gebhart/patrepeval huggingface dataset:
Epitaxial lateral overgrowth of (112¯2) semipolar GaN on (11¯00) m-plane sapphire by metalorganic chemical vapor deposition (2007)

The authors report the growth of semipolar (112¯2) GaN films on nominally on-axis (101¯0) m-plane sapphire substrates using metal organic chemical vapor deposition. High-resolution x-ray diffraction (XRD) results indicate a preferred (112¯2) GaN orientation. Moreover, epitaxial lateral overgrowth (ELO) of GaN was carried out on the (112¯2) oriented GaN templates. When the ELO stripes were aligned along [112¯0]sapphire, the Ga-polar wings were inclined by 32° with respect to the substrate plane with smooth extended nonpolar a-plane GaN surfaces and polar c-plane GaN growth fronts. When compared with the template, the on-axis and off-axis XRD rocking curves indicated significant improvement in the crystalline quality by ELO for this mask orientation (on-axis 1700arcsec for the template, 380arcsec for the ELO sample, when rocked toward the GaN m axis), as verified by transmission electron microscopy (TEM). For growth mask stripes aligned along [0001]sapphire with GaN m-plane as growth fronts, the surface was composed of two {101¯1} planes making a 26° angle with the substrate plane. For this mask orientation XRD and TEM showed no improvement in the crystalline quality by ELO when compared to the non-ELO template.
Creation of a Shikimate Pathway Variant (2004)

The competition between the Escherichia coli carbohydrate phosphotransferase system and 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase for phosphoenolpyruvate limits the concentration and yield of natural products microbially synthesized via the shikimate pathway. To circumvent this competition for phosphoenolpyruvate, a shikimate pathway variant has been created. 2-Keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases encoded by Escherichia coli dgoA and Klebsiella pneumoniae dgoA are subjected to directed evolution. The evolved KDPGal aldolase isozymes exhibit 4-8-fold higher specific activities relative to that for native KDPGal aldolase with respect to catalyzing the condensation of pyruvate and d-erythrose 4-phosphate to produce DAHP. To probe the ability of the created shikimate pathway variant to support microbial growth and metabolism, growth rates and synthesis of 3-dehydroshikimate are examined for E. coli constructs that lack phosphoenolpruvate-based DAHP synthase activity and rely on evolved KDPGal aldolase for biosynthesis of shikimate pathway intermediates and products.
Gene organization and structure of the Streptomyces lividans gal operon (1988)

We present the gene organization and DNA sequence of the Streptomyces lividans galactose utilization genes. Complementation of Escherichia coli galE, galT, or galK mutants and DNA sequence analysis were used to demonstrate that the galactose utilization genes are organized within an operon with the gene order galT, galE, and galK. Comparison of the inferred protein sequences for the S. lividans gal gene products to the corresponding E. coli and Saccharomyces carlbergensis sequences identified regions of structural homology within each of the galactose utilization enzymes. Finally, we discuss a potential relationship between the gene organization of the operon and the functional roles of the gal enzymes in cellular metabolism.
Positive Progress in ImmunoPET—Not Just a Coincidence (2010)

The identification of tumor tissue biomarkers has led to the production, validation, and Food and Drug Administration-approval of a number of antibody-based targeted therapeutics in the past two decades. As a result of the significant role that these immunotherapeutics play in the management of cancer, and the potential utility of complementary imaging agents, immunoPET imaging has generated considerable interest. This update discusses the important factors to consider when designing a PET (positron emission tomography) imaging agent from the molecular target to the biological targeting molecule and radionuclide combination and also reviews recent preclinical and clinical findings in the immunoPET field. Although there are a variety of radionuclides that are currently utilized in PET studies, this update focuses on four of the positron emitters commonly used in labeling proteins: iodine-124, zirconium-89, copper-64, and fluorine-18. Notable advances in the preclinical setting include the continued development of immunoPET probes to predict the biodistribution of related radioimmunotherapeutics, the success of nontraditional radionuclide and antibody fragment combinations, the broader use of zirconium-89, and the recent emergence of (18)F-labeled diabodies for same-day imaging. Antibody-based PET probes constitute a valuable class of molecular imaging agents, and the progress made preclinically should expedite the transition of these targeted diagnostics to clinical applications.
Nulliparous versus primiparous crossbred females for beef. (1991)

Feedlot and carcass traits of nulliparous and primiparous females representing eight breed types, including Bos taurus and Bos indicus x Bos taurus crosses, were evaluated. Nulliparous females (heifers) were in the feedlot for 4 mo; primiparous females (heiferettes) were fed for 2 1/3 mo after their calves were weaned at 6 mo of age. Heifers averaged higher (P less than .01) in dressing percentage, percentage of kidney fat, carcass grade (P less than .10), and color of lean (P less than .05) compared with heiferettes. Heiferettes exceeded the nulliparous group in feedlot ADG (P less than .01), fat thickness (P less than .05), and percentage of steak, roast, and bone (P less than .01). Parity effects on carcass weight, longissimus area, marbling, pH, and shear force value were not statistically significant. Dam breed types differed in several traits, including marbling (P less than .05) and percentage of steak (P less than .10), roast (P less than .01), and bone (P less than .01). Dam breed x parity interactions were nonsignificant. Results show that beef derived from heiferettes is competitive with heifer beef.
An Engineered Zinc Finger Protein Activator of the Endogenous Glial Cell Line-Derived Neurotrophic Factor Gene Provides Functional Neuroprotection in a Rat Model of Parkinson's Disease (2010)

Loss of dopaminergic neurons is primarily responsible for the onset and progression of Parkinson's disease (PD); thus, neuroprotective and/or neuroregenerative strategies remain critical to the treatment of this increasingly prevalent disease. Here we explore a novel approach to neurotrophic factor-based therapy by engineering zinc finger protein transcription factors (ZFP TFs) that activate the expression of the endogenous glial cell line-derived neurotrophic factor (GDNF) gene. We show that GDNF activation can be achieved with exquisite genome-wide specificity. Furthermore, in a rat model of PD, striatal delivery of an adeno-associated viral vector serotype 2 encoding the GDNF activator resulted in improvements in forelimb akinesia, sensorimotor neglect, and amphetamine-induced rotations caused by 6-hydroxydopamine (6-OHDA) lesion. Our results suggest that an engineered ZFP TF can drive sufficient GDNF expression in the brain to provide functional neuroprotection against 6-OHDA; therefore, targeted activation of the endogenous gene may provide a method for delivering appropriate levels of GDNF to PD patients.
TEC FAMILY KINASES IN T LYMPHOCYTE DEVELOPMENT AND FUNCTION (2004)

The Tec family tyrosine kinases are now recognized as important mediators of antigen receptor signaling in lymphocytes. Three members of this family, Itk, Rlk, and Tec, are expressed in T cells and activated in response to T cell receptor (TCR) engagement. Although initial studies demonstrated a role for these proteins in TCR-mediated activation of phospholipase C-gamma, recent data indicate that Tec family kinases also regulate actin cytoskeletal reorganization and cellular adhesion following TCR stimulation. In addition, Tec family kinases are activated downstream of G protein-coupled chemokine receptors, where they play parallel roles in the regulation of Rho GTPases, cell polarization, adhesion, and migration. In all these systems, however, Tec family kinases are not essential signaling components, but instead function to modulate or amplify signaling pathways. Although they quantitatively reduce proximal signaling, mutations that eliminate Tec family kinases in T cells nonetheless qualitatively alter T cell development and differentiation.
Receptor Proximity, Not Intermolecular Orientation, Is Critical for Triggering T-cell Activation (2001)

Engagement of antigen receptors on the surface of T-cells with peptides bound to major histocompatibility complex (MHC) proteins triggers T-cell activation in a mechanism involving receptor oligomerization. Receptor dimerization by soluble MHC oligomers is sufficient to induce several characteristic activation processes in T-cells including internalization of engaged receptors and up-regulation of cell surface proteins. In this work, the influence of intermolecular orientation within the activating receptor dimer was studied. Dimers of class II MHC proteins coupled in a variety of orientations and topologies each were able to activate CD4+ T-cells, indicating that triggering was not dependent on a particular receptor orientation. In contrast to the minimal influence of receptor orientation, T-cell triggering was affected by the inter-molecular distance between MHC molecules, and MHC dimers coupled through shorter cross-linkers were consistently more potent than those coupled through longer cross-linkers. These results are consistent with a mechanism in which intermolecular receptor proximity, but not intermolecular orientation, is the key determinant for antigen-induced CD4+ T-cell activation.
Effects of diode laser welding with dye‐enhanced glue on tensile strength of sutures commonly used in urology (1996)

Background and Objective Tissue welding using laser-activated protein solders may soon become an alternative to sutured tissue approximation. In most cases, approximating sutures are used both to align tissue edges and provide added tensile strength. Collateral thermal injury, however, may cause disruption of tissue alignment and weaken the tensile strength of sutures. The objective of this study was to evaluate the effect of laser welding on the tensile strength of suture materials used in urologic surgery. Study Design/Material and Methods: Eleven types of sutures were exposed to diode laser energy (power density = 15.9 W/cm2) for 10, 30, and 60 seconds. Each suture was compared with and without the addition of dye-enhanced albumin-based solder. After exposure, each suture material was strained (2′/min) until untimate breakage on a tensometer and compared to untreated sutures using ANOVA. Results The strength of undyed sutures were not significantly affected; however, violet and green-dyed sutures were in general weakened by laser exposure in the presence of dye-enhanced glue. Laser activation of the smallest caliber, dyed sutures (7-0) in the presence of glue caused the most significant loss of tensile strength of all sutures tested. Conclusion These results indicate that the thermal effects of laser welding using our technique decrease the tensile strength of dyed sutures. A thermally resistant suture material (undyed or clear) may prevent disruption of wounds closed by laser welding techniques. © 1996 Wiley-Liss, Inc.
Immunohistochemical Localization of Lipocortin 1 in Rat Brain Is Sensitive to pH, Freezing, and Dehydration (1997)

Lipocortin 1 (LC1, annexin 1) has received considerable attention as a substrate for protein kinases, as a Ca++- and phosphatidylserine-binding protein, and as a mediator of glucocorticoid anti-inflammatory effects. However, there has been confusion over localization of LC1 immunoreactivity (LC1-ir), which reportedly localizes to neurons and/or to astrocytes or microglia in rat brain. To test whether these contradictory data arise from unusual properties of the antigen, we developed a novel brain slice model to determine fixation and staining variables. The specificity of anti-LC1 sera was ensured by pre-absorption and affinity purification with immobilized recombinant LC1. Specific LC1-ir was detected in ramified microglia of brains perfused with acidified aldehydes and embedded in paraffin. However, commonly used immunohistochemical procedures have unexpected profound effects. LC1-ir was eliminated by fixation with neutral/alkaline aldehydes, by freezing before strong acid-aldehyde fixation, or by staining without partial de/rehydration before the primary serum. The sensitivity of LC1 epitopes to proton and water activities may reflect molecular properties important to LC1's roles in vivo. True LC1-ir was not detected in normal neurons or astrocytes.
Phase Separation within a Binary Self-Assembled Monolayer on Au{111} Driven by an Amide-Containing Alkanethiol (2001)

We report the phase separation of a self-assembled monolayer formed from a binary mixture of adsorbates, n-decanethiol, and an amide-containing alkanethiol of similar length (3-mercapto-N-nonylpropionamide), as studied by scanning tunneling microscopy. While mixtures of n-alkanethiols of similar length (i.e., n-decanethiol and n-dodecanethiol) show no phase separation, the introduction of a hydrogen-bonding functionality buried deep within the film induces the formation of single-component domains on the nanometer scale. Phase separation occurs at all relative compositions studied, and for these molecules maintains the same exposed terminal functionality across the entire film. In nonequimolar concentrations of adsorbates, we observe that the solution component present in greater concentration will dominate the composition of the adsorbed monolayer in super proportion to that in solution, consistent with enthalpic contributions from both the solvent and intermolecular interactions of adsorbates.
Ensembl 2004 (2003)

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.
Deadline differentiated pricing of deferrable electric power service (2012)

As the penetration of wind and solar energy into the electric grid continues to grow, there will be an increasing need to evolve demand-side solutions capable of compensating the inherent variability in power supply from such renewable resources. Today, demand is largely treated as inelastic. However, the power requirements of many commercial and residential loads are such that a fraction of power demand at any given moment is inherently deferrable in time subject to a deadline constraint on the total energy supplied. Examples include thermal systems such as refrigerators, water heaters, HVAC systems, data centers, and, assuming mass adoption of plug-in electric vehicles, batteries. In this paper, we discuss some limitations of dynamic pricing mechanisms (e.g., real-time pricing) as a means of inducing demand response and suggest a novel forward contracting mechanism for deadline-differentiated deferrable energy contracts to alleviate some of these difficulties. Essentially, consumers who consent to deferral of their consumption in time - subject to a pre-specified deadline - will receive a discounted per-unit price for said energy. In this way, the supplier is capable of extracting flexibility in the delivery of energy to participating deferrable loads, while consumers receive a discount on energy with an associated deadline guarantee on delivery. The supply side is modeled as random to capture variability in renewable power supply. Using a general model for consumer preferences to capture the effect of consumption deferral on utility, we prove the existence of a competitive equilibrium and provide a characterization of deadline-differentiated prices yielding such an equilibrium. We also discuss provably optimal online scheduling policies to dynamically allocate the variable supply to a bundle of deadline-differentiated energy tasks.
Regulation of TLR7/9 responses in plasmacytoid dendritic cells by BST2 and ILT7 receptor interaction (2009)

Plasmacytoid dendritic cells (pDCs) produce copious type I interferon (IFN) upon sensing nucleic acids through Toll-like receptor (TLR) 7 and TLR9. Uncontrolled pDC activation and IFN production are implicated in lymphopenia and autoimmune diseases; therefore, a mechanism controlling pDC IFN production is essential. Human pDCs specifically express an orphan receptor, immunoglobulin-like transcript 7 (ILT7). Here, we discovered an ILT7 ligand expressed by human cell lines and identified it as bone marrow stromal cell antigen 2 (BST2; CD317). BST2 directly binds to purified ILT7 protein, initiates signaling via the ILT7-FcepsilonRIgamma complex, and strongly inhibits production of IFN and proinflammatory cytokines by pDCs. Readily induced by IFN and other proinflammatory cytokines, BST2 may modulate the human pDC's IFN responses through ILT7 in a negative feedback fashion.
Gene Therapy of Experimental Autoimmune Thyroiditis by In Vivo Administration of Plasmid DNA Coding for Fas Ligand (1999)

Fas-Fas ligand (FasL) interaction is required for the maintenance of immune homeostasis and seems to be responsible for the privileged immune status of some tissues. Experimental autoimmune thyroiditis (EAT), which is characterized by autoreactive T and B cell responses and a marked lymphocytic infiltration of the thyroid, is a model of choice to study the therapeutic effects of FasL. Here, we provide evidence that direct injection of DNA expression vectors encoding FasL into the inflamed thyroid inhibited development of lymphocytic infiltration of the thyroid and induced death of infiltrating T cells. These results were paralleled by a total abrogation of anti-Tg cytotoxic T cell response in FasL-treated animals vs controls. In summary, our results show that FasL expression on thyrocytes may have a curative effect on ongoing EAT by inducing death of pathogenic autoreactive infiltrating T lymphocytes.
Farnesyltransferase inhibition causes morphological reversion of ras-transformed cells by a complex mechanism that involves regulation of the actin cytoskeleton. (1994)

A potent and specific small molecule inhibitor of farnesyl-protein transferase, L-739,749, caused rapid morphological reversion and growth inhibition of ras-transformed fibroblasts (Rat1/ras cells). Morphological reversion occurred within 18 h of L-739,749 addition. The reverted phenotype was stable for several days in the absence of inhibitor before the transformed phenotype reappeared. Cell enlargement and actin stress fiber formation accompanied treatment of both Rat1/ras and normal Rat1 cells. Significantly, inhibition of Ras processing did not correlate with the initiation or maintenance of the reverted phenotype. While a single treatment with L-739,749 was sufficient to morphologically revert Rat1/ras cells, repetitive inhibitor treatment was required to significantly reduce cell growth rate. Thus, the effects of L-739,749 on transformed cell morphology and cytoskeletal actin organization could be separated from effects on cell growth, depending on whether exposure to a farnesyl-protein transferase inhibitor was transient or repetitive. In contrast, L-739,749 had no effect on the growth, morphology, or actin organization of v-raf-transformed cells. Taken together, the results suggest that the mechanism of morphological reversion is complex and may involve farnesylated proteins that control the organization of cytoskeletal actin.
Bifunctional antibody-Renilla luciferase fusion protein for in vivo optical detection of tumors (2006)

An anti-carcinoembryonic antigen (CEA) antibody fragment, the anti-CEA diabody, was fused to the bioluminescence enzyme Renilla luciferase (RLuc) to generate a novel optical imaging probe. Native RLuc or one of two stabilized variants (RLucC124A, RLuc8) was used as the bioluminescent moiety. A bioluminescence ELISA showed that diabody-luciferase could simultaneously bind to CEA and emit light. In vivo optical imaging of tumor-bearing mice demonstrated specific targeting of diabody-RLuc8 to CEA-positive xenografts, with a tumor:background ratio of 6.0 +/- 0.8 at 6 h after intravenous injection, compared with antigen-negative tumors at 1.0 +/- 0.1 (P = 0.05). Targeting and distribution was also evaluated by microPET imaging using (124)I-diabody-RLuc8 and confirmed that the optical signal was due to antibody-mediated localization of luciferase. Renilla luciferase, fused to biospecific sequences such as engineered antibodies, can be administered systemically to provide a novel, sensitive method for optical imaging based on expression of cell surface receptors in living organisms.
A micromachined silicon electron tunneling sensor (2002)

An electron tunneling sensor that takes advantage of the extreme position sensitivity of electron tunneling and the unique properties of micromachined silicon is presented. Anisotropic etchants, such as EDP, are used to create micrometer- and millimeter-scale structures such as single-crystal silicon springs, electrodes, and tunneling tips, which are then incorporated in the sensor. The electrostatic force between a pair of planar electrodes is used to control the separation between the tunneling tip and the surface. The thermal drift, hysteresis, and creep of conventional piezoelectric actuators is thereby avoided. Because the structure is composed entirely of silicon, the usual problems associated with differential thermal expansion in piezoelectric-based tunnel devices are greatly reduced.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A family of suboptimum detectors for coherent multiuser communications (1990)

Consideration is given to a class of suboptimum detectors for data transmitted asynchronously by K users employing direct-sequence spread-spectrum multiple access (DS/SSMA) on the additive white Gaussian noise (AWGN) channel. The general structure of these detectors consists of a bank of matched filters, a linear transformation that operates on the matched-filter outputs, and a set of threshold devices. The linear transformations are chosen to minimize either a mean-squared-error or a weighted-squared-error performance criterion. Each detector can be implemented using a tapped delay line. The number of computations performed per detected bit is linear in K in each case, and the resulting detectors are thus much simpler than the optimum detector. Under typical operating conditions, these detectors will perform much better than the conventional receiver and often nearly as well as the optimum detector.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A comparison between caudal block versus splash block for postoperative analgesia following inguinal herniorrhaphy in children (2011)

We conclude that a splash block can have a similar analgesic effect as that of a caudal block for the postoperative herniorrhaphy pain of children.