gebhart/patrepeval huggingface dataset:
α2A/α2C-Adrenergic Receptor Third Loop Chimera Show That Agonist Interaction with Receptor Subtype Backbone Establishes G Protein-coupled Receptor Kinase Phosphorylation (2000)

The alpha(2A)-adrenergic receptor (AR) undergoes rapid agonist-promoted desensitization due to phosphorylation by G protein-coupled receptor kinases (GRKs) 2 and 3 at serines in the third intracellular loop of the receptor. In contrast, the alpha(2C)AR fails to display such desensitization or phosphorylation, which has been presumed to be due to this receptor lacking GRK phosphorylation sites. However, the alpha(2C)AR has multiple serines and threonines in putative favorable motifs within its third intracellular loop. We considered that the conformation of the third intracellular loop imposed by agonists binding to the transmembrane-spanning domains could be the basis of this subtype-specific property, rather than the presence or absence of phosphoacceptors per se. To address this, alpha(2A)/alpha(2C) third loop chimeric receptors were constructed. In whole cell phosphorylation studies, the alpha(2A) with the alpha(2C) third loop receptor underwent agonist-promoted phosphorylation while the alpha(2C) with the alpha(2A) third loop receptor did not, indicating that the agonist interaction with the parent receptor backbone establishes the phosphorylation phenotype. We postulated then that agonists with diverse structures that distinctly interact with alpha(2)AR should display different degrees of phosphorylation independent of receptor activation. Indeed, several full and partial agonists were identified, which evoked phosphorylation that was not related to intrinsic activity as established by [(35)S]guanosine 5'-3-O-(thio)triphosphate binding. Taken together, it appears that phosphorylation of the alpha(2)AR evoked by agonist is highly sensitive to the conformation of the third intracellular loop induced/stabilized by agonist to such an extent that these properties dictate the extent of phosphorylation of the loop when phosphoacceptors are present, and are the basis for subtype-specific phosphorylation.
Redox-Magnetohydrodynamic Microfluidics Without Channels and Compatible with Electrochemical Detection Under Immunoassay Conditions (2010)

A unique capability of redox-magnetohydrodynamics (redox-MHD) for handling liquids on a small scale was demonstrated. A 1.2 muL solution plug was pumped from an injection site to a detector without the need for a channel to direct the flow. The redox pumping species did not interfere with enzymatic activity in a solution compatible with enzyme-linked immunoassays. Alkaline phosphatase (AP), a common enzyme label, converted p-aminophenyl phosphate (PAPP) to p-aminophenol (PAP(R)) in the presence of 2.5 mM Ru(NH(3))(6)Cl(2) and 2.5 mM Ru(NH(3))(6) Cl(3), in 0.1 M Tris buffer (pH = 9). A solution plug containing PAPP (no AP) was pumped through the surrounding solution containing AP (no PAPP), and the enzymatically generated PAP(R) was easily detected and distinguishable electrochemically from the pumping species with square wave voltammetry down to 0.1 mM concentrations. The test device consisted of a silicon chip containing individually addressable microband electrodes, placed on a 0.5 T NdFeB permanent magnet with the field oriented perpendicular to the chip. A 8.0 mm wide x 15.5 mm long x 1.5 mm high volume of solution was contained by a poly(dimethylsiloxane) gasket and capped with a glass slide. A steady-state fluid velocity of approximately 30 mum/s was generated in a reinforcing flow configuration between oppositely polarized sets of pumping electrodes with approximately 2.1 muA.
Complex Formation with Focal Adhesion Kinase: A Mechanism to Regulate Activity and Subcellular Localization of Src Kinases (1999)

Tyrosine phosphorylation of focal adhesion kinase (FAK) creates a high-affinity binding site for the src homology 2 domain of the Src family of tyrosine kinases. Assembly of a complex between FAK and Src kinases may serve to regulate the subcellular localization and the enzymatic activity of members of the Src family of kinases. We show that simultaneous overexpression of FAK and pp60(c-src) or p59(fyn) results in the enhancement of the tyrosine phosphorylation of a limited number of cellular substrates, including paxillin. Under these conditions, tyrosine phosphorylation of paxillin is largely cell adhesion dependent. FAK mutants defective for Src binding or focal adhesion targeting fail to cooperate with pp60(c-src) or p59(fyn) to induce paxillin phosphorylation, whereas catalytically defective FAK mutants can direct paxillin phosphorylation. The negative regulatory site of pp60(c-src) is hypophosphorylated when in complex with FAK, and coexpression with FAK leads to a redistribution of pp60(c-src) from a diffuse cellular location to focal adhesions. A FAK mutant defective for Src binding does not effectively induce the translocation of pp60(c-src) to focal adhesions. These results suggest that association with FAK can alter the localization of Src kinases and that FAK functions to direct phosphorylation of cellular substrates by recruitment of Src kinases.
Comparative Opsonic and Protective Activities of Staphylococcus aureus Conjugate Vaccines Containing Native or Deacetylated Staphylococcal Poly- N -Acetyl-β-(1-6)-Glucosamine (2005)

Staphylococcus aureus and Staphylococcus epidermidis both synthesize the surface polysaccharide poly-N-acetyl-beta-(1-6)-glucosamine (PNAG), which is produced in vitro with a high level (>90%) of the amino groups substituted by acetate. Here, we examined the role of the acetate substituents of PNAG in generating opsonic and protective antibodies. PNAG and a deacetylated form of the antigen (dPNAG; 15% acetylation) were conjugated to the carrier protein diphtheria toxoid (DT) and used to immunize animals. Mice responded in a dose-dependent fashion to both conjugate vaccines, with maximum antibody titers observed at the highest dose and 4 weeks after the last of three weekly immunizations. PNAG-DT and dPNAG-DT vaccines were also very immunogenic in rabbits. Antibodies raised to the conjugate vaccines in rabbits mediated the opsonic killing of various staphylococcal strains, but the specificity of the opsonic killing was primarily to dPNAG, as this antigen inhibited the killing of S. aureus strains by both PNAG- and dPNAG-specific antibodies. Passive immunization of mice with anti-dPNAG-DT rabbit sera showed significant levels of clearance of S. aureus from the blood (54 to 91%) compared to control mice immunized with normal rabbit sera, whereas PNAG-specific antibodies were ineffective at clearing S. aureus. Passive immunization of mice with a goat antiserum raised to the dPNAG-DT vaccine protected against a lethal dose of three different S. aureus strains. Overall, these data show that immunization of animals with a conjugate vaccine of dPNAG elicit antibodies that mediated opsonic killing and protected against S. aureus infection, including capsular polysaccharide types 5 and 8 and an untypable strain.
Mixed interleukins and thymosin fraction V synergistically induce T lymphocyte development in hydrocortisone-treated aged mice (1992)

Analysis of the role of interleukins in T cell ontogeny in vitro indicates that the regulation of T cell development involves interleukins (ILs) as well as thymic hormones (THs). In order to assess their respective roles in T lymphocyte development in vivo, chemically thymectomized mice were treated with ILs and THs. After 2 days of hydrocortisone treatment, aged mice showed acute thymic involution (weight was less than 30% of control) and reduced spleen size (less than 80% of control) with progressive recovery to 8 days. After 2 days of hydrocortisone treatment, adult mice were injected for 5 days with mixed buffy coat interleukins (BC-IL; 50 units IL2 equivalence), purified IL2 (50 units), rIL1 beta (4 ng), and thymosin fraction V (TF5; 100 micrograms). The animals were sacrificed and spleens and thymuses were analyzed for weight, cellularity, T cell number, subsets, and function as determined by proliferative responses to concanavalin A and ILs. BC-IL treatment increased the recovery of spleen and thymus weights and cellularity with corresponding augmentation of number and function of T lymphocytes; neither IL1 or IL2 or their combination had this effect. TF5 had no effect alone but strongly potentiated the effect of BC-IL on T lymphocyte function. These data indicate that BC-IL in combination with thymic peptides potently promotes T lymphocyte development. The combination may be therapeutically relevant for immunorestoration.
The processing routes determined by negatively charged residues in DR1-restricted T cell determinants (1997)

The presentation pathways followed by DR1-restricted determinants from the fusion protein of measles virus were studied. By assessing the capacity of various APC preparations to stimulate fusion protein-specific T cells, it was shown that the determinant contained within the fusion protein sequence 254-268 (F254) relies on newly synthesized DR1 protein for its presentation. By contrast, the determinant contained within the fusion protein sequence 314-328 (F314) is captured by DR1 protein recycled from the plasma membrane. In vitro binding analyses showed that the F254 and F314 peptides optimally bind to DR1 at pH 4 and pH 5, respectively. In addition, it was found that binding of the F254 peptide to DR1 is much poorer at pH 7 than at pH 4, while binding of the F314 peptide was decreased only moderately at pH 7 as compared with pH 5. Substitution of the glutamic acid 261 for an alanine in the F254 peptide resulted in an analogue with an improved capacity of binding to DR1 at neutral pH. By contrast, replacement of the valine 319 by a glutamic acid in the F314 peptide generated an analogue with a decreased binding capacity at pH 7. These findings indicated that determinants that do not bear acidic residues are captured efficiently by DR1 molecules over a broader range of pH than determinants containing acidic residues. Binding analyses between DR1 and four additional peptides further supported this conclusion. Altogether, these results suggested that acidic residues, by tuning the optimal pH for the assembly of peptide-DR1 complexes, determine the processing pathway followed by the determinants.
Temperature and dose-rate effects in gamma irradiated rare-earth doped fibers (2008)

Rare-earth-doped fibers, such as Er<sup>3+</sup>- and Yb<sup>3+</sup>-doped aluminosilicates can be advantageous in space-based systems due to their stability, their high-bandwidth transmission properties and their lightweight, small-volume properties. In such environments the effect of ionizing-radiation on the optical transmission of these fibers is of paramount importance. For the present work, gamma-radiation experiments were conducted in which un-pumped Yb<sup>3+</sup> and Er<sup>3+</sup> doped sample fibers were irradiated with a Cobalt-60 source under different dose-rate and temperature conditions. In-situ spectral transmittance data over the near IR was monitored during the irradiations for total doses of up to tens of krad (Si). It was found that there was a dose-rate dependence in which higher rates resulted in more photodarkening. Higher temperatures were not found to significantly affect the rate of photodarkening at the dose rates used.
Glucocorticoid treatment and endocrine pancreas function: implications for glucose homeostasis, insulin resistance and diabetes (2014)

Glucocorticoids (GCs) are broadly prescribed for numerous pathological conditions because of their anti-inflammatory, antiallergic and immunosuppressive effects, among other actions. Nevertheless, GCs can produce undesired diabetogenic side effects through interactions with the regulation of glucose homeostasis. Under conditions of excess and/or long-term treatment, GCs can induce peripheral insulin resistance (IR) by impairing insulin signalling, which results in reduced glucose disposal and augmented endogenous glucose production. In addition, GCs can promote abdominal obesity, elevate plasma fatty acids and triglycerides, and suppress osteocalcin synthesis in bone tissue. In response to GC-induced peripheral IR and in an attempt to maintain normoglycaemia, pancreatic β-cells undergo several morphofunctional adaptations that result in hyperinsulinaemia. Failure of β-cells to compensate for this situation favours glucose homeostasis disruption, which can result in hyperglycaemia, particularly in susceptible individuals. GC treatment does not only alter pancreatic β-cell function but also affect them by their actions that can lead to hyperglucagonaemia, further contributing to glucose homeostasis imbalance and hyperglycaemia. In addition, the release of other islet hormones, such as somatostatin, amylin and ghrelin, is also affected by GC administration. These undesired GC actions merit further consideration for the design of improved GC therapies without diabetogenic effects. In summary, in this review, we consider the implication of GC treatment on peripheral IR, islet function and glucose homeostasis.
Prognostic and therapeutic value of mitochondrial serine hydroxyl-methyltransferase 2 as a breast cancer biomarker (2016)

Mitochondrial serine hydroxylmethyltransferase 2 (SHMT2) is a key enzyme in the serine/glycine synthesis pathway. SHMT2 has been implicated as a critical component for tumor cell survival. The aim of the present study was to evaluate the prognostic value and efficiency of SHMT2 as a biomarker in patients with breast cancer. Individual and pooled survival analyses were performed on five independent breast cancer microarray datasets. Gene signatures enriched by SHMT2 were also analyzed in these datasets. SHMT2 protein expression was detected using immunohistochemistry (IHC) assay in 128 breast cancer cases. Gene set enrichment analysis revealed that SHMT2 was significantly associated with gene signatures of mitochondrial module, cancer invasion, metastasis and poor survival among breast cancer patients (p<0.05). The clinical relevance of SHMT2 was validated on IHC data. The mitochondrial localization of SHMT2 protein was visualized on IHC staining. Independent and pooled analysis confirmed that SHMT2 expression was associated with breast cancer tumor aggressiveness (TNM staging and Elson grade) in a dose-dependent manner (p<0.05). The prognostic performance of SHMT2 mRNA was comparable to other gene signatures and proved superior to TNM staging. Further analysis results indicated that SHMT2 had better prognostic value for estrogen receptor (ER)-negative breast cancer patients, compared to ER-positive patients. In cases involving stage IIb breast cancer, chemotherapy significantly extended survival time among patients with high SHMT2 expression. These results indicate that SHMT2 may be a valuable prognostic biomarker in ER-negative breast cancer cases. Furthermore, SHMT2 may be a potential target for breast cancer treatment and drug discovery.
The Heparin/Heparan Sulfate 2-O-Sulfatase from Flavobacterium heparinum (2003)

In the previous paper (Myette, J. R., Shriver, Z., Claycamp, C., McLean, M. W., Venkataraman, G., and Sasisekharan, R. (2003) J. Biol. Chem. 278, 12157-12166), we described the molecular cloning, recombinant expression, and preliminary biochemical characterization of the heparin/heparan sulfate 2-O-sulfatase from Flavobacterium heparinum. In this paper, we extend our structure-function investigation of the 2-O-sulfatase. First, we have constructed a homology-based structural model of the enzyme active site, using as a framework the available crystallographic data for three highly related arylsulfatases. In this model, we have identified important structural parameters within the enzyme active site relevant to enzyme function, especially as they relate to its substrate specificity. By docking various disaccharide substrates, we identified potential structural determinants present within these substrates that would complement this unique active site architecture. These determinants included the position and number of sulfates present on the glucosamine, oligosaccharide chain length, the presence of a Delta4,5-unsaturated double bond, and the exolytic versus endolytic potential of the enzyme. The predictions made from our model provided a structural basis of substrate specificity originally interpreted from the biochemical and kinetic data. Our modeling approach was further complemented experimentally using peptide mapping in tandem with mass spectrometry and site-directed mutagenesis to physically demonstrate the presence of a covalently modified cysteine (formylglycine) within the active site. This combinatorial approach of structure modeling and biochemical studies provides insight into the molecular basis of enzyme function.
Speed/accuracy trade-offs for modern convolutional object detectors (2016)

The goal of this paper is to serve as a guide for selecting a detection architecture that achieves the right speed/memory/accuracy balance for a given application and platform. To this end, we investigate various ways to trade accuracy for speed and memory usage in modern convolutional object detection systems. A number of successful systems have been proposed in recent years, but apples-to-apples comparisons are difficult due to different base feature extractors (e.g., VGG, Residual Networks), different default image resolutions, as well as different hardware and software platforms. We present a unified implementation of the Faster R-CNN [Ren et al., 2015], R-FCN [Dai et al., 2016] and SSD [Liu et al., 2015] systems, which we view as "meta-architectures" and trace out the speed/accuracy trade-off curve created by using alternative feature extractors and varying other critical parameters such as image size within each of these meta-architectures. On one extreme end of this spectrum where speed and memory are critical, we present a detector that achieves real time speeds and can be deployed on a mobile device. On the opposite end in which accuracy is critical, we present a detector that achieves state-of-the-art performance measured on the COCO detection task.
Topiramate inhibits cortical spreading depression in rat and cat: impact in migraine aura (2005)

Cortical spreading depression is thought to be the pathophysiological correlate of the neurological symptoms in migraine with aura. Topiramate is an anti-epileptic drug that is also used as a migraine preventive. Ion homeostasis and excitatory amino acid efflux are major components of cortical spreading depression; so given the broad range of actions of topiramate, we examined its effect on cortical spreading depression. Cortical spreading depression was elicited by a needle stick in the cortex in surgically prepared rats and cats; laser Doppler probes were used to measure the cerebral blood flow and a recording electrode was used to measure electrical nerve cell activity. Topiramate at 30 mg kg(-1) was able to inhibit regional cerebral blood flow changes and cortical depolarization and spreading depression in all rats, and in 8 of 13 cats. We conclude that topiramate may act on mechanisms involved in the initiation and propagation of spreading depression, and that these mechanisms may be similar to those involved in the therapeutic role.
Microscope Projection Photolithography for Rapid Prototyping of Masters with Micron-Scale Features for Use in Soft Lithography (2001)

This paper demonstrates the application of projection photolithography, using a standard commercial microscope, for the generation of masters for soft lithography. The procedure is rapid and convenient and produces features smaller in size (as small as 0.6 μm) than those available from other methods of rapid prototyping, albeit over a limited area (∼4 × 104 μm2 per exposure). A transparency photomask (prepared using high-resolution printing) is inserted into the light path of the microscope and projected through the microscope objective onto a photoresist-coated substrate. Features on the order of 1 μm can be produced routinely over the area of sharp focus (a circle of radius r ≅ 100 μm with a 100× objective) by this method without modification or precise calibration of the microscope. The microscope platform also provides two other useful functions, both characteristic of commercial steppers: step-and-repeat exposures and pattern alignment. The developed photoresist is used as a master for the fabrication of stamps and replica molds for soft lithography. These elements are used in demonstrations of fabrication of microstructures with feature sizes in the range from 1 to 10 μm. Although the technique is limited in the area it can produce in a single exposure, it can fabricate many kinds of structures useful in chemistry, biology, and materials science.
IL-6 controls Th17 immunity in vivo by inhibiting the conversion of conventional T cells into Foxp3+regulatory T cells (2008)

The conditions leading to the induction of adaptive Foxp3(+) regulatory T cells (T-regs) from peripheral T cells in vivo are incompletely understood. Here, we show that unresponsiveness of T cells to IL-6 by T cell-selective deletion of gp130 or immunization of wild-type mice with antigen in incomplete Freund's adjuvant (IFA), which fails to induce IL-6, promotes the conversion of peripheral CD4(+) T cells into adaptive Foxp3(+) T-regs. Thus, both T cell-conditional gp130 knockout (KO) mice immunized with MOG35-55 in complete Freund's adjuvant (CFA) and wild-type mice immunized with MOG35-55 in IFA develop overwhelming antigen-specific T-reg responses and are protected from experimental autoimmune encephalomyelitis (EAE). Depletion of T-regs restores T helper (Th)17 responses and clinical EAE in MOG/CFA-immunized T cell-conditional gp130 KO mice, but not in MOG/IFA-immunized wild-type mice. We conclude that in the absence of T-regs, IL-6 signaling is dispensable for the induction of Th17 cells, and alternative pathways exist to induce Th17 cells and EAE in the absence of IL-6 signaling. However, IL-6 signaling is dominant in inhibiting the conversion of conventional T cells into Foxp3(+) T-regs in vivo, and in the absence of IL-6 signaling, no other cytokine can substitute in inhibiting T-reg conversion. These data identify IL-6 as an important target to modulate autoimmune responses and chronic inflammation.
Targeting of Tumor Blood Vessels: A Phage-Displayed Tumor-Homing Peptide Specifically Binds to Matrix Metalloproteinase-2-Processed Collagen IV and Blocks Angiogenesis In vivo (2009)

Proteolytic degradation of the basement membrane by the matrix metalloproteinase-2 and -9 is an essential step in tumor angiogenesis. On proteolytic degradation, cryptic sites in collagen IV are formed, which serve as a migration signal for endothelial cells and are specific for angiogenic blood vessels. The aim of this study was to generate peptides that bind specifically to proteolytically processed collagen IV and to test whether these peptides accumulate in tumor vasculature and are able to block angiogenesis. To obtain such peptides, we performed a combined in vivo and in vitro phage display screen using a recombinant phage-displayed peptide library. We found a phage displaying the peptide sequence TLTYTWS that specifically binds to collagen IV modified by matrix metalloproteinase-2. We then tested the ability of the phage to bind to the vasculature in xenograft tumors and found indeed a significant accumulation of the phage in tumors but not in control organs. The tumor homing of the TLTYTWS phage is specific, as it can be blocked by coinjection chemically synthesized cognate peptide. Moreover, TLTYTWS peptide inhibits angiogenesis in an in vivo assay in a concentration-dependent manner and significantly reduces endothelial differentiation in vitro. In conclusion, we report about a novel tumor-homing peptide that specifically binds to proteolytically processed collagen IV, accumulates in tumors, and blocks angiogenesis. This peptide may be a new useful tool for diagnostic and therapeutic procedures in oncology.