the intestine against dietary proteins and commensal flora is characterized by regulatory mechanisms (tolerance) that prevent harmful consequences. Intestinal dendritic cells (DCs) have a central role in the development of immunosuppressive regulatory T cells owing to their ability to produce TGF-β and retinoic acid (RA). However, the article under evaluation shows an unexpected effect of RA - that of promoting a proinflammatory phenotype in intestinal DCs involved in the generation of inflammatory immune responses to dietary antigens. By using a double transgenic murine model that resembles human celiac disease, it was demonstrated that RA synergizes with IL-15 in promoting the breakdown of gluten tolerance and the development of enteropathy. The tissue microenvironment modulates DC function, and immune therapies that are based on RA aiming to restore oral tolerance should be used with caution because the presence of IL-15 (and/or other proinflammatory cytokines) may have undesirable effects.
O‐2A progenitors of the mouse optic nerve exhibit a developmental pattern of antigen expression different from the rat (1995)

In a previous study we demonstrated that differentiation and development of mouse oligodendrocytes is similar to that of the rat after the stage at which O4 is acquired. In this present study we compare directly the early differentiation of oligodendrocytes in the mouse and rat post natal optic nerve and show that the two species differ at the O-2A progenitor and proligodendroblast stages. Mouse progenitors show a variety of morphologies compared to the typical bipolar appearance in the rat. Many murine cells fail to immunolabel with A2B5, GD3, O4, and RmAb, classical markers for rat progenitors, proligodendroblasts, and immature oligodendrocytes. We find that these "unlabeled" cells stain for GAP-43 and that expression of GAP-43 overlaps A2B5 and GD3 in the earlier progenitors and O4, RmAb, and O1 in the later proligodendroblasts and immature oligodendrocytes. Our data suggest that in the development of the mouse O-2A progenitor cells there is a developmental discontinuity between the earlier markers such as A2B5 and GD3 and the later marker O4, which can be filled by GAP-43. We therefore consider that GAP-43 could be used in the mouse, in addition to the classical O-2A markers, for the study of the early oligodendrocyte lineage as it labels an otherwise undetectable O-2A population.
Rab11 regulates recycling through the pericentriolar recycling endosome. (1996)

Small GTPases of the rab family are crucial elements of the machinery that controls membrane traffic. In the present study, we examined the distribution and function of rab11. Rab11 was shown by confocal immunofluorescence microscopy and EM to colocalize with internalized transferrin in the pericentriolar recycling compartment of CHO and BHK cells. Expression of rab11 mutants that are preferentially in the GTP- or GDP-bound state caused opposite effects on the distribution of transferrin-containing elements; rab11-GTP expression caused accumulation of labeled elements in the perinuclear area of the cell, whereas rab11-GDP caused a dispersion of the transferrin labeling. Functional studies showed that the early steps of uptake and recycling for transferrin were not affected by overexpression of rab11 proteins. However, recycling from the later recycling endosome was inhibited in cells overexpressing the rab11-GDP mutant. Rab5, which regulates early endocytic trafficking, acted before rab11 in the transferrin-recycling pathway as expression of rab5-GTP prevented transport to the rab11-positive recycling endosome. These results suggest a novel role for rab11 in controlling traffic through the recycling endosome.
Herpes simplex virus type 1 DNA synthesis requires the product of the UL8 gene: isolation and characterization of an ICP6::lacZ insertion mutation (1989)

We investigated the role of the herpes simplex virus type 1 UL8 gene product in viral DNA replication. First, we unambiguously fine mapped the mutation in tsS38 (complementation group 1-26) to an open reading frame, designated UL8, predicted to encode an 80-kilodalton protein. Previous studies indicated that tsS38 was capable of synthesizing low to moderate levels of viral DNA at the nonpermissive temperature (C. T. Chu, D. S. Parris, R. A. F. Dixon, F. E. Farber, and P. A. Schaffer, Virology 98:168-181, 1979); thus, it was not clear whether the UL8 gene product is essential for viral DNA synthesis. Therefore, a deletion-insertion mutation was constructed in the UL8 gene by removing most of its coding sequences and replacing them with the Escherichia coli lacZ gene under control of the viral ICP6 regulatory signals. The resulting recombinant, hr80, was propagated in helper cells (S22) which express the wild-type version of the UL8 gene, but was incapable of forming plaques in Vero cells. Furthermore, hr80 was totally defective in the synthesis of viral DNA and late proteins under nonpermissive growth conditions. These results demonstrated that the UL8 gene product is essential for viral DNA synthesis.
Labels and event processes in the asbestos operating system (2005)

Asbestos, a new prototype operating system, provides novel labeling and isolation mechanisms that help contain the effects of exploitable software flaws. Applications can express a wide range of policies with Asbestos's kernel-enforced label mechanism, including controls on inter-process communication and system-wide information flow. A new event process abstraction provides lightweight, isolated contexts within a single process, allowing the same process to act on behalf of multiple users while preventing it from leaking any single user's data to any other user. A Web server that uses Asbestos labels to isolate user data requires about 1.5 memory pages per user, demonstrating that additional security can come at an acceptable cost.
Mutual Coupling in MIMO Wireless Systems: A Rigorous Network Theory Analysis (2004)

A new framework for the analysis of multiple-input multiple-output (MIMO) wireless systems is introduced to account for mutual coupling effects in the antenna arrays. The multiport interactions at transmit and receive are characterized by representing the channel using a scattering parameter matrix. A new power constraint that limits the average radiated power is also introduced. The capacity of the MIMO system with mutual coupling is defined as the maximum mutual information of the transmit and receive vectors over all possible transmit signaling and receive loading. Full-wave electromagnetic antenna simulations combined with a simple path-based channel model are used to demonstrate the utility of the method.
A temporal and ultrastructural relationship between heparan sulfate proteoglycans and AA amyloid in experimental amyloidosis. (1991)

Previous histochemical studies have suggested a close temporal relationship between the deposition of highly sulfated glycosaminoglycans (GAGs) and amyloid during experimental AA amyloidosis. In the present investigation, we extended these initial observations by using specific immunocytochemical probes to analyze the temporal and ultrastructural relationship between heparan sulfate proteoglycan (HSPG) accumulation and amyloid deposition in a mouse model of AA amyloidosis. Antibodies against the basement membrane-derived HSPG (either protein core or GAG chains) demonstrated a virtually concurrent deposition of HSPGs and amyloid in specific tissue sites regardless of the organ involved (spleen or liver) or the induction protocol used (amyloid enhancing factor + silver nitrate, or daily azocasein injections). Polyclonal antibodies to AA amyloid protein and amyloid P component also demonstrated co-localization to sites of HSPG deposition in amyloid sites, whereas no positive immunostaining was observed in these locales with a polyclonal antibody to the protein core of a dermatan sulfate proteoglycan (known as "decorin"). Immunogold labeling of HSPGs (either protein core or GAG chains) in amyloidotic mouse spleen or liver revealed specific localization of HSPGs to amyloid fibrils. In the liver, heparan sulfate GAGs were also immunolocalized to the lysosomal compartment of hepatocytes and/or Kupffer cells adjacent to sites of amyloid deposition, suggesting that these cells are involved in HSPG production and/or degradation. The close temporal and ultrastructural relationship between HSPGs and AA amyloid further implies an important role for HSPGs during the initial stages of AA amyloidosis.
An optical pointer for infrared remote controllers (2005)

An infrared optical pointing system is described for interactive remote controllers to allow the positioning of a cursor on a TV screen. A simple lens and 4 quadrant photodetector in the remote controller are used to measure the angle of incidence of light received from an infrared reference beam.
Quantification of Posture Induced Changes in Wearable Seismocardiogram Signals for Heart Failure Patients (2016)

Our goal is to characterize the effects of posture-supine, seated, and standing-on the seismocardiogram (SCG) signal for patients with heart failure (HF). Posture can (1) distort the SCG signal, for example due to altering the body's mechanical vibration response, and (2) affect a person's cardiovascular physiology, for example due to changes in venous return. This work focuses on characterizing the former, such that in future studies we can use the SCG to assess physiological changes in patients with HF at home. Our team has developed a circular patch (7 cm in diameter) which, when placed on the sternum, simultaneously measures the electrocardiogram (ECG) along with SCG signals in the dorso-ventral and head-to-foot directions. We recruited six HF patients thus far for this ongoing study. Each subject was asked to lie down in a supine position on a patient bed for 1 minute followed by 1 minute in each of the seated and standing postures. A novel algorithm was implemented to compare distortion in the shape of the SCG signals in the supine and seated postures as compared to the standing upright posture. The frequency domain analysis of the SCG signals revealed presence of high energy in bands greater than 8 Hz for supine and seated postures. Based on the findings of this paper, features can be derived to correct for posture related changes in the measured SCG signals for accurate assessment of patients with HF at home.
Variations in the number of peptide-MHC class I complexes required to activate cytotoxic T cell responses. (1995)

We determined equilibrium constants for the binding of 16 peptides (based on four T cell epitopes) to three MHC class I proteins (A2, Kb, and Ld) on intact cells and estimated the number of accessible peptide-binding sites on these cells. From these results, and the concentrations of peptides required to sensitize target cells for lysis by CD8+ CTL, we conclude that the critical number of peptide-MHC complexes required per target cell for the activation of CTL responses varies with different combinations of peptide-MHC complexes and CTL clones from several thousand complexes to fewer than ten per target cell.
Production and purification of recombinant protective antigen and protective efficacy against Bacillus anthracis (1998)

Recombinant protective antigen (rPA), expressed by Bacillus subtilis WB600 (pPA 101), has been purified to homogeneity and the protective efficacy against a Bacillus anthracis challenge has been investigated. rPA was fractionated from culture supernatant fluid by ammonium sulphate, followed by anion exchange chromatography using DEAE Streamline, anion-exchange chromatography on FPLC MonoQ HR 10/10 and finally, gel filtration chromatography on FPLC Superose 12 HR 10/30, to yield 7 mg rPA per litre of culture. The protective efficacy of rPA against an airborne challenge with the AMES strain of B. anthracis was determined in the presence of the adjuvants, alhydrogel and Ribi, and compared to that achieved by the current UK human vaccine in guinea pigs. rPA combined with the Ribi adjuvant was found to provide 100% protection against challenge.
Basic Mechanisms in Blood Coagulation (1975)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Syntheses, Properties, and Potential Applications of Multicomponent Magnetic Nanoparticles (2008)

Abstract Multicomponent hybrid nanostructures that contain two or more nanometer‐scale components have attracted much attention recently owing to the synergistic properties induced by interactions between these different nanometer‐scale objects. Herein, we give an overview of the efforts to synthesize multicomponent nanoparticles with at least one component being magnetic, and focus on our recent developments. The syntheses are based on heterogeneous nucleation and growth of a second and third component onto seed nanoparticles. These multicomponent nanoparticles show interesting magnetic, magneto‐optical, plasmonic, and semiconducting properties that can be modulated by interfacial interactions between different nanocomponents. This opens up a new avenue to advanced multifunctional nanomaterials for device concepts and applications.
The Design and Analysis of an Infeed System for Forest Residue Baler (1985)

ABSTRACT A hydraulically operated, inverted grapple infeed system was developed to feed heterogeneous wood residue into a baler. Finite element analysis was conducted to check the integrity of the design. Input data for the analysis was collected during field trials with the infeed system. The analyses and the results obtained under different loading conditions are discussed.
HMM adaptation using vector taylor series for noisy speech recognition (2000)

In this paper we address the problem of robustness of speech recognition systems in noisy environments. The goal is to estimate the parameters of a HMM that is matched to a noisy environment, given a HMM trained with clean speech and knowledge of the acoustical environment. We propose a method based on truncated vector Taylor series that approximates the performance of a system trained with that corrupted speech. We also provide insight on the approximations used in the model of the environment and compare them with the lognormal approximation in PMC.