gebhart/patrepeval huggingface dataset:
Quantitative analysis of the human immunodeficiency virus type 1 (HIV-1)-specific cytotoxic T lymphocyte (CTL) response at different stages of HIV-1 infection: differential CTL responses to HIV-1 and Epstein-Barr virus in late disease. (1993)

Major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) are part of the cellular immune response to human persistent virus infections. Measurements of the frequency and specificity of human immunodeficiency virus type 1 (HIV-1)-specific CTL and their variation with time may indicate their relative importance in modulating the progression of HIV-1 infection. We have used limiting dilution analysis (LDA) to derive quantitative estimates of the frequency of HIV-1-specific CTL precursors in a cross-sectional study of 23 patients at different clinical stages of HIV-1 infection and to compare these with the frequency of CTL precursors specific for another persistent virus (Epstein-Barr virus [EBV]) in the same patients. Peripheral blood mononuclear cells (PBMC) were stimulated in vitro with autologous HIV-1-infected lymphoblasts and assayed for cytotoxicity in 51Cr release assays against autologous and MHC-mismatched lymphoblastoid B cells infected with recombinant vaccinia viruses expressing the three HIV-1 structural gene products. The frequency of MHC-restricted precursors was high in asymptomatic HIV-1-infected patients (env-specific CTL precursors up to 73/10(6) PBMC; gag-specific CTL precursors up to 488/10(6) PBMC), although the relative frequency against the different structural gene products varied from patient to patient. The HIV-1-specific CTL precursor frequency was reduced in patients who had more severe (< 400/microliters) CD4+ lymphocyte depletion, while in the majority of such patients the frequency of CTL precursors against EBV was maintained at levels observed in healthy controls. Direct CTL activity in unstimulated PBMC was observed in three of nine patients but no correlation was found between the presence of an activated CTL response and the magnitude of the CTL response detected after stimulation in LDA. Thus, CTL precursors were detected against all three HIV-1 structural gene products in patients with CD4+ lymphocyte counts > 400/microliters, at frequencies that are high compared with those reported for other persistent viruses. A CTL response directed against multiple protein antigens of HIV-1 may protect the patient against epitope variation. The fact that the EBV-specific CTL precursor frequencies were maintained in advanced HIV-1 infection suggests that there may be selective impairment of the HIV-1-specific CTL response associated with disease progression.
A Pictet-Spengler ligation for protein chemical modification (2012)

Aldehyde- and ketone-functionalized proteins are appealing substrates for the development of chemically modified biotherapeutics and protein-based materials. Their reactive carbonyl groups are typically conjugated with α-effect nucleophiles, such as substituted hydrazines and alkoxyamines, to generate hydrazones and oximes, respectively. However, the resulting C=N linkages are susceptible to hydrolysis under physiologically relevant conditions, which limits the utility of such conjugates in biological systems. Here we introduce a Pictet-Spengler ligation that is based on the classic Pictet-Spengler reaction of aldehydes and tryptamine nucleophiles. The ligation exploits the bioorthogonal reaction of aldehydes and alkoxyamines to form an intermediate oxyiminium ion; this intermediate undergoes intramolecular C-C bond formation with an indole nucleophile to form an oxacarboline product that is hydrolytically stable. We used the reaction for site-specific chemical modification of glyoxyl- and formylglycine-functionalized proteins, including an aldehyde-tagged variant of the therapeutic monoclonal antibody Herceptin. In conjunction with techniques for site-specific introduction of aldehydes into proteins, the Pictet-Spengler ligation offers a means to generate stable bioconjugates for medical and materials applications.
Localization of points of interest from georeferenced and oriented photographs (2013)

The geographic coordinates automatically assigned to photos by the built-in GPS devices of cameras register the location a photo was taken at, rather than the location of the main point of interest within the depicted scene. While scientific advances have been made in the efforts to accurately locate the actual positions of such points of interest, these resort to either crude clustering-based approaches or expensive content-based approaches in order to estimate their geographic coordinates. In this paper we propose a novel technique that incorporates the compass direction supplied by modern cameras, allowing us to compute the most probable locations of the point of interest by analyzing intersections between the lines of sight originating from the cameras focusing on the same scene. Since the accuracy of the digital devices that supply the geographic coordinates and the compass direction can vary, we take these imprecisions into account when estimating the location.
Antigen targeting to myeloid-specific human Fc gamma RI/CD64 triggers enhanced antibody responses in transgenic mice. (1996)

Besides their phagocytic effector functions, myeloid cells have an essential role as accessory cells in the induction of optimal humoral immune responses by presenting captured antigens and activating lymphocytes. Antigen presentation by human monocytes was recently found to be enhanced in vitro through the high-affinity Fc receptor for IgG (Fc gamma RI; CD64), which is exclusively present on myeloid cells. To evaluate a comparable role of Fc gamma RI in antigen presentation in vivo, we generated human Fc gamma RI transgenic mice. Under control of its endogenous promoter, human Fc gamma RI was selectively expressed on murine myeloid cells at physiological expression levels. As in humans, expression was properly regulated by the cytokines IFN-gamma, G-CSF, IL-4, and IL-10, and was up-regulated during inflammation. The human receptor expressed by murine macrophages bound monomeric human IgG and mediated particle phagocytosis and IgG complex internalization. To evaluate whether specific targeting of antigens to Fc gamma RI can induce enhanced antibody responses, mice were immunized with an anti-human Fc gamma RI antibody containing antigenic determinants. Transgenic mice produced antigen-specific antibody responses with high IgG1 titers and substantial IgG2a and IgG2b responses. These data demonstrate that human Fc gamma RI on myeloid cells is highly active in mediating enhanced antigen presentation in vivo, and show that anti-Fc gamma RI mAbs are promising vaccine adjuvants.
Melanoma-associated Chondroitin Sulfate Proteoglycan (MCSP)-targeted delivery of soluble TRAIL potently inhibits melanoma outgrowth in vitro and in vivo (2010)

Anti-MCSP:TRAIL has promising pre-clinical anti-melanoma activity that appears to result from combined inhibition of tumorigenic MCSP-signaling and concordant activation of TRAIL-apoptotic signaling. Anti-MCSP:TRAIL alone, or in combination with rimcazole, may be of potential value for the treatment of malignant melanoma.
A Simulation Model for Meandering Rivers (1996)

A computer model for the dynamics of meandering rivers has been used to study the interplay between the migrating river and the changing sedimentary environment created by the meandering river itself. The model is based on the theory of Ikeda et al . [1981] and is closely related to that proposed by Howard [1983]. Coarser sands, which are often associated with high credibility, are deposited in the point bars formed when the river migrates away from its former bank. Fine‐grained material eventually fills the oxbow lakes created by cutoff processes and forms erosion‐resistant plugs. In the simulations, geometric forms of individual meanders observed in different natural sedimentary environments have been reproduced by changing the credibility of the corresponding sedimentary materials, such as point bar deposits, flood plain deposits, and oxbow lake deposits. The simulations indicate that the typical meander wavelength is determined mainly by hydraulic factors such as the flow in the channel and the inclination of the underlying flood plain and is independent of the difference in the credibilities of sedimentary deposits. The computational approach permits exploration of long‐term changes in the floodplain geology, mediated by the meandering river. As an initial demonstration, the formation of meander belts is investigated using the model. The results suggest that a meander belt will be formed by a river's own cutoff loops only if the characteristic time of deposition and solidification of an oxbow lake is longer than the typical time that it takes the river to migrate downstream over the distance of a meander‐loop wavelength.
Molecular Wiring in Smart Dressings: Opening a New Route to Monitoring Wound pH (2015)

It has been proposed that fluctuations in wound pH can give valuable insights into the healing processes in chronic wounds, but acquiring such data can be a technological challenge especially where there is little sample available. Developments in voltammetric pH sensing have opened up new avenues for the design of probes that can function in ultra-small volumes and can be inherently disposable but, as yet few can meet the demands of wound monitoring. A preliminary investigation of the pH response of a new redox wire prepared from a peptide homopolymer of tryptophan is presented and its potential applicability as a sensing material for use in smart dressings is critically discussed.
Clinical Research Update (1991)

This article reviews the molecular bases of alpha- and beta-thalassemias in Sardinia. In addition, it describes the characteristics and the effects of a genetic program designed to prevent homozygous beta-thalassemia. In the large majority of the cases (95.7%), beta-thalassemia is caused by the nonsense mutation at codon 39, followed by frameshifts at codon 6 (2.1%). Homozygous beta-thalassemia most commonly results in thalassemia major, but in a small proportion this genotype produces milder forms referred to as thalassemia intermedia. The reasons for the attenuated forms were determined only in a small proportion of the cases. The reduced clinical severity was due to either of two factors: (a) There could be the presence of cytosine-thymidine (C----T) substitution of position - 158 G gamma, which is able to increase the G gamma chain output (as in homozygotes for frameshift at codon 6 or compound heterozygote for frameshift at codon 6 and codon 39 nonsense mutation). (b) Reduced clinical severity could be the result of co-inheritance of alpha-thalassemia in the form of two alpha-globin gene deletions of functional loss of the alpha 2-globin gene (homozygote for codon 39 nonsense mutation). The most prominent clinical form of alpha-thalassemia is hemoglobin H disease, which may result from the compound heterozygous state for deletion alpha 0- and alpha(+)-thalassemia (in 83.1% of cases) or deletion and nondeletion alpha-thalassemia (in 16.9%). Deletion Hb disease shows a milder clinical picture as compared to the nondeletion form. The most common nondeletion alpha-thalassemia is the ATG----ACG substitution at the initiation codon of the alpha 2 gene. Double heterozygotes of alpha (-alpha/-alpha) and beta-thalassemia or delta- and beta-thalassemia are relatively common and may cause confusion in carrier identification. The preventive program aimed to control beta-thalassemia is based on voluntary carrier screening., counselling, and prenatal diagnosis. Prenatal diagnosis is carried out by dot blot analysis with allelic specific oligonucleotides on amplified trophoblast DNA. This procedure gave very reliable results; in fact, no misdiagnosis has occurred so far. The preventive program was highly effective, resulting in a decline of the incidence of thalassemia major from 1:250 to 1:1,000 live births.
Human Nasal and Tracheo-Bronchial Respiratory Epithelial Cell Culture (2012)

Human airway epithelial (hAE) cell cultures are instrumental for studying basic and applied aspects of respiratory tract biology, disease, and therapy. When primary epithelial cells from the human nasal passages or tracheo-bronchial airways are grown on porous supports at an air-liquid interface (ALI) they undergo mucociliary differentiation, reproducing both the in vivo morphology and key physiologic processes. These cultures are useful for studying basic biology, disease pathogenesis, gene therapy and aerosol administration of drugs. This chapter gives detailed protocols for tissue procurement, cell isolation, production of complex media, and cell culture initiation and maintenance needed for hAE cell ALI cultures with non-proprietary reagents.
The Human SepSecS-tRNA Sec Complex Reveals the Mechanism of Selenocysteine Formation (2009)

Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism. The crystal structure of human tRNA(Sec) in complex with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro enzyme assays, supports a pyridoxal phosphate-dependent mechanism of Sec-tRNA(Sec) formation. Two tRNA(Sec) molecules, with a fold distinct from other canonical tRNAs, bind to each SepSecS tetramer through their 13-base pair acceptor-TPsiC arm (where Psi indicates pseudouridine). The tRNA binding is likely to induce a conformational change in the enzyme's active site that allows a phosphoserine covalently attached to tRNA(Sec), but not free phosphoserine, to be oriented properly for the reaction to occur.
Synthesis ofα,β-Unsaturated Amides by Olefin Cross-Metathesis (2001)

Electronic and steric properties of the substituents on the amide nitrogen atom govern the yield and rate of the cross-metathesis between a variety of α,β-unsaturated amides and olefins with 1 as the catalyst. This influence is the result of deactivation of the catalyst by chelation of the carbonyl group to the metal. However, an increase in catalyst loading compensates for the chelation effect. Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Super-resolution reconstruction of continuous image sequences (2003)

Super-resolution reconstruction algorithms perform a fusion of several low quality images of the same scene into a single improved quality image. As opposed to this STATIC recovery problem, in this paper we define a DYNAMIC super-resolution task: the restoration of a blurred, decimated, and noisy image sequence. We first model this problem through state-space equations, showing that this problem can be viewed as a sequence of STATIC super-resolution problems. Two efficient reconstruction algorithms are proposed, both being adaptive filtering approximations of the Kalman filter; the R-SD and the R-LMS. Computer simulations on synthetic sequences indicate the computational feasibility of these algorithms.
Hermitian Precoding for Distributed MIMO Systems with Individual Channel State Information (2013)

We consider a distributed multiple-input multiple-output (MIMO) system in which multiple transmitters cooperatively serve a common receiver. It is usually very costly to acquire full channel state information at the transmitter (CSIT) in such a scenario, especially for large-scale antenna systems. In this paper, we assume individual CSIT (I-CSIT), i.e., each transmitter has perfect CSI of its own link but only slow fading factors of the others. A linear Hermitian precoding technique is proposed to enhance the system performance. The optimality of the proposed precoding technique is analyzed. Numerical results demonstrate that the performance loss incurred by the I-CSIT assumption is negligible as compared to the full-CSIT case.
Changes in Haematological Indices, Blood Viscosity and Inhibitors of Coagulation during Treatment of Endometriosis with Danazol (1994)

The effects of treatment with danazol (600 mg daily) on haemostatic and haematological function were investigated in 18 pre-menopausal women with endometriosis. Blood samples were taken at 2 pre-treatment visits, at 6, 12 and 24 weeks on treatment, and at 6 weeks after discontinuation of the drug. Haemoglobin, red cell count, haematocrit and platelet count all rose significantly during treatment with danazol (p < 0.01 vs. baseline). Plasma fibrinogen levels fell significantly (p < 0.01), while whole blood viscosity increased during treatment and remained significantly elevated at follow-up. The prothrombin time shortened, but remained within normal limits, and there were no significant changes in factor VII:C, VIIa, or fibrinopeptide A. No significant changes were found in platelet function. Plasma B-beta 15-42 increased significantly. Functional levels of protein C, protein S, and antithrombin III, all rose significantly, above the normal range, while C4b-binding protein levels fell. We conclude that the observed changes in coagulation inhibitors and fibrinolytic activity may be considered beneficial in the context of venous thromboembolism. The rheological effects, however, indicate a degree of caution in the use of the drug in individuals considered to be at risk from arterial cardiovascular disease.
Matrix methods for solving protein substructures of chlorine and sulfur from anomalous data (2001)

The weak signal obtained from the anomalous scattering (at lambda = 1.54 A) of naturally occurring elements such as sulfur, phosphorus and ordered solvent chloride ions is used to determine the atomic positions of these atoms. Two examples are discussed: the sulfur and chlorine substructure of tetragonal hen egg-white lysozyme and an oligonucleotide containing ten P atoms. The substructure of lysozyme was also solved from Cu K(alpha) radiation data collected on a standard rotating-anode generator. The results presented here are an illustration of the power of the matrix methods, which are to be implemented in next distribution of the direct methods package CRUNCH.
The JAK3 inhibitor CP-690550 selectively reduces NK and CD8+ cell numbers in cynomolgus monkey blood following chronic oral dosing (2004)

Janus kinase 3 (JAK3) is a cytoplasmic tyrosine kinase associated with the common gamma chain, an integral component of cytokine receptors of the interleukin (IL)-2 family, including IL-4, -7, -9, -15, and -21. CP-690550 is a JAK3 inhibitor with immunosuppressive properties under development for transplantation. We evaluated alterations in circulating lymphocyte subsets in cynomolgus monkey blood following chronic (3-week), oral CP-690550 administration. Natural killer (NK) and CD8+ T cell numbers were reduced in a dose- and time-dependent manner; the latter was a primary effect on memory subsets. CD4+ T and B cell numbers were unaffected or slightly increased, respectively. NK cell numbers were reduced approximately 80% (vs. 35% in vehicle-treated animals) and returned to baseline levels within 3 weeks following treatment cessation. CD8+ T cells declined by a maximum 43% (vs. 25% for vehicle-treated animals) but rebounded significantly (300%) within 2 weeks after the last dose. Although CP-690550 did not result in reduction of CD4+ T cell number, these cells also increased (225%) within 2 weeks of treatment cessation. IL-15 is important for maintaining homeostasis of these cell types, and CP-690550 inhibited IL-15-induced CD69 expression in NK cells [inhibitory concentration 50% (IC50)=48.0+/-8.4 nM] and CD8+ T cells (IC50=16.2+/-1.5 nM).
A 20-kDa protein associated with the murine T-cell antigen receptor is phosphorylated in response to activation by antigen or concanavalin A. (1985)

Antigen or concanavalin A activation of a murine T-cell hybrid specific for pigeon cytochrome c and restricted to the Ek alpha:Ek beta immune response-associated (Ia) molecule resulted in phosphorylation of a 20-kDa protein that was specifically coprecipitated by a monoclonal antibody binding the T-cell antigen receptor. There was no evidence for phosphorylation of the antigen receptor itself. The phosphorylation of the 20-kDa polypeptide was dependent on the concentration of antigen or lectin used to activate the T-cell hybrid and reached a maximum 40 min after the addition of antigen. Moreover, the phosphorylation induced by antigen in the presence of Ia molecule-bearing B cells was specifically blocked by the addition of appropriate anti-Ia molecule monoclonal antibodies. The 20-kDa protein was also radioiodinated with a hydrophobic photoactivatable labeling reagent. The amount of iodinated 20-kDa protein immunoprecipitable with the anti-receptor antibody did not increase with T-cell activation, indicating that the phosphorylation occurred on a molecule that was constitutively associated with the antigen receptor. Concanavalin A also induced phosphorylation of a 20-kDa polypeptide in a second antigen-specific major histocompatibility complex-restricted T-cell hybrid. Again, the phosphorylated polypeptide was precipitated only by a monoclonal antibody specific for the antigen receptor on this hybrid. Thus, the antigen or concanavalin A-induced activation of T-cell hybrids results in the rapid phosphorylation of a 20-kDa protein that is associated with the T-cell antigen receptor.
Topological constraints in nucleic acid hybridization kinetics (2005)

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.
The effect of carbon monoxide on red cell life span in sickle cell disease (1975)

Carbon monoxide at a concentration of 1000-2000 ppm was administered to sickle cell disease patients. In each of two patients, one 51Cr red cell survival study was carried out before CO administration, and a second study was initiated a few days before CO administration was started. In both, significant prolongation of red cell survival was observed, suggesting that the rheologic properties of sickle cells were favorably influenced in vivo. The administration of carbon monoxide is not recommended as a treatment for sickle cell disease. However, further trials would seem to be justified if conducted under carefully controlled conditions.
Scanned Probe Microscopy of Electronic Transport in Carbon Nanotubes (2000)

We use electrostatic force microscopy and scanned gate microscopy to probe the conducting properties of carbon nanotubes at room temperature. Multiwalled carbon nanotubes are shown to be diffusive conductors, while metallic single-walled carbon nanotubes are ballistic conductors over micron lengths. Semiconducting single-walled carbon nanotubes are shown to have a series of large barriers to conduction along their length. These measurements are also used to probe the contact resistance and locate breaks in carbon nanotube circuits.