gebhart/patrepeval huggingface dataset:
Activation of the Lck tyrosine protein kinase by hydrogen peroxide requires the phosphorylation of Tyr-394. (1995)

Exposure of cells to H2O2 mimics many of the effects of treatment of cells with extracellular ligands. Among these is the stimulation of tyrosine phosphorylation. In this study, we show that exposure of cells to H2O2 increases the catalytic activity of the lymphocyte-specific tyrosine protein kinase p56lck (Lck) and induces tyrosine phosphorylation of Lck at Tyr-394, the autophosphorylation site. Using mutant forms of Lck, we found that Tyr-394 is required for H2O2-induced activation of Lck, suggesting that phosphorylation of this site may activate Lck. In addition, H2O2 treatment induced phosphorylation at Tyr-394 in a catalytically inactive mutant of Lck in cells that do not express endogenous Lck. This demonstrates that a kinase other than Lck itself is capable of phosphorylating Lck at the so-called autophosphorylation site and raises the possibility that this as yet unidentified tyrosine protein kinase functions as an activator of Lck. Such an activating enzyme could play an important role in signal transduction in T cells.
Pulsed-light system as a novel food decontamination technology: a review (2007)

In response to consumer preferences for high quality foods that are as close as possible to fresh products, athermal technologies are being developed to obtain products with high levels of organoleptic and nutritional quality but free of any health risks. Pulsed light is a novel technology that rapidly inactivates pathogenic and food spoilage microorganisms. It appears to constitute a good alternative or a complement to conventional thermal or chemical decontamination processes. This food preservation method involves the use of intense, short-duration pulses of broad-spectrum light. The germicidal effect appears to be due to both photochemical and photothermal effects. Several high intensity flashes of broad spectrum light pulsed per second can inactivate microbes rapidly and effectively. However, the efficacy of pulsed light may be limited by its low degree of penetration, as microorganisms are only inactivated on the surface of foods or in transparent media such as water. Examples of applications to foods are presented, including microbial inactivation and effects on food matrices.
Lattice-based FHE as secure as PKE (2014)

We show that (leveled) fully homomorphic encryption (FHE) can be based on the hardness of O(n1.5+ε)-approximation for lattice problems (such as GapSVP) under quantum reductions for any ε 〉 0 (or O(n2+ε)-approximation under classical reductions). This matches the best known hardness for "regular" (non-homomorphic) lattice based public-key encryption up to the ε factor. A number of previous methods had hit a roadblock at quasipolynomial approximation. (As usual, a circular security assumption can be used to achieve a non-leveled FHE scheme.)
Compact dual-frequency microstrip antenna (2002)

A new type of compact dual-frequency microstrip antenna is presented, which is designed by utilizing a cross-slot and two shorting-pins. Comparing with the conventional rectangular patch antenna, the bandwidths for dual-frequency are both extended to more than 3.8 times and the spacing between the feed and shorting-pin position is larger and easier for manufacturing. The finite-difference time-domain (FDTD) method is used to calculate the return loss and input impedance properties.
Gene Therapy for Cancer (1992)

<h3>SELECTED CASES</h3><h3>CASE 1.</h3> —A 26-year-old woman was referred to the Surgery Branch, National Cancer Institute, Bethesda, Md, with metastatic melanoma. A year earlier the patient had noted an enlarging mole on her right upper extremity; the results of the biopsy revealed a melanoma. She underwent a wide local excision and right axillary lymph node dissection. Of 30 lymph nodes, two contained melanoma. Despite experimental treatment with vaccinia tumor oncolysate, her disease progressed. On presentation to the National Institutes of Health in June 1989, she had about 30 subcutaneous deposits of melanoma, multiple lung metastases, and oral lesions on her tonsils and soft palate. On June 21,1989, she underwent resection of six separate subcutaneous lesions ranging in diameter from 2 to 5 cm to harvest tumor-infiltrating lymphocytes (TIL) (T cells that infiltrate into animal and human tumors and can be grown in culture with interleukin 2 [IL-2]).<sup>1</sup>Eight days
Nucleophilic Catalysis of the Iodine–Zinc Exchange Reaction: Preparation of Highly Functionalized Diaryl Zinc Compounds (2004)

Sensitive functional groups are tolerated in an iodine–zinc exchange reaction catalyzed by Li(acac). Aryl and heteroaryl diorganozinc compounds with keto, aldehyde, or isothiocyanate substituents can be prepared by this method (see example in scheme; acac=acetylacetone, NMP=1-methyl-2-pyrrolidinone). Such zinc reagents serve as substrates for a wide variety of coupling reactions.
Structural role of amino acids 99–110 in recombinant human erythropoietin (1991)

Erythropoietin is the prime regulator of red blood cell production. Previous studies demonstrated that antipeptide antibodies to amino acids 99-119 and 111-129 bind to two non-overlapping domains and inhibit the hormone's action (Sytkowski, A.J. & Donahue, K. A. (1987) J. Biol. Chem. 262, 1161-1165). Oligonucleotide-directed mutagenesis now shows that amino acids 99-110 (domain 1) but not 119-129 (domain 2) are important to erythropoietin's structure and function. Mutagenesis of wild-type human erythropoietin cDNA was used to produce a series of mutant proteins with sequential deletion of three adjacent amino acids and insertion of the sequence Glu-Phe across the two domains. Transient expression in COS-7 cells revealed 2.0-kb transcripts encoded by all of the cDNAs. Domain 2 mutants exhibited specific biological activities similar to that of the wild type. In contrast, domain 1 mutants were not secreted. In vitro transcription and translation of the domain 1, domain 2 and wild-type cDNAs resulted in the isolation of 23.5-kDa and 32-kDa proteins in the absence or presence of pancreatic microsomes, respectively, consistent with efficient translation of all of the mutants and equivalent post-translational processing of each protein. The data suggest that mutation within domain 1 results in the intracellular biosynthesis of erythropoietins with altered structure, rendering them subject to rapid degradation. The bioassay of erythropoietins synthesized entirely in vitro demonstrated that domain 1 mutants were inactive, whereas both wild type and domain 2 mutant hormones exhibited biologic activity. The results are consistent with a critical role for amino acids 99-110 in the structure of human erythropoietin.
The A 2B adenosine receptor modulates pulmonary hypertension associated with interstitial lung disease (2012)

Development of pulmonary hypertension is a common and deadly complication of interstitial lung disease. Little is known regarding the cellular and molecular mechanisms that lead to pulmonary hypertension in patients with interstitial lung disease, and effective treatment options are lacking. The purpose of this study was to examine the adenosine 2B receptor (A(2B)R) as a regulator of vascular remodeling and pulmonary hypertension secondary to pulmonary fibrosis. To accomplish this, cellular and molecular changes in vascular remodeling were monitored in mice exposed to bleomycin in conjunction with genetic removal of the A(2B)R or treatment with the A(2B)R antagonist GS-6201. Results demonstrated that GS-6201 treatment or genetic removal of the A(2B)R attenuated vascular remodeling and hypertension in our model. Furthermore, direct A(2B)R activation on vascular cells promoted interleukin-6 and endothelin-1 release. These studies identify a novel mechanism of disease progression to pulmonary hypertension and support the development of A(2B)R antagonists for the treatment of pulmonary hypertension secondary to interstitial lung disease.
Room-Temperature Ferromagnetism in Transparent Transition Metal-Doped Titanium Dioxide (2001)

Dilute magnetic semiconductors and wide gap oxide semiconductors are appealing materials for magnetooptical devices. From a combinatorial screening approach looking at the solid solubility of transition metals in titanium dioxides and of their magnetic properties, we report on the observation of transparent ferromagnetism in cobalt-doped anatase thin films with theconcentration of cobalt between 0 and 8%. Magnetic microscopy images reveal a magnetic domain structure in the films, indicating the existence of ferromagnetic long-range ordering. The materials remain ferromagnetic above room temperature with a magnetic moment of 0.32 Bohr magnetons per cobalt atom. The film is conductive and exhibits a positive magnetoresistance of 60% at 2 kelvin.
Immunohistochemical localization of syndecan‐1 in normal and pathological human uterine cervix (1994)

Expression of syndecan-1, a cell surface proteoglycan that binds growth factors and extracellular matrix components, was studied in normal and pathological human uterine cervix using immunohistochemical methods. Normal cervical squamous epithelium showed positive staining for syndecan-1 in all cell layers, except the basal cell layer, whereas endocervical columnar epithelium stained weakly. In non-neoplastic reactive lesions, metaplastic squamous cells were positive for syndecan-1, whereas columnar cells showed weak or negative staining. In cervical condylomas, cells showing koilocytotic atypia were positive for syndecan-1. The progression of cervical intraepithelial neoplasia (CIN) grade I to grade III was associated with reduced syndecan-1 expression and localization of syndecan-1 to more superficial cell layers. In squamous cell carcinomas (SCCs), syndecan-1 expression correlated with histological differentiation, being absent from most poorly differentiated tumours. The results suggest that loss of syndecan-1 from atypical cells is an early event during cervical carcinogenesis and show a close association of syndecan-1 expression with preserved epithelial morphology and differentiation.
Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides (2005)

We report four-color DNA sequencing by synthesis (SBS) on a chip, using four photocleavable fluorescent nucleotide analogues (dGTP-PC-Bodipy-FL-510, dUTP-PC-R6G, dATP-PC-ROX, and dCTP-PC-Bodipy-650) (PC, photocleavable; Bodipy, 4,4-difluoro-4-bora-3alpha,4alpha-diaza-s-indacene; ROX, 6-carboxy-X-rhodamine; R6G, 6-carboxyrhodamine-6G). Each nucleotide analogue consists of a different fluorophore attached to the 5 position of the pyrimidines and the 7 position of the purines through a photocleavable 2-nitrobenzyl linker. After verifying that these nucleotides could be successfully incorporated into a growing DNA strand in a solution-phase polymerase reaction and the fluorophore could be cleaved using laser irradiation ( approximately 355 nm) in 10 sec, we then performed an SBS reaction on a chip that contains a self-priming DNA template covalently immobilized by using 1,3-dipolar azide-alkyne cycloaddition. The DNA template was produced by PCR, using an azido-labeled primer, and the self-priming moiety was attached to the immobilized DNA template by enzymatic ligation. Each cycle of SBS consists of the incorporation of the photocleavable fluorescent nucleotide into the DNA, detection of the fluorescent signal, and photocleavage of the fluorophore. The entire process was repeated to identify 12 continuous bases in the DNA template. These results demonstrate that photocleavable fluorescent nucleotide analogues can be incorporated accurately into a growing DNA strand during a polymerase reaction in solution and on a chip. Moreover, all four fluorophores can be detected and then efficiently cleaved using near-UV irradiation, thereby allowing continuous identification of the DNA template sequence. Optimization of the steps involved in this SBS approach will further increase the read-length.
A model of myelofibrosis and osteosclerosis in mice induced by overexpressing thrombopoietin (mpl ligand): reversal of disease by bone marrow transplantation (1996)

We have previously shown that mice induced to overexpress thrombopoietin (TPO) by retroviral-mediated gene transfer into bone marrow (BM) cells develop myelofibrosis and osteosclerosis. It was speculated that these effects were secondary to TPO, resulting from high levels of megakaryocytes and platelets. Also, it was proposed that these mice represent a model for myelofibrosis and osteosclerosis. In this report, we show that levels of both transforming growth factor-beta 1 and platelet-derived growth factor are increased twofold to fivefold in the platelet-poor plasma of TPO overexpressing mice compared with control mice. These data suggest that the increased megakaryocytes produce elevated levels of these cytokines that lead to the pathogenesis of disease. Further, we retransplanted TPO overexpressing mice, at 40 to 42 weeks after primary transplantation, with normal BM cells. After the secondary transplantation, megakaryocytes and platelets returned to normal levels and the myelofibrosis and osteosclerosis were completely corrected. These data extend our initial studies of the effects of overexpression of TPO and show the potential use of this model to explore the underlying cause of myelofibrosis and osteosclerosis and potential treatments for these diseases.
Synthesis, DNA Affinity, and Antiprotozoal Activity of Fused Ring Dicationic Compounds and Their Prodrugs (2005)

Dicationic guanidine, N-alkylguanidine, and reversed amidine derivatives of fused ring systems have been synthesized from their corresponding bis-amines. DNA binding studies suggest that the diguanidines and the N-alkyl diguanidines fluorenes bind in the minor groove in a manner similar to that of the previously reported dicationic carbazole derivatives. The diguanidines and the N-alkyl diguanidines showed promising in vitro activity against both Trypanosoma brucei rhodesiense and Plasmodium falciparum. Promising in vivo biological results were obtained for the dicationic N-isopropylguanidino-9H-fluorene, giving 4/4 cures of the treated animals in the STIB900 animal model for African trypanosomiasis. The N-methyl analogue showed high activity as well. In addition, with the goal of enhancing the oral bioavailability, two novel classes of potential guanidine prodrugs were prepared. The N-alkoxyguanidine derivatives were not effective as prodrugs. In contrast, a number of the carbamates showed promising activity. The value of the carbamate prodrugs was clearly demonstrated by the results, which gave 4/4 cures on oral administration in the STIB900 mouse model.
Meat Flavor Generation in Complex Maillard Model Systems (2010)

Formation of non-sulfur compounds (4-hydroxy-5-methyl-3(2H)-furanone, 4-hydroxy-2,5-dimethyl-3(2H)-furanone, 5-hydroxymethylfurfural, 2-furfural) and sulfur compounds (2-methyl-3-furanthiol, 2-furfurylthiol) that contribute to meat flavor were investigated in Maillard complex model systems containing mixtures of sugars and amino acids. Customized fractional factorial design was used to select the composition of the systems. Volatiles were quantified by GC-MS and responses analyzed by regression analysis. Significant (p<0.05) synergetic and/or competition effects were observed between reactants. The presence of more than one sugar and/or amino acid had a clear impact on the formation of key meat volatiles as well as on the mixture’s final sensory profile. Preliminary insight on the Maillard reaction mechanism in complex mixtures as they occur in real food products is given.
Thrombosis in stem cell transplantation (2012)

Hemostatic changes and thrombotic events are frequent in patients undergoing stem cell transplantation. Arterial and venous thromboses are major causes of morbidity and mortality. Thrombotic complications can be classified into four groups including: catheter-related thrombosis, venous thromboembolic (VTE) events, sinusoidal obstructive syndrome (SOS)/veno-occlusive disease, and transplant-associated thrombotic microangiopathy (TAM). The incidence of catheter-related thrombosis is 8-20% in patients undergoing autologous hematopoietic stem cell transplantation (HSCT), and the incidence is low in syngeneic and allogeneic transplant patients. Venous duplex Doppler ultrasound, venogram, and computed tomography scan are required to visualize the venous thrombus. The treatment should be aimed at the prevention of pulmonary embolism, the avoidance of thrombus extension, and the preservation of catheter patency. Patients undergoing HSCT may have risk factors for VTE including underlying malignancy, traumatic brain injury, prolonged hospitalization, administration of conditioning regimens, and central venous catheters. Important risk factors are presence of history of VTE and graft-versus-host disease. One-year incidence of symptomatic VTE is 3.7%. SOS, also known as veno-occlusive disease, is a serious liver disease, seen in approximately 50-60% of HSCT patients. The mortality rate from the severe form of SOS is 84.3% and majority of the patients have multi-organ failure. The frequency is quite low after autologous transplantation. Risk factors for SOS include pre-existing hepatic damage, previous high-dose chemotherapy and abdominal irradiation, female gender and donor-recipient human leukocyte antigen disparity. Cyclophosphamide and busulphan are the most common agents with the highest incidence and fatal SOS. Histopathologic features of SOS include dilatation of sinusoids, necrosis of perivenular hepatocytes, and obstruction of small intrahepatic central venules by microthrombi and fibrin deposition. Signs of SOS usually occur within first 30 days after HSCT including hyperbilirubinemia, hepatomegaly, ascites, and weight gain. Symptoms of liver failure, including encephalopathy, coagulopathy, and renal failure will appear in severe form. A hepatic venous pressure gradient above 10 mmHg is highly specific for SOS. Early use of defibrotide has been shown to be effective in the treatment of high-risk SOS. TAM is a distinct, infrequent, and significant life-threatening complication of HSCT. TAM is seen in the range of 0·5-76% and was reported to be 10-25% in patients undergoing allogeneic HSCT with a mortality rate around 50%. It can also be seen after autologous HSCT and mainly affects the glomerular capillaries. There has been no standard therapy for TAM. Few case series reported good response to rituximab and high-dose corticosteroids were used with limited success. Trials with complement inhibitors such as eculizumab are currently underway.
Magnetization dynamics in nanocontact current controlled oscillators (2007)

This work focuses on the magnetization dynamics driven by spin-polarized currents in nonconfined systems when a point-contact geometry is used. We demonstrate that a generalized formulation of the spin-torque efficiency function, which includes space and angular dependences, combined with the usage of abrupt absorbing boundary conditions, which has been found to be suitable to eliminate spin-wave reflection at the computational boundaries, leads to a quantitative agreement between simulations and experimental observations. A study of the properties of spin waves excited close to the threshold clearly indicates the robustness of Slonczewski's prediction. Nevertheless, full-scale investigations reveal the necessity of introducing additional nonlinearities in the equation of motion under the large-angle oscillation regime.
Gradient echo acquisition for superparamagnetic particles with positive contrast (GRASP): Sequence characterization in membrane and glass superparamagnetic iron oxide phantoms at 1.5T and 3T (2005)

Iron oxides are used for cell trafficking and identification of macrophages in plaque using MRI. Due to the negative contrast, differentiation between signal loss caused by iron and native low signal in tissue may be problematic. It is, therefore, preferable to achieve positive contrast. The purpose of this study was to test the efficacy of a new MRI sequence GRASP (GRe Acquisition for Superparamagnetic Particles) to generate a positive signal in phantoms containing iron. Membrane phantoms were constructed containing Ferumoxide at 7 concentrations. Standard GRE sequences were modified with user controlled z-gradient rephasing (+/- 100%). CNR values were determined as a function of echo time (TE) and % rephasing at 1.5T and 3T. T(2)* values were determined using multiple double-echo GRE. The GRASP sequence generated positive signal enhancement in phantoms containing iron. For all rephasing values <or=30%, positive contrast was observed. The CNR generated at 1.5T was greater than the values at 3T for all concentrations tested. Correlation between CNR at 0% and 100% rephasing was observed at 1.5T(R = 0.84). Additionally, correlation between field change across the volume and CNR was observed. In conclusion, GRASP sequences may be used to generate positive signal enhancement in the presence of iron using MRI.
Mesh Parameterization Methods and Their Applications (2007)

We present a survey of recent methods for creating piecewise linear mappings between triangulations in 3D and simpler domains such as planar regions, simplicial complexes, and spheres. We also discuss emerging tools such as global parameterization, inter-surface mapping, and parameterization with constraints. We start by describing the wide range of applications where parameterization tools have been used in recent years. We then briefly review the pertinent mathematical background and terminology, before proceeding to survey the existing parameterization techniques. Our survey summarizes the main ideas of each technique and discusses its main properties, comparing it to other methods available. Thus it aims to provide guidance to researchers and developers when assessing the suitability of diﬀerent methods for various applications. This survey focuses on the practical aspects of the methods available, such as time complexity and robustness and shows multiple examples of parameterizations generated using diﬀerent methods, allowing the reader to visually evaluate and compare the results.
Expectation-Maximization Attention Networks for Semantic Segmentation (2019)

Self-attention mechanism has been widely used for various tasks. It is designed to compute the representation of each position by a weighted sum of the features at all positions. Thus, it can capture long-range relations for computer vision tasks. However, it is computationally consuming. Since the attention maps are computed w.r.t all other positions. In this paper, we formulate the attention mechanism into an expectation-maximization manner and iteratively estimate a much more compact set of bases upon which the attention maps are computed. By a weighted summation upon these bases, the resulting representation is low-rank and deprecates noisy information from the input. The proposed Expectation-Maximization Attention (EMA) module is robust to the variance of input and is also friendly in memory and computation. Moreover, we set up the bases maintenance and normalization methods to stabilize its training procedure. We conduct extensive experiments on popular semantic segmentation benchmarks including PASCAL VOC, PASCAL Context and COCO Stuff, on which we set new records.