gebhart/patrepeval huggingface dataset:
Third Keystone Symposium on Cellular Immunology and the Immunotherapy of Cancer Antigen Processing and Presentation Autologous Human Dendriphages Pulsed with Synthetic or Natural Tumor Peptides Elicit Tumor-Specific CTLs In Vitro (1998)

The recent identification of tumor-associated antigens and tumor-associated antigen-derived peptide epitopes recognized by cytolytic T lymphocytes (CTLs) in the context of major histocompatibility complex (MHC) class I molecules has prompted the development of peptide-based vaccines for the treatment of human cancers, particularly melanoma. The design of such clinical protocols requires an understanding of the inherent immunogenicity of the peptide(s) and a choice of a facilitating adjuvant promoting cellular immunity against these peptides. We have evaluated the abilities of a series of defined synthetic peptide epitopes derived from MART-1/Melan-A, gp100, tyrosinase, and MAGE-3 or unfractionated peptides naturally presented by melanoma MHC molecules to elicit HLA-A2-restricted and melanoma-reactive CTLs from the peripheral blood of normal donors or patients with metastatic melanoma. Autologous peripheral blood dendritic cells (DCs), which were easily generated from all donors when cultured in the presence of recombinant human interleukin-4 and recombinant human granulocyte-macrophage colony-stimulating factor were pulsed with melanoma peptides and used to "prime" and/or "boost" CTL cultures in vitro. Our results suggest that antimelanoma CTLs may be reproducibly generated in short-term in vitro cultures in this manner using either a subset of the defined synthetic peptides (MART-1/Melan-A27-35, MART-1/Melan-A32-40, gp100(280-288), tyrosinase368-376, and MAGE-3(271-279)) or unfractionated peptides (containing both idiotypic and shared melanoma epitopes) derived from freshly isolated autologous melanoma lesions. These in vitro data support the use of autologous DCs prepulsed with such peptides as an appropriate antigen adjuvant delivery system in melanoma peptide-based vaccines.
Sickle erythrocyte adherence to large vessel and microvascular endothelium under physiologic flow is qualitatively different. (1992)

Complications in sickle syndromes are thought to result from regional disturbances of normal blood flow with subsequent ischemic damage. Adherence of sickle erythrocytes has been implicated in the pathophysiology of occlusive complications. Most previous studies have explored adherence of sickle erythrocytes to endothelial cells from large vessels, even though the majority of the pathophysiologic models implicate the microvascular system. To explore potential variation in endothelial interactions at low shear rates, adherence of sickle erythrocytes to large vessel umbilical vein endothelium and microvascular endothelium was compared under flow conditions in a parallel-plate flow chamber at a shear stress of 1.0 dyne/cm2. Autologous plasma promotes high levels of sickle red cell adherence to microvascular endothelial cells, but only low levels of adherence to human umbilical vein endothelium. On average, autologous plasma promotes sixfold more sickle cell red adherence to microvascular endothelial cells. In contrast to umbilical vein endothelium, high molecular von Willebrand factor does not elevate sickle cell adherence to microvascular endothelial cells, and the integrin receptor agonist peptide, RGD, does not inhibit adherence to microvascular endothelial cells. These results demonstrate that sickle erythrocyte adherence to large vessel and microvascular endothelium is quantitatively and qualitatively different and that plasma factors may have significant impact on sickle erythrocyte adherence to endothelium in the microvessels. Since microvascular occlusion has been suggested as an antecedent of ischemic damage in sickle syndromes, plasma enhanced adherence to microvascular endothelium may contribute to the pathophysiology of episodic occlusion in sickle cell anemia.
Reduction of Maximum Entropy Models to Hidden Markov Models (2012)

We show that maximum entropy (maxent) models can be modeled with certain kinds of HMMs, allowing us to construct maxent models with hidden variables, hidden state sequences, or other characteristics. The models can be trained using the forward-backward algorithm. While the results are primarily of theoretical interest, unifying apparently unrelated concepts, we also give experimental results for a maxent model with a hidden variable on a word disambiguation task; the model outperforms standard techniques.
Prevalence of Trichomonas vaginalis and Coinfection with Chlamydia trachomatis and Neisseria gonorrhoeae in the United States as Determined by the Aptima Trichomonas vaginalis Nucleic Acid Amplification Assay (2012)

Our aim was to determine Trichomonas vaginalis prevalence using the Aptima Trichomonas vaginalis assay (ATV; Gen-Probe) and the prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae coinfections in U.S. women undergoing screening for C. trachomatis/N. gonorrhoeae. Discarded urogenital samples from 7,593 women (18 to 89 years old) undergoing C. trachomatis/N. gonorrhoeae screening using the Aptima Combo 2 assay (Gen-Probe) in various clinical settings were tested with ATV. Overall, T. vaginalis, C. trachomatis, and N. gonorrhoeae prevalences were 8.7%, 6.7%, and 1.7%, respectively. T. vaginalis was more prevalent than C. trachomatis or N. gonorrhoeae in all age groups except the 18- to 19-year-old group. The highest T. vaginalis prevalence was in women ≥ 40 years old (>11%), while the highest C. trachomatis prevalence (9.2%) and N. gonorrhoeae prevalence (2.2%) were in women <30 years old. Coinfection prevalences were 1.3% for C. trachomatis/T. vaginalis, 0.61% for C. trachomatis/N. gonorrhoeae and N. gonorrhoeae/T. vaginalis, and 0.24% for C. trachomatis/N. gonorrhoeae/T. vaginalis and highest in women <30 years old. T. vaginalis prevalence differed by race/ethnicity, with the highest prevalence in black women (20.2%). T. vaginalis prevalence ranged from 5.4% in family planning clinics to 22.3% in jails. Multivariate analysis determined that ages of ≥ 40 years, black race, and patient locations were significantly associated with T. vaginalis infection. T. vaginalis is the most common sexually transmitted infection (STI) in women of >40 years, while C. trachomatis and N. gonorrhoeae prevalence is lowest in that age group. Higher T. vaginalis prevalence in women of >40 years is probably attributed to the reason for testing, i.e., symptomatic status versus routine screening in younger women. Coinfections were relatively low. High T. vaginalis prevalence in all age groups suggests that women screened for C. trachomatis/N. gonorrhoeae, whether asymptomatic or symptomatic, should be screened for T. vaginalis.
Procalcitonin to Guide Initiation and Duration of Antibiotic Treatment in Acute Respiratory Infections: An Individual Patient Data Meta-Analysis (2012)

Use of procalcitonin to guide initiation and duration of antibiotic treatment in patients with ARIs was effective in reducing antibiotic exposure across settings without an increase in the risk of mortality or treatment failure. Further high-quality trials are needed in critical-care patients.
F11 Elemental analysis of soils by X-ray fluorescence using glass disks— invited (2006)

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Characterization of novel microsphere chain fiber optic tips for potential use in ophthalmic laser surgery (2012)

Ophthalmic surgery may benefit from use of more precise fiber delivery systems during laser surgery. Some current ophthalmic surgical techniques rely on tedious mechanical dissection of tissue layers. In this study, chains of sapphire microspheres integrated into a hollow waveguide distal tip are used for erbium:YAG laser ablation studies in contact mode with ophthalmic tissues, ex vivo. The laser's short optical penetration depth combined with the small spot diameters achieved with this fiber probe may provide more precise tissue removal. One-, three-, and five-microsphere chain structures were characterized, resulting in FWHM diameters of 67, 32, and 30 μm in air, respectively, with beam profiles comparable to simulations. Single Er:YAG pulses of 0.1 mJ and 75-μs duration produced ablation craters with average diameters of 44, 30, and 17 μm and depths of 26, 10, and 8 μm, for one-, three-, and five-sphere structures, respectively. Microsphere chains produced spatial filtering of the multimode Er:YAG laser beam and fiber, providing spot diameters not otherwise available with conventional fiber systems. Because of the extremely shallow treatment depth, compact focused beam, and contact mode operation, this probe may have potential for use in dissecting epiretinal membranes and other ophthalmic tissues without damaging adjacent retinal tissue.
Self organization in mobile ad hoc networks: the approach of Terminodes (2001)

The Terminodes project is designing a wide-area mobile ad hoc network which is meant to be used in a public environment; in our approach, the network is run by users themselves. We give a global description of the building blocks used by the basic operation of the network; they all rely on various concepts of self-organization. Routing uses a combination of geography-based information and local MANET-like protocols. Terminode positioning is obtained by either GPS or a relative positioning method. Mobility management uses self-organized virtual regions. Terminodes employ a form of virtual money called nuglets as an incentive to collaborate. Lastly, we discuss directions for providing some level of security.
All or Nothing: 1910–1912 (1995)

The political life of Vladimir Ilich Lenin was avidly scrutinised by the subjects of the former Russian empire from 1917, and foreign politicians and commentators strove to stay abreast of his career. Few statesmen had attracted an examination of this intensity. Not since the days of Napoleon Bonaparte had an individual so deeply intrigued and exercised world opinion. This extraordinary fascination was evoked by the nature of the new regime’s projects. The first socialist state had been born. The objective of pan-European revolution was triumphantly proclaimed. The natural reflex of contemporaries was to enquire what sort of man had led the Bolshevik march on power. Faulty communications inside Russia and the disruption caused in Europe by the battles on the Western and Eastern fronts made it difficult to gather information on him; but his articles in Pravda provided much material. Many decrees of the new Soviet government were written by him; he also granted occasional interviews. Books which he had written before the First World War were republished with large print-runs. Diplomats reported back to their governments from Petrograd. Few observers doubted that the main inspirer of the October Revolution was Lenin. His declaration that the era of European socialist revolution was imminent, and that the Bolsheviks of Russia would inaugurate it, caused ubiquitous frissons of excitement.
Atypical Protein Kinase Cι Plays a Critical Role in Human Lung Cancer Cell Growth and Tumorigenicity (2005)

Atypical protein kinase C (aPKC) isozymes function in epithelial cell polarity, proliferation, and survival and have been implicated in cellular transformation. However, the role of these enzymes in human cancer is largely unexplored. Here, we report that aPKCiota is highly expressed in human non-small cell lung cancer cell lines, whereas the closely related aPKC isozyme PKCzeta is undetectable in these cells. Disruption of PKCiota signaling reveals that PKCiota is dispensable for adherent growth of non-small cell lung cancer cells but is required for transformed growth in soft agar in vitro and for tumorigenicity in vivo. Molecular dissection of signaling down-stream of PKCiota demonstrates that Rac1 is a critical molecular target for PKCiota-dependent transformation, whereas PKCiota is not necessary for NFkappaB activation in vitro or in vivo. Expression of the PB1 domain of PKCiota (PKCiota-(1-113)) blocks PKCiota-dependent Rac1 activity and inhibits cellular transformation indicating a role for this domain in the transforming activity of PKCiota. Taken together, our data demonstrate that PKCiota is a critical lung cancer gene that activates a Rac1-->Pak-->Mek1,2-->Erk1,2 signaling pathway required for transformed growth. Our data indicate that PKCiota may be an attractive molecular target for mechanism-based therapies for treatment of lung cancer.
Sensitive and Specific Monoclonal Antibody-Based Capture Enzyme Immunoassay for Detection of Nucleocapsid Antigen in Sera from Patients with Severe Acute Respiratory Syndrome (2004)

A rapid antigen test for the diagnosis of severe acute respiratory syndrome (SARS) is essential for control of this disease at the point of management. The nucleocapsid (N) protein of SARS-associated coronavirus (SARS-CoV) is abundantly expressed in infected-cell culture filtrate as demonstrable by Western blotting using convalescent-phase sera from patients with SARS. We used monoclonal antibodies specifically directed against N protein to establish a sensitive antigen capture sandwich enzyme-linked immunosorbent assay (ELISA) for the detection of SARS-CoV. The assay employed a mixture of three monoclonal antibodies for capture and rabbit polyclonal antibodies for detection of serum antigen in 32 cases of clinically probable SARS as defined by the World Health Organization during the epidemic in Guangzhou, China. Recombinant N protein was used as a standard to establish a detection sensitivity of approximated 50 pg/ml. The linear range of detection in clinical specimens was from 100 pg/ml to 3.2 ng/ml. Using a panel of sera collected at different points in time, the amount of circulating N antigen was found to peak 6 to 10 days after the onset of symptoms. The sensitivity of the assay was 84.6% in 13 serologically confirmed SARS patients with blood taken during the first 10 days after the onset of symptoms (11 of 13). The specificity of the assay was 98.5% in 1,272 healthy individuals (1,253 of 1,272). There was no cross-reaction with other human and animal coronaviruses in this assay. In conclusion, a sensitive and quantitative antigen capture ELISA was established for the early diagnosis and disease monitoring of SARS-CoV infection.
Activation and phosphorylation of a pleckstrin homology domain containing protein kinase (RAC-PK/PKB) promoted by serum and protein phosphatase inhibitors. (1996)

Treatment of quiescent Swiss 3T3 fibroblasts with serum, or with the phosphatase inhibitors okadaic acid and vanadate, induced a 2- to 11-fold activation of the serine/ threonine RAC protein kinase (RAC-PK). Kinase activation was accompanied by decreased mobility of RAC-PK on SDS/PAGE such that three electrophoretic species (a to c) of the kinase were detected by immunoblot analysis, indicative of differentially phosphorylated forms. Addition of vanadate to arrested cells increased the RAC-PK phosphorylation level 3-to 4-fold. Unstimulated RAC-PK was phosphorylated predominantly on serine, whereas the activated kinase was phosphorylated on both serine and threonine residues. Treatment of RAC-PK in vitro with protein phosphatase 2A led to kinase inactivation and an increase in electrophoretic mobility. Deletion of the N-terminal region containing the pleckstrin homology domain did not affect RAC-PK activation by okadaic acid, but it reduced vanadate-stimulated activity and also blocked the serum-induced activation. Deletion of the serine/threonine rich C-terminal region impaired both RAC-PKalpha basal and vanadate-stimulated activity. Studies using a kinase-deficient mutant indicated that autophosphorylation is not involved in RAC-PKalpha activation. Stimulation of RAC-PK activity and electrophoretic mobility changes induced by serum were sensitive to wortmannin. Taken together the results suggest that RAC-PK is a component of a signaling pathway regulated by phosphatidylinositol (PI) 3-kinase, whose action is required for RAC-PK activation by phosphorylation.
Functional expression of adhesive peptides as fusions to Escherichia coli flagellin (1997)

An expression system for studying epitopes of adhesion proteins based on fusion of gene fragments into fliC(H7) of Escherichia coli is described. We constructed the system by an in-frame insertion of DNA fragments encoding one, two or three of the fibronectin-binding D repeats present in the fibronectin-binding protein A (FnBPA) of Staphylococcus aureus, into the fliC(H7) gene region encoding the variable domain of the H7 flagellin. The constructs were expressed by in trans complementation in the E. coli strain JT1 which harbours knock-out mutations for the expression of FliC as well as of the mannoside-binding fimbrial adhesin. The resulting chimeric flagella, which contained 39, 77 or 115 heterologous amino acid residues, efficiently bound soluble and immobilized human plasma and cellular fibronectin, and the binding was most efficient with the flagella containing the three D repeats of FnBPA. The chimeric flagella bound to frozen sections of human kidney and to cultured human cells. Antibodies raised against the chimeric flagella bound to Protein A-deficient S. aureus cells and inhibited the binding of staphylococci to immobilized fibronectin. We also expressed peptides, ranging in size between 48 and 302 amino acids, of the collagen-binding YadA adhesin of Yersinia enterocolitica. A fragment of 302 amino acids representing the middle region of YadA was needed for collagen binding. Chimeric flagellar filaments expressing hundreds of intimately associated adhesive epitopes offer versatile tools to analyze adhesin-receptor interactions and functional epitopes of adhesion proteins.
Presence of sympathetically denervated but viable myocardium and its electrophysiologic correlates after early revascularised, acute myocardial infarction (2004)

After early reperfusion for myocardial infarction, viable but denervated myocardium is frequent and correlates with slow depolarisation and repolarisation. However, in patients with small infarct size and preserved left ventricular function, these findings seem to have little influence on outcome.
TCP splitter: a TCP/IP flow monitor in reconfigurable hardware (2003)

This flow-monitoring circuit delivers an ordered byte stream to a client application for every TCP/IP connection it processes. Using an active flow-processing algorithm, TCP Splitter is a lightweight, efficient design that supports the monitoring of an almost unlimited number of flows at multigigabit line rates.
A physiologic model of glucose metabolism in man and its use to design and assess improved insulin therapies for diabetes (1985)

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1985.
Mathematical Simulation Experiment of Single-freedom Vibration System's Characteristic Based on Matlab (2005)

Taking spring-mass system as mechanics model to research single-freedom vibration system's characteristic has universal practical value.This text bases on single-freedom vibration system's mathematical model,using Matlab to design the mathematical simulation experiment of single-freedom vibration system.The experiment gives the result of vibration differential equation's numerical solution and draws the answer curves in different damping,obtains some helpful conclusion.
Elevated Levels of NAP-1/Interleukin-8 Are Present in the Airspaces of Patients with the Adult Respiratory Distress Syndrome and Are Associated with Increased Mortality (1992)

The adult respiratory distress syndrome (ARDS) is characterized by increased neutrophils within the airspaces of the lungs. In order to determine if neutrophil activating protein (NAP)-1/interleukin-8 (NAP-1/IL-8) could be an important cause of neutrophil influx and activation in ARDS, we examined fluid, which was either directly aspirated or lavaged with saline from the lungs of patients with ARDS. NAP-1/IL-8 was present in significantly higher concentrations in the fluids of patients with ARDS compared with control subjects. There was a significant correlation between the percentage of neutrophils in the lavage fluids and the NAP-1/IL-8 concentration (r2 = 0.74). Furthermore, the NAP-1/IL-8 concentration of the pulmonary edema fluid was equivalent to the optimal concentration required to induce neutrophil chemotaxis in vitro. Although not all of the chemotactic activity of the edema fluid was removed by an anti-NAP-1/IL-8 affinity column, the data established that NAP-1/IL-8 is an important neutrophil chemotaxin in the airspaces of patients with ARDS. In addition, those patients with very high concentrations of NAP-1/IL-8 in their bronchoalveolar lavage fluids had a higher mortality rate than those patients with lower concentrations of NAP-1/IL-8. The correlation between NAP-1/IL-8 concentration and mortality is not paralleled by total protein concentration and mortality.
Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship (2011)

We describe herein the structure-activity relationship (SAR) and cocrystal structures of a series of Nek2 inhibitors derived from the published polo-like kinase 1 (Plk1) inhibitor (R)-1. Our studies reveal a nonlinear SAR for Nek2 and our cocrystal structures show that compounds in this series bind to a DFG-out conformation of Nek2 without extending into the enlarged back pocket commonly found in this conformation. These observations were further investigated, and structure-based design led to Nek2 inhibitors derived from (R)-1 with more than a hundred-fold selectivity against Plk1.
Reaction products of dialkyl acetylenedicarboxylates with 2,3‐diaminopyridine (1995)

Abstract The condensation of dialkyl acetylenedicarboxylates 1 and 2 with 2,3‐diaminopyridine (3) or its 5‐bromo derivative 4 in ethanol gave pyrido[2,3‐ b ]pyrazinones with a common side chain ‐CH 2 ‐COOR at their 2‐position, 5–7 , but in the presence of sulfuric acid the reaction afforded their isomers with the same side chain at the 3‐position, 8–10 . All of the products were shown to exist in enamine form, in which a ring double bond has been displaced onto their side chain (CHCOOR) being facilitated by an internal chelation as demonstrated by their ir and 1 H nmr spectra.
Molecular analysis of the mouse agouti gene and the role of dominant agouti-locus mutations in obesity and insulin resistance (1994)

The lethal yellow (A{sup y/-}) and viable yellow (A{sup vy/-}) mouse agouti mutants have a predominantly yellow pelage and display a complex syndrome that includes obesity, hyperinsulinemia, and insulin resistance, hallmark features of obesity-associated noninsulin-dependent diabetes mellitus (NIDDM) in humans. A new dominant agouti allele, A{sup iapy}, has recently been identified; like the A{sup vy} allele, it is homozygous viable and confers obesity and yellow fur in heterozygotes. The agouti gene was cloned and characterized at the molecular level. The gene is expressed in the skin during hair growth and is predicted to encode a 131 amino acid protein, that is likely to be a secreted factor. In both Ay/- and A{sup iapy}/- mice, the obesity and other dominant pleiotropic effects are associated with an ectopic expression of agouti in many tissues where the gene product is normally not produced. In Ay, a 170-kb deletion has occurred that causes an upstream promoter to drive the ectopic expression of the wild-type agouti coding exons. In A{sup iapy}, the coding region of the gene is expressed from a cryptic promoter within the LTR of an intracisternal A-particle (IAP), which has integrated within the region just upstream of the first agouti coding exon. Transgenic mice ubiquitously expressing the cloned agouti gene under the influence of the beta-actin and phosphoglycerate kinase promoters display obesity, hyperinsulinemia, and yellow coat color. This demonstrates unequivocally that ectopic expression of agouti is responsible for the yellow obese syndrome.