gebhart/patrepeval huggingface dataset:
THE EVOLUTION OF ADAPTIVE IMMUNITY (2006)

Approximately 500 mya two types of recombinatorial adaptive immune systems appeared in vertebrates. Jawed vertebrates generate a diverse repertoire of B and T cell antigen receptors through the rearrangement of immunoglobulin V, D, and J gene fragments, whereas jawless fish assemble their variable lymphocyte receptors through recombinatorial usage of leucine-rich repeat (LRR) modular units. Invariant germ line-encoded, LRR-containing proteins are pivotal mediators of microbial recognition throughout the plant and animal kingdoms. Whereas the genomes of plants and deuterostome and chordate invertebrates harbor large arsenals of recognition receptors primarily encoding LRR-containing proteins, relatively few innate pattern recognition receptors suffice for survival of pathogen-infected nematodes, insects, and vertebrates. The appearance of a lymphocyte-based recombinatorial system of anticipatory immunity in the vertebrates may have been driven by a need to facilitate developmental and morphological plasticity in addition to the advantage conferred by the ability to recognize a larger portion of the antigenic world.
Star coupler based WDM switch employing tunable devices with reduced tunability range (1992)

High capacity star coupler based WDM switches require tunable devices with a wide tunability range beyond the reach of the present device technology. The Letter describes a new design principle for such WDM switches that incorporates available tunable devices that are short of the required tunability range. The proposed design, which is based on the conventional three-stage switch architecture, requires less hardware than previously needed, but at the cost of increased switch control complexity.
Lattice Tilt and Misfit Dislocations in (11\bar22) Semipolar GaN Heteroepitaxy (2010)

Epilayer lattice tilt has been observed by X-ray diffraction for heteroepitaxial AlGaN and InGaN films on (1122) semipolar GaN substrates. Complementary transmission electron microscopy demonstrates that epilayer tilt is a consequence of interfacial misfit dislocations with Burgers vectors a/3[1120] that glide on the (0001) basal plane [inclined ∼58° to (1122)]. The dislocation lines are parallel to [1100], consistent with the anisotropy of the tilt observed in X-ray scans parallel to orthogonal in-plane directions. The dislocations had an in-plane Burgers vector component that relieved misfit strain, and a perpendicular component responsible for lattice tilt. Dislocation densities predicted by tilt agree well with TEM measurements.
Both the stroma and thylakoid lumen of tobacco chloroplasts are competent for the formation of disulphide bonds in recombinant proteins (2007)

Plant chloroplasts are promising vehicles for recombinant protein production, but the process of protein folding in these organelles is not well understood in comparison with that in prokaryotic systems, such as Escherichia coli. This is particularly true for disulphide bond formation which is crucial for the biological activity of many therapeutic proteins. We have investigated the capacity of tobacco (Nicotiana tabacum) chloroplasts to efficiently form disulphide bonds in proteins by expressing in this plant cell organelle a well-known bacterial enzyme, alkaline phosphatase, whose activity and stability strictly depend on the correct formation of two intramolecular disulphide bonds. Plastid transformants have been generated that express either the mature enzyme, localized in the stroma, or the full-length coding region, including its signal peptide. The latter has the potential to direct the recombinant alkaline phosphatase into the lumen of thylakoids, giving access to this even less well-characterized organellar compartment. We show that the chloroplast stroma supports the formation of an active enzyme, unlike a normal bacterial cytosol. Sorting of alkaline phosphatase to the thylakoid lumen occurs in the plastid transformants translating the full-length coding region, and leads to larger amounts and more active enzyme. These results are compared with those obtained in bacteria. The implications of these findings on protein folding properties and competency of chloroplasts for disulphide bond formation are discussed.
The effect of viscoelastic fluids on flows generated by spherical objects during sedimentation (2012)

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012.
Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: The phenylacetyl-CoA catabolon (1998)

Fourteen different genes included in a DNA fragment of 18 kb are involved in the aerobic degradation of phenylacetic acid by Pseudomonas putida U. This catabolic pathway appears to be organized in three contiguous operons that contain the following functional units: (i) a transport system, (ii) a phenylacetic acid activating enzyme, (iii) a ring-hydroxylation complex, (iv) a ring-opening protein, (v) a beta-oxidation-like system, and (vi) two regulatory genes. This pathway constitutes the common part (core) of a complex functional unit (catabolon) integrated by several routes that catalyze the transformation of structurally related molecules into a common intermediate (phenylacetyl-CoA).
Interaction between Clostridium thermocellum endoglucanase CelD and polypeptides derived from the cellulosome-integrating protein CipA: stoichiometry and cellulolytic activity of the complexes (1997)

Four mini-scaffoldins were constructed from modules derived from the Clostridium thermocellum cellulosome-integrating protein CipA. Cip7 and Cip6 contained one and two cohesin modules respectively. Cip14 and Cip16, also containing one and two cohesin modules respectively, were flanked by a cellulose-binding domain. Endoglucanase CelD formed stable complexes with all mini-scaffoldins. Analytical ultracentrifugation of the complexes showed that 1 mol of CelD bound per mol of Cip14, and 2 mol of CelD bound per mol of Cip16. Under the conditions used for assaying cellulase activity, 96% of CelD alone bound to Avicel. Association with Cip14 or Cip16 increased the cellulose binding of CelD to 99%, while association with Cip7 or Cip6 decreased binding to 79 and 75% respectively. The hydrolytic activity of CelD against Avicel was increased 3-fold in complexes with Cip14 and Cip16, but remained substantially the same in complexes with Cip6 and Cip7. Addition of whole CipA also enhanced the efficiency of Avicel hydrolysis by CelD. However, even at an optimal ratio of the components, CelD-CipA complexes were somewhat less active than complexes of CelD with Cip14 or Cip16. These results suggest that the synergism observed between CelD and Cip14 or Cip16 is mostly due to the presence of the cellulose-binding domain, which promotes productive binding of the enzyme.
Effects of Tylosin Use on Erythromycin Resistance in Enterococci Isolated from Swine (2004)

The effect of tylosin on erythromycin-resistant enterococci was examined on three farms; farm A used tylosin for growth promotion, farm B used tylosin for treatment of disease, and farm C did not use tylosin for either growth promotion or disease treatment. A total of 1,187 enterococci were isolated from gestation, farrowing, suckling, nursery, and finishing swine from the farms. From a subset of those isolates (n = 662), 59% (124 out of 208), 28% (80 out of 281), and 2% (4 out of 170) were resistant to erythromycin (MIC >/= 8 microg/ml) from farms A, B, and C, respectively. PCR analysis and Southern blotting revealed that 95% (65 out of 68) of isolates chosen from all three farms for further study were positive for ermB, but all were negative for ermA and ermC. By using Southern blotting, ermB was localized to the chromosome in 56 of the isolates while 9 isolates from farms A and B contained ermB on two similar-sized plasmid bands (12 to 16 kb). Pulsed-field gel electrophoresis revealed that the isolates were genetically diverse and represented a heterogeneous population of enterococci. This study suggests that although there was resistance to a greater number of enterococcal isolates on a farm where tylosin was used as a growth promotant, resistant enterococci also existed on a farm where no antimicrobial agents were used.
A family of neuromuscular stimulators with optical transcutaneous control (1991)

A family of miniature implantable neuromuscular stimulators has been developed using surface-mounted Philips 4000-series integrated circuits. The electronic components are mounted by hand on printed circuits (platinum/gold on alumina) and the electrical connections are made by reflow soldering. The plastic integrated-circuit packages, ceramic resistors and metal interconnections are protected from the body fluids by a coating of biocompatible silicone rubber. This simple technology provides reliable function for at least 4 months under implanted conditions. The circuits have in common a single lithium cell power-supply (3.2 V) and an optical sensor which can be used to detect light flashes through the skin after the device has been implanted. This information channel may be used to switch the output of a device on or off, or to cycle through a series of pre-set programs. The devices are currently finding application in studies which provide an experimental basis for the clinical exploitation of electrically stimulated skeletal muscle in cardiac assistance, sphincter reconstruction or functional electrical stimulation of paralysed limbs.
Effect of Colicin E3 upon the 30S Ribosomal Subunit of Escherichia coli (1971)

The properties of 30S ribosomal subunits from untreated and from colicin E3-treated (E3-30S) bacteria have been compared. Polyacrylamide gel electrophoresis of ribosomal proteins revealed no difference, but several studies indicated that the 16S RNA from E3-30S particles was modified. E3-16S RNA showed slightly increased resistance to heat-induced degradation and had a reduced (15 S) sedimentation coefficient on sucrose gradients. Fingerprint analyses of E3-16S RNA revealed that the 3'-terminus of the molecule had been deleted. It was concluded that a primary effect of colicin E3 is the activation of a highly specific RNase that degrades 30S ribosomal RNA in situ, and that the resulting fragment(s) are probably retained within the 30S particle.
Theoretical Eye Model with Aspherics* (1971)

A model for the human eye is proposed, similar to Gullstrand’s well-known 4-radius model, however with the front surface of the cornea and the back surface of the crystalline lens taken to be rotationally symmetric aspherics. Whereas for the cornea a polynomial is used based on experimental data of Bonnet, a second-order parabola was tentatively adopted for the back surface of the lens. This model results in slight spherical undercorrection, in agreement with experimental findings. On the other hand, the sine condition is not well satisfied, probably due to neglect of the shell structure of the lens. By ray tracing, astigmatism and coma as well as the meridional and sagittal focal lengths were computed up to a visual angle of 90°. Calculations were also made for the same model preceded by a plano-concave contact lens (Goldmann 3-mirror contact glass), showing that this combination results in considerably reduced astigmatism.
Brittle crack propagation in silicon single crystals (1991)

Viewing the brittle-to-ductile transition of fracture in intrinsically brittle solids as a crack tip initiated critical event of either nucleation of dislocation loops from the crack tip or the motion away of such dislocations from the crack tip, experiments have been devised to measure the critical activation energy of such events by measuring the arrest temperature of cleavage cracks with different velocities in experiments that were conducted on large Si single crystals subjected to a steep temperature gradient. While such experiments can provide precise information that can be related directly to mechanisms of crack tip bifurcation behavior, they are hampered by nontrivial perturbations that must be controlled. Here in the first of a series of communications we discuss the nature of these perturbations in Si single crystals, cleaving either on the {111} or the {110} planes.
SecureMR: A Service Integrity Assurance Framework for MapReduce (2009)

MapReduce has become increasingly popular as a powerful parallel data processing model. To deploy MapReduce as a data processing service over open systems such as service oriented architecture, cloud computing, and volunteer computing, we must provide necessary security mechanisms to protect the integrity of MapReduce data processing services. In this paper, we present SecureMR, a practical service integrity assurance framework for MapReduce. SecureMR consists of five security components, which provide a set of practical security mechanisms that not only ensure MapReduce service integrity as well as to prevent replay and denial of service (DoS) attacks, but also preserve the simplicity, applicability and scalability of MapReduce. We have implemented a prototype of SecureMR based on Hadoop, an open source MapReduce implementation. Our analytical study and experimental results show that SecureMR can ensure data processing service integrity while imposing low performance overhead.
Nondegenerate three-wave mixing with the Josephson ring modulator (2013)

The Josephson ring modulator (JRM) is a device, based on Josephson tunnel junctions, capable of performing nondegenerate mixing in the microwave regime without losses. The generic scattering matrix of the device is calculated by solving coupled quantum Langevin equations. Its form shows that the device can achieve quantum-limited noise performance both as an amplifier and a mixer. Fundamental limitations on simultaneous optimization of performance metrics like gain, bandwidth, and dynamic range (including the effect of pump depletion) are discussed. We also present three possible integrations of the JRM as the active medium in a different electromagnetic environment. The resulting circuits, named Josephson parametric converters (JPC), are discussed in detail, and experimental data on their dynamic range are found to be in good agreement with theoretical predictions. We also discuss future prospects and requisite optimization of JPC as a preamplifier for qubit readout applications.
Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses (2007)

In microbial mat communities of Yellowstone hot springs, ribosomal RNA (rRNA) sequence diversity patterns indicate the presence of closely related bacterial populations along environmental gradients of temperature and light. To identify the functional bases for adaptation, we sequenced the genomes of two cyanobacterial (Synechococcus OS-A and OS-B') isolates representing ecologically distinct populations that dominate at different temperatures and are major primary producers in the mat. There was a marked lack of conserved large-scale gene order between the two Synechococcus genomes, indicative of extensive genomic rearrangements. Comparative genomic analyses showed that the isolates shared a large fraction of their gene content at high identity, yet, differences in phosphate and nitrogen utilization pathways indicated that they have adapted differentially to nutrient fluxes, possibly by the acquisition of genes by lateral gene transfer or their loss in certain populations. Comparisons of the Synechococcus genomes to metagenomic sequences derived from mats where these Synechococcus stains were originally isolated, revealed new facets of microbial diversity. First, Synechococcus populations at the lower temperature regions of the mat showed greater sequence diversity than those at high temperatures, consistent with a greater number of ecologically distinct populations at the lower temperature. Second, we found evidence of a specialized population that is apparently very closely related to Synechococcus OS-B', but contains genes that function in the uptake of reduced ferrous iron. In situ expression studies demonstrated that these genes are differentially expressed over the diel cycle, with highest expression when the mats are anoxic and iron may be in the reduced state. Genomic information from these mat-specific isolates and metagenomic information can be coupled to detect naturally occurring populations that are associated with different functionalities, not always represented by isolates, but which may nevertheless be important for niche partitioning and the establishment of microbial community structure.
A New Idea of Pure Mode-I Fracture Test of Bonded Bi-Materials (2010)

Bi-material systems in which two dissimilar materials are adhesively joined by a thin adhesive interlayer have been widely used in a variety of modern industries and engineering structures. There are two fundamental issues that need to be adequately addressed: (1) Fracture of bonded bi-materials is mixed mode: Mode-I (pure peel) and Mode-II (pure shear). Fracture test implementation of bi-material systems with the traditional Mode-I methods will induce a noticeable mixed mode fracture due to the disrupted symmetry by the bi-material configuration; (2) The popular cohesive zone models (CZMs) for accurate fracture simulations require more than a single parameter (toughness) as is the case in the traditional linear elastic fracture mechanics (LEFM). Thus, J-integral is highly preferred. It can not only capture more accurate toughness value by considering the root rotation effect, but also facilitate the experimental characterizations of the interfacial cohesive laws, which naturally include all required parameters by CZMs. Motivated by these two important issues, a novel idea is proposed in the present work to realize and characterize the pure Mode-I nonlinear interface fracture between bonded dissimilar materials: Despite the approximation with the elementary beam theories, the accuracy is validated by numerical simulations. The proposed approach may be considered as a promising candidate for the future standard Mode-I test method of adhesively bonded dissimilar materials due to its obvious simplicity and accuracy.
Oclacitinib (APOQUEL®) is a novel Janus kinase inhibitor with activity against cytokines involved in allergy (2014)

Janus kinase (JAK) enzymes are involved in cell signaling pathways activated by various cytokines dysregulated in allergy. The objective of this study was to determine whether the novel JAK inhibitor oclacitinib could reduce the activity of cytokines implicated in canine allergic skin disease. Using isolated enzyme systems and in vitro human or canine cell models, potency and selectivity of oclacitinib was determined against JAK family members and cytokines that trigger JAK activation in cells. Oclacitinib inhibited JAK family members by 50% at concentrations (IC50 's) ranging from 10 to 99 nm and did not inhibit a panel of 38 non-JAK kinases (IC50 's > 1000 nM). Oclacitinib was most potent at inhibiting JAK1 (IC50 = 10 nM). Oclacitinib also inhibited the function of JAK1-dependent cytokines involved in allergy and inflammation (IL-2, IL-4, IL-6, and IL-13) as well as pruritus (IL-31) at IC50 's ranging from 36 to 249 nM. Oclacitinib had minimal effects on cytokines that did not activate the JAK1 enzyme in cells (erythropoietin, granulocyte/macrophage colony-stimulating factor, IL-12, IL-23; IC50 's > 1000 nM). These results demonstrate that oclacitinib is a targeted therapy that selectively inhibits JAK1-dependent cytokines involved in allergy, inflammation, and pruritus and suggests these are the mechanisms by which oclacitinib effectively controls clinical signs associated with allergic skin disease in dogs.
Use of glucose starvation to limit growth and induce protein production in Escherichia coli (1992)

The use of glucose starvation to uncouple the production of recombinant beta-galactosidase from cell growth in Escherichia coli was investigated. A lacZ operon fusion to the carbon starvation-inducible cst-1 locus was used to control beta-galactosidase synthesis. beta-Galactosidase induction was observed only under aerobic starvation conditions, and its expression continued for 6 h following the onset of glucose starvation. The cessation of beta-galactosidase expression closely correlated with the exhaustion of acetate, an overflow metabolite of glucose, from the culture medium. Our results suggest the primary role of acetate in cst-1-controlled protein expression is that of an energy source. Using this information, we metered acetate to a glucose-starved culture and produced a metabolically sluggish state, where growth was limited to a low linear rate and production of recombinant beta-galactosidase occurred continuously throughout the experiment. The cst-1 controlled beta-galactosidase synthesis was also induced at low dilution rates in a glucose-limited chemostat, suggesting possible applications to high-density cell systems such as glucose-limited recycle reactors. This work demonstrates that by using an appropriate promoter system and nutrient limitation, growth can be restrained while recombinant protein production is induced and maintained.
Current and Novel Approaches to the Drug Treatment of Schizophrenia (2001)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTCurrent and Novel Approaches to the Drug Treatment of SchizophreniaMichael Rowley, Linda J. Bristow, and Peter H. HutsonView Author Information Merck Sharp and Dohme, The Neuroscience Research Centre, Terlings Park, Eastwick Road, Harlow, Essex CM20 2QR, U.K. Cite this: J. Med. Chem. 2001, 44, 4, 477–501Publication Date (Web):February 8, 2001Publication History Received7 June 2000Published online8 February 2001Published inissue 1 February 2001https://pubs.acs.org/doi/10.1021/jm0002432https://doi.org/10.1021/jm0002432review-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views2642Altmetric-Citations108LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Amines,Antagonists,Central nervous system,Receptors,Rodent models Get e-Alerts
Solving Index-1 DAEs in MATLAB and Simulink (1999)

This paper describes mathematical and software developments needed for the effective solution of differential algebraic equations of index 1 in the integrated computing environment MATLAB and the dynamic simulation package Simulink. The developments are applicable to other problem-solving environments and some are applicable to general scientific computation.
Adverse Outcomes and Predictors of Underuse of Antithrombotic Therapy in Medicare Beneficiaries With Chronic Atrial Fibrillation (2000)

The underuse of antithrombotic therapy in Medicare beneficiaries who have NVAF is associated with measurable adverse outcomes. The benefit of warfarin therapy may extend to frail, elderly patients, a group that was excluded from randomized controlled trials. The role of antiplatelet therapy in this population deserves further study because many of these patients have relative contraindications to warfarin.