gebhart/patrepeval huggingface dataset:
High performance quantum computing (2011)

The architecture scalability afforded by recent proposals of a large-scale photonic-based quantum computer allows us to move on to a discussion of massively scaled Quantum Information Processing (QIP). In this paper, we consider the quantum analogue of High Performance Computing (HPC), where a dedicated server farm is utilized by many users to run algorithms and share quantum data. We introduce both a trusted mainframe model as a quantum extension of classical HPC and a model where quantum security is achieved during computation. The scaling structure of the optical architecture leads to an attractive future for server based QIP, where dedicated mainframes can be constructed and/or expanded to serve an increasingly hungry user base with the ideal resource for individual quantum information processing.
Micromachined circuits for millimeter- and sub-millimeter-wave applications (1993)

Two approaches for the development of micromachined circuits for millimeter- and submillimeter-wave applications are discussed. These technologies provide a means to overcome the drawbacks typically associated with conventional planar transmission lines, such as microstrip and coplanar waveguides. Examples demonstrating the use of micromachining to effectively incorporate a third dimension into the geometry of monolithic circuits are presented. This introduces additional parameters in the design and results in structures with superior electrical performance, such as membrane-supported circuits, and reduced volume and weight, such as micromachined-shielded circuits. Micromachined circuits which incorporate miniaturized shielding packages in a monolithic design are described. The performance of these circuits shows that the low-volume, low-weight packaging is effective in reducing signal loss, without degrading the desired frequency response.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Farnesoid X Receptor (2005)

Bile acids are the end products of cholesterol metabolism. They are synthesized in the liver and secreted via bile into the intestine, where they aid in the absorption of fat-soluble vitamins and dietary fat. Subsequently, bile acids return to the liver to complete their enterohepatic circulation. The Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily and has emerged as a key player in the control of multiple metabolic pathways. On its activation by bile acids, FXR regulates bile acid synthesis, conjugation, and transport, as well as various aspects of lipid and glucose metabolism. This review summarizes recent advances in deciphering the role of FXR in the context of hepatic lipid and glucose homeostasis and discusses the potential of FXR as a pharmacological target for therapeutic applications.
Genetic Abnormalities and Challenges in the Treatment of Acute Myeloid Leukemia (2011)

Acute myeloid leukemia (AML) is a hematopoietic disorder in which there are too many immature blood-forming cells accumulating in the bone marrow and interfering with the production of normal blood cells. It has long been recognized that AML is a clinically heterogeneous disease characterized by a multitude of chromosomal abnormalities and gene mutations, which translate to marked differences in responses and survival following chemotherapy. The cytogenetic and molecular genetic aberrations associated with AML are not mutually exclusive and often coexist in the leukemic cells. AML is a disease of the elderly, with a mean age of diagnosis of 70 years. Adverse cytogenetic abnormalities increase with age, and within each cytogenetic group, prognosis with standard treatment worsens with age. In the past 20 years, there has been little improvement in chemotherapeutic regimens and hence the overall survival for patients with AML. A huge unmet need exists for efficacious targeted therapies for elderly patients that are less toxic than available chemotherapy regimens. The multitude of chromosomal and genetic abnormalities makes the treatment of AML a challenging prospect. A detailed understanding of the molecular changes associated with the chromosomal and genetic abnormalities in AML is likely to provide a rationale for therapy design and biomarker development. This review summarizes the variety of cytogenetic and genetic changes observed in AML and gives an overview of the clinical status of new drugs in development.
Oligonucleotide Loading Determines Cellular Uptake of DNA-Modified Gold Nanoparticles (2007)

The cellular internalization of oligonucleotide-modified nanoparticles is investigated. Uptake is dependent on the density of the oligonucleotide loading on the surface of the particles, where higher densities lead to greater uptake. Densely functionalized nanoparticles adsorb a large number of proteins on the nanoparticle surface. Nanoparticle uptake is greatest where a large number of proteins are associated with the particle.
Peptide YY Is Critical for Acylethanolamine Receptor Gpr119-Induced Activation of Gastrointestinal Mucosal Responses (2010)

Peptide YY (PYY) is released following food intake and regulates intestinal function and glucose homeostasis, but the mechanisms underpinning these processes are unclear. Enteroendocrine L cells contain PYY and express the acylethanolamine receptor, Gpr119. Here, we show that Gpr119 activation inhibited epithelial electrolyte secretion in human and mouse colon in a glucose-sensitive manner. Endogenous PYY selectively mediated these effects, since PYY(-/-) mice showed no Gpr119 response, but responses were observed in NPY(-/-) mice. Importantly, Gpr119 responses in wild-type (WT) mouse tissue and human colon were abolished by Y(1) receptor antagonism, but were not enhanced by dipeptidylpeptidase IV blockade, indicating that PYY processing to PYY(3-36) was not important. In addition, Gpr119 agonism reduced glycemic excursions after oral glucose delivery to WT mice but not PYY(-/-) mice. Taken together, these data demonstrate a previously unrecognized role of PYY in mediating intestinal Gpr119 activity and an associated function in controlling glucose tolerance.
A knowledge based framework for the detection of measurement uncertainties in derived sea surface current fields (2010)

In [6] we presented an approach to measure sea surface currents from satellite images by computing the displacement vectors of distinctive image features or measuring the optical flow between successive images of the same scene. These algorithms are based on the assumption that the image flow observed is caused by the motion of surface films with the currents to be measured. Optical flow due to other image features, e.g. ship wakes, does not correspond to the motion field and causes systematic errors. The decision whether a derived measurement is valid or not by domain experts is very time-consuming. We present first steps towards an automatic knowledge-based approach that uses description logic to validate the measurements of sea surface currents. The terminological knowledge is based on the expert's knowledge of the domain in conjunction with a geographical database containing factual knowledge about the scene. The combination of different sources of knowledge makes it possible to infer about the validity of sea surface current measurements from image data by reasoning based on the local context of the image features.
Phosphatidylinositol 3-Kinase as a Mediator of TNF-Induced NF-κB Activation (2000)

The activation of transcription factor NF-kappa B by TNF involves the stimulation of a novel signaling cascade. In this paper we show that phosphatidylinositol 3-kinase (PI 3-kinase) may play a pivotal role in TNF-mediated activation of NF-kappa B-dependent genes. Consistent with its involvement in TNF signaling, PI 3-kinase activities in HepG2 and U937 cells can be stimulated by TNF in a rapid but transient manner through a mechanism that may involve its association with the insulin receptor substrate-1. A dominant-negative mutant of the p85 regulatory subunit of PI 3-kinase, which is a potent inhibitor of PI 3-kinase signaling, effectively blocked the TNF-induced expression of an NF-kappa B-dependent reporter gene. Although PI 3-kinase may be required for NF-kappa B activation, overexpression of its p110 catalytic subunit alone was unable to induce an NF-kappa B/chloramphenicol acetyltransferase (CAT) reporter gene. However, when TNF was added to p110-overexpressing cells, there was a synergistic activation of the NF-kappa B/CAT reporter, suggesting that other TNF-inducible signals may cooperate with PI 3-kinase to activate NF-kappa B. Consistent with its role in NF-kappa B activation, inhibition of PI 3-kinase activity by wortmannin or LY294002 greatly potentiated TNF-induced apoptosis. This TNF/wortmannin-induced apoptosis was markedly prevented in cells overexpressing Rel A. Taken together, our results indicate that a PI 3-kinase-regulated step in TNF-signaling is critical for the expression of NF-kappa B-dependent genes.
Ketone Bodies as a Therapeutic for Alzheimer's Disease (2008)

An early feature of Alzheimer's disease (AD) is region-specific declines in brain glucose metabolism. Unlike other tissues in the body, the brain does not efficiently metabolize fats; hence the adult human brain relies almost exclusively on glucose as an energy substrate. Therefore, inhibition of glucose metabolism can have profound effects on brain function. The hypometabolism seen in AD has recently attracted attention as a possible target for intervention in the disease process. One promising approach is to supplement the normal glucose supply of the brain with ketone bodies (KB), which include acetoacetate, beta-hydroxybutyrate, and acetone. KB are normally produced from fat stores when glucose supplies are limited, such as during prolonged fasting. KB have been induced both by direct infusion and by the administration of a high-fat, low-carbohydrate, low-protein, ketogenic diets. Both approaches have demonstrated efficacy in animal models of neurodegenerative disorders and in human clinical trials, including AD trials. Much of the benefit of KB can be attributed to their ability to increase mitochondrial efficiency and supplement the brain's normal reliance on glucose. Research into the therapeutic potential of KB and ketosis represents a promising new area of AD research.
Laser Frequency Combs for Astronomical Observations (2008)

A direct measurement of the universe's expansion history could be made by observing in real time the evolution of the cosmological redshift of distant objects. However, this would require measurements of Doppler velocity drifts of approximately 1 centimeter per second per year, and astronomical spectrographs have not yet been calibrated to this tolerance. We demonstrated the first use of a laser frequency comb for wavelength calibration of an astronomical telescope. Even with a simple analysis, absolute calibration is achieved with an equivalent Doppler precision of approximately 9 meters per second at approximately 1.5 micrometers-beyond state-of-the-art accuracy. We show that tracking complex, time-varying systematic effects in the spectrograph and detector system is a particular advantage of laser frequency comb calibration. This technique promises an effective means for modeling and removal of such systematic effects to the accuracy required by future experiments to see direct evidence of the universe's putative acceleration.
Unusual mechanism of hydrocarbon formation in the housefly: cytochrome P450 converts aldehyde to the sex pheromone component (Z)-9-tricosene and CO2. (1994)

An unusual mechanism for hydrocarbon biosynthesis is proposed from work examining the formation of (Z)-9-tricosene (Z9-23:Hy), the major sex pheromone component of the female housefly, Musca domestica. Incubation of (Z)-15-[1-14C]- and (Z)-15-[15,16-3H2]tetracosenoic acid (24:1 fatty acid) with microsomes from houseflies gave equal amounts of [3H]Z9-23:Hy and 14CO2. The formation of CO2 and not CO, as reported for hydrocarbon formation in plants, animals, and microorganisms [Dennis, M. & Kolattukudy, P. E. (1992) Proc. Natl. Acad. Sci. USA 89, 5306-5310], was verified by trapping agents and by radio-GLC analysis. Incubation of (Z)-15-[15,16-3H2]tetracosenoyl-CoA with microsomal preparations in the presence of NADPH and O2 gave almost equal amounts of (Z)-15-3H2]tetrasosenal (24:1 aldehyde) and Z9-23:Hy. Addition of increasing amounts of hydroxylamine (aldehyde trapping agent) caused a decrease in hydrocarbon formation with a concomitant increase in oxime (aldehyde derivative) formation. The 24:1 aldehyde was efficiently converted to (Z)-9-tricosene only in the presence of both NADPH and O2. Bubbling carbon monoxide (20:80 CO/O2) or including an antibody against housefly cytochrome P450 reductase inhibited the formation Z9-23:Hy from 24:1 aldehyde. These data demonstrate an unusual mechanism for hydrocarbon formation in insects in which the acyl-CoA is reduced to the corresponding aldehyde and then carbon-1 is removed as CO2. The requirement for NADPH and O2 and the inhibition by CO and the antibody to cytochrome P450 reductase strongly implicate the participation of a cytochrome P450 in this reaction.
Translation initiation in Escherichia coli: sequences within the ribosome‐binding site (1992)

The translational roles of the Shine-Dalgarno sequence, the initiation codon, the space between them, and the second codon have been studied. The Shine-Dalgarno sequence UAAGGAGG initiated translation roughly four times more efficiently than did the shorter AAGGA sequence. Each Shine-Dalgarno sequence required a minimum distance to the initiation codon in order to drive translation; spacing, however, could be rather long. Initiation at AUG was more efficient than at GUG or UUG at each spacing examined; initiation at GUG was only slightly better than UUG. Translation was also affected by residues 3' to the initiation codon. The second codon can influence the rate of initiation, with the magnitude depending on the initiation codon. The data are consistent with a simple kinetic model in which a variety of rate constants contribute to the process of translation initiation.
Endoprotease Activities Other Than Furin and PACE4 with a Role in Processing of HIV-I gp160 Glycoproteins in CHO-K1 Cells (1997)

We addressed the question of whether furin is the endoprotease primarily responsible for processing the human immunodeficiency virus type I (HIV-I) envelope protein gp160 in mammalian cells. The furin-deficient Chinese hamster ovary (CHO)-K1 strain RPE.40 processed gp160 as efficiently as wild-type CHO-K1 cells in vivo. Although furin can process gp160 in vitro, this processing is probably not physiologically relevent, because it occurs with very low efficiency. PACE4, a furin homologue, allowed processing of gp160 when both were expressed in RPE.40 cells. Further, PACE4 participated in the activation of a calcium-independent protease activity in RPE.40 cells, which efficiently processed the gp160 precursor in vitro. This calcium-independent protease activity was not found in another furin-deficient cell strain, 7.P15, selected from the monkey kidney cell line COS-7.
Low power 1T DRAM/NVM versatile memory featuring steep sub-60-mV/decade operation, fast 20-ns speed, and robust 85&#x00B0;C-extrapolated 10<sup>16</sup> endurance (2015)

In this work, we report a one-transistor (1T) versatile memory; the memory transistor characteristics achieve sub-60-mV/dec operation and considerably low off-state leakage of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−15</sup> A/µm at a supply voltage below 0.5V. The versatile memory features DRAM/NVM functions of large ΔV <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> window of 2.8V, fast 20-ns speed, 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> s retention at 85°C, and long extrapolated 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</sup> endurance at 85°C, which show the potential for 3D memory application with severe requirement on both high density and low power consumption.
Formal methods for the validation of automotive product configuration data (2003)

In the automotive industry, the compilation and maintenance of correct product configuration data is a complex task. Our work shows how formal methods can be applied to the validation of such business critical data. Our consistency support tool BIS works on an existing database of Boolean constraints expressing valid configurations and their transformation into manufacturable products. Using a specially modified satisfiability checker with an explanation component, BIS can detect inconsistencies in the constraints set and thus help increase the quality of the product data. BIS also supports manufacturing decisions by calculating the implications of product or production environment changes on the set of required parts. In this paper, we give a comprehensive account of BIS: the formalization of the business processes underlying its construction, the modifications of satisfiability-checking technology we found necessary in this context, and the software technology used to package the product as a client–server information system.
Convergent Message-Passing Algorithms for Inference over General Graphs with Convex Free Energies (2012)

Inference problems in graphical models can be represented as a constrained optimization of a free energy function. It is known that when the Bethe free energy is used, the fixedpoints of the belief propagation (BP) algorithm correspond to the local minima of the free energy. However BP fails to converge in many cases of interest. Moreover, the Bethe free energy is non-convex for graphical models with cycles thus introducing great difficulty in deriving efficient algorithms for finding local minima of the free energy for general graphs. In this paper we introduce two efficient BP-like algorithms, one sequential and the other parallel, that are guaranteed to converge to the global minimum, for any graph, over the class of energies known as "convex free energies". In addition, we propose an efficient heuristic for setting the parameters of the convex free energy based on the structure of the graph.
Understanding Immunosenescence in Aging-Related DiseasesWith Quantitative Proteomics (2014)

Immunosenescence refers to the gradual deterioration of the immune system during aging. It is widely accepted that immunosenescence is characterized by diminished immune response, low-grade inflammation, and increased propensity for autoimmunity. These changes in the immune system increase the risk and mortality of diseases among the elderly. Poor response to immunotherapies as a result of immunosenescence can further worsen this situation. Fundamental understanding of immunosenescence is helpful for the prevention and treatment of aging-related diseases. Genomics, transcriptomics, proteomics, and metabolomics can give insight to molecular mechanisms of immunosenescence and its contribution to aging-related diseases. In particular, work presented in this dissertation takes advantage of proteomics methods to understand immunosenescence in two aging-related diseases-sepsis and Alzheimer’s disease (AD). To better study sepsis and AD, novel proteomics platforms are developed in this dissertation. Firstly, a robust platform is developed to improve the coverage of the human plasma proteome and establish statistical criteria for the determination of differentially-expressed proteins. Secondly, a novel data acquisition method using pulsed Q dissociation (PQD) in triple-stage mass spectrometry (MS3) is developed for isobaric tags-based quantitation. This method increases the number of identified and quantified proteins without compromising quantitative accuracy. 
In sepsis studies, proteins involved in inflammation, acute phase response, coagulation, and lipid metabolism are associated with age-related risk of severe sepsis among community-acquired pneumonia patients. In AD studies, a human double transgenic knock-in amyloid precursor protein/presenilin-1 (APP/PS-1) mouse model is employed. The proteome of T-cells and other immune cells (e.g., B-cells and macrophages) from this model is characterized and provides a reference map for future studies. T-cells from APP/PS-1 mice have increased oxidative stress during the progression of AD. Proteomics analysis of T-cells from this mouse model provides molecular basis for this phenomenon. Proteins related to cytoskeleton, energy metabolism, apoptosis, and molecular chaperones are also differentially expressed during AD progression.
Overall, works in this dissertation provide novel platforms for protein identification and quantitation. Application of proteomics platforms to the studies of sepsis and AD provides insight to the molecular mechanisms of immunosenescence. Results from these studies may be helpful for the development of novel diagnosis and treatments.
Harrison's Infectious Diseases (2010)

Infectious Diseases - as only Harrison's can cover it. A Doody's Core Title for 2015. Featuring a superb compilation of chapters related to infectious diseases that appear in Harrison's Principles of Internal Medicine, Eighteenth Edition, this concise, full-color clinical companion delivers the latest knowledge in the field backed by the scientific rigor and authority that have defined Harrison's. You will find content from renowned editors and contributors in a carry-anywhere presentation that is ideal for the classroom, clinic, ward, or exam/certification preparation. Features: current, complete coverage of need-to-know topics, including infections in organ systems, bacterial infections, viral infections, prion diseases, fungal infections, and protozoal infections; addresses underlying epidemiologic, pathophysiologic, and genetic factors; important material on HIV infections and AIDS by Anthony S. Fauci and H. Clifford Lane; two image-based chapters comprise atlases valuable to clinical assessment: rashes associated with fever and blood smears of the various stages of the parasites causing malaria and babesiosis; integration of pathophysiology with clinical management 121 high-yield questions and answers drawn from Harrison's Principles of Internal Medicine Self-Assessment and Board Review, 18e. It also includes content updates and new developments since the publication of Harrison's Principles of Internal Medicine, 18e; 132 chapters written by physicians who are recognized experts in the field of infectious diseases; and, helpful appendix of laboratory values of clinical importance.
The transcriptional regulatory strategy of the rat tissue kallikrein gene family (1997)

We have analysed the transcriptional regulatory strategy of the rat tissue kallikrein gene family, a strategy that provides universal submandibular gland expression of all family members coupled with otherwise disparate expression of individual members in a wide variety of organs. To test whether a locus control region (LCR) or individual gene enhancers control the family, the expression patterns of rat kallikrein genes were examined in transgenic mice bearing a series of rat genomic fragments spanning the kallikrein locus. Each fragment, present in recombinant P1 phage clones, contained two or three linked members of the rat family. Rat (r) genes KLK1, KLK2, KLK3, KLK7, KLK8, KLK9 and KLK10 on four different P1 clones were all correctly expressed at high levels in the submandibular glands of transgenic mice and in general showed the correct extra-salivary patterns characteristic of each family member. Moreover, when the neighbouring family members rKLK1 and rKLK3 were separated on non-overlapping fragments and tested in mice, each transgene was expressed correctly in the submandibular gland and in other organs characteristic of that gene. Thus the family locus is not controlled by an LCR; rather each gene appears to have an associated transcriptional enhancer that specifies high submandibular expression and contributes to the additional organ specificity of the family member.