gebhart/patrepeval huggingface dataset:
Antipneumococcal effects of C-reactive protein and monoclonal antibodies to pneumococcal cell wall and capsular antigens (1989)

Antibodies to pneumococcal capsular polysaccharides are well known for their ability to protect against pneumococcal infection. Recent studies indicate that antibodies to cell wall antigens, including pneumococcal surface protein A and the phosphocholine (PC) determinant of teichoic acids as well as human C-reactive protein (which also binds to PC), can protect mice against pneumococcal infection. In the present study we compared the protective effects of these agents as measured by mouse protection, the blood bactericidal assay, and clearance of pneumococci from the blood and peritoneal cavity. Our findings extend previous results indicating that human C-reactive protein and antibodies to noncapsular antigens are generally less protective than anticapsular antibodies. The new results obtained indicate the following: (i) mouse protection studies with intraperitoneal and intravenous infections provide very similar results; (ii) monoclonal immunoglobulin G2a (IgG2a) antibodies to PC, like IgG1, IgG2b, and IgG3 antibodies to PC, are highly protective against pneumococcal infection in mice; (iii) human antibody to PC is able to protect against pneumococcal infection in mice; (iv) antibodies to PspA are effective at mediating blood and peritoneal clearance of pneumococci; (v) complement is required for the in vivo protective effects of both IgG and IgM antibodies to PC; (vi) IgG1, IgG2b, and IgG3 anti-PC antibodies all mediate complement-dependent lysis of PC-conjugated erythrocytes; and (vii) antibodies and human C-reactive proteins that are reactive with capsular antigens but not cell wall antigens are able to mediate significant antibacterial activity in the blood bactericidal assay.
Nonviral in vivo delivery of therapeutic small interfering RNAs. (2007)

Since its discovery in the late 1990s, RNA interference (RNAi) has gained much attention as a powerful strategy for silencing activity. Instrumental for this naturally occurring targeting mechanism is the intracellular presence of a target gene-specific small interfering RNA (siRNA). Therefore, the in vivo delivery of highly specific siRNA molecules represents one major goal in the further development of RNAi-based approaches for clinical applications. For the non-viral delivery of siRNAs, except for local or topical administration, various routes of application and delivery vehicles/strategies have been explored so far, including the systemic injection of pure, unmodified or chemically modified siRNAs, physical methods such as hydrodynamic injection or electropulsation, encapsulation of siRNAs in liposomes, lipoplexes or cationic lipids, formation of nanoplexes through complexation of siRNAs in cationic or other carriers, or chemical coupling of siRNAs to specific carrier molecules. Therefore, approaches to establish the clinical application of RNAi may rely on a combination of biosciences and nanotechnology; in particular, for the identification of optimal siRNAs against optimal target molecules, and the development of sophisticated delivery systems.
Important Role of the Amino Acid Attached to tRNA in Formylation and in Initiation of Protein Synthesis in Escherichia coli (1996)

In attempts to convert an elongator tRNA to an initiator tRNA, we previously generated a mutant elongator methionine tRNA carrying an anticodon sequence change from CAU to CUA along with the two features important for activity of Escherichia coli initiator tRNA in initiation. This mutant tRNA (Mi:2 tRNA) was active in initiation in vivo but only when aminoacylated with methionine by overproduction of methionyl-tRNA synthetase. Here we show that the Mi:2 tRNA is normally aminoacylated in vivo with lysine and that the tRNA aminoacylated with lysine is a very poor substrate for formylation compared with the same tRNA aminoacylated with methionine. By introducing further changes at base pairs 4:69 and 5:68 in the acceptor stem of the Mi:2 tRNA to those found in the E. coli initiator tRNA, we show that change of the U4:A69 base pair to G4:C69 and overproduction of lysyl-tRNA synthetase and methionyl-tRNA transformylase results in partial formylation of the mutant tRNA and activity of the formyllysyl-tRNAs in initiation of protein synthesis. Thus, the G4: C69 base pair contributes toward formylation of the tRNA and protein synthesis in E. coli can be initiated with formyllysine. We also discuss the implications of these and other results on recognition of tRNAs by E. coli lysyl-tRNA synthetase and on competition in cells among aminoacyl-tRNA synthetases.
Use of the norepinephrine transporter as a reporter gene for non‐invasive imaging of genetically modified cells (2004)

Transduction of tumor cells with NET cDNA causes highly specific uptake and significant retention of catecholamine analogs in vitro and in vivo. These characteristics make the NET suitable as a reporter gene for non-invasive monitoring of gene transfer.
Modulation of fluorouracil by leucovorin in patients with advanced colorectal cancer: evidence in terms of response rate. Advanced Colorectal Cancer Meta-Analysis Project. (1992)

These results confirm the advantage of 5-FU plus leucovorin over 5-FU alone in terms of objective tumor response. They also suggest that in planning future trials, tumor response should not be considered a valid surrogate end point for survival in patients with advanced colorectal cancer.
Breast Cancer Cell Lines Contain Functional Cancer Stem Cells with Metastatic Capacity and a Distinct Molecular Signature (2009)

Tumors may be initiated and maintained by a cellular subcomponent that displays stem cell properties. We have used the expression of aldehyde dehydrogenase as assessed by the ALDEFLUOR assay to isolate and characterize cancer stem cell (CSC) populations in 33 cell lines derived from normal and malignant mammary tissue. Twenty-three of the 33 cell lines contained an ALDEFLUOR-positive population that displayed stem cell properties in vitro and in NOD/SCID xenografts. Gene expression profiling identified a 413-gene CSC profile that included genes known to play a role in stem cell function, as well as genes such as CXCR1/IL-8RA not previously known to play such a role. Recombinant interleukin-8 (IL-8) increased mammosphere formation and the ALDEFLUOR-positive population in breast cancer cell lines. Finally, we show that ALDEFLUOR-positive cells are responsible for mediating metastasis. These studies confirm the hierarchical organization of immortalized cell lines, establish techniques that can facilitate the characterization of regulatory pathways of CSCs, and identify potential stem cell markers and therapeutic targets.
13C NMR studies of the binding of medium-chain fatty acids to human serum albumin. (1994)

Binding of the medium-chain fatty acids (MCFA), octanoic (OCT) and decanoic (DEC) acid, to human serum albumin (HSA) has been studied by 13C NMR spectroscopy. NMR spectra at 35 degrees C showed an apparently homogeneous binding environment (a single, narrow resonance for the 13C-enriched carboxyl carbon) at different mole ratios and pH values. Changes in the chemical shift of this peak with mole ratio and protein concentration demonstrated rapid equilibration (< or = msec) of bound and unbound MCFA and permitted a direct quantitation of bound/unbound MCFA. Spectra of OCT/HSA mixtures at 6 degrees C revealed at least three distinct binding sites that fill sequentially. The observed heterogeneity of binding at low temperature, compared to 35 degrees C, is attributed to a slower exchange rate of OCT between binding sites. The highest affinity sites for both OCT and DEC have properties similar to those of binding sites for longer-chain fatty acids, such as the close proximity of the fatty acid carboxylate to basic amino acid residue(s). Interestingly, chemical shift data showed that the first mole of OCT and DEC either bind differently to the same site or bind to different sites on HSA. The rapid desorption of MCFA from HSA binding sites has implications for dietary regimens with medium chain triglycerols.
Allosteric Inhibitor Development Targeting HIV‐1 Integrase (2011)

HIV-1 integrase (IN) is one of three essential enzymes for viral replication, and is a focus of ardent antiretroviral drug discovery and development efforts. Diligent research has led to the development of the strand-transfer-specific chemical class of IN inhibitors, with two compounds from this group, raltegravir and elvitegravir, advancing the farthest in the US Food and Drug Administration (FDA) approval process for any IN inhibitor discovered thus far. Raltegravir, developed by Merck & Co., has been approved by the FDA for HIV-1 therapy, whereas elvitegravir, developed by Gilead Sciences and Japan Tobacco, has reached phase III clinical trials. Although this is an undoubted success for the HIV-1 IN drug discovery field, the emergence of HIV-1 IN strand-transfer-specific drug-resistant viral strains upon clinical use of these compounds is expected. Furthermore, the problem of strand-transfer-specific IN drug resistance will be exacerbated by the development of cross-resistant viral strains due to an overlapping binding orientation at the IN active site and an equivalent inhibitory mechanism for the two compounds. This inevitability will result in no available IN-targeted therapeutic options for HIV-1 treatment-experienced patients. The development of allosterically targeted IN inhibitors presents an extremely advantageous approach for the discovery of compounds effective against IN strand-transfer drug-resistant viral strains, and would likely show synergy with all available FDA-approved antiretroviral HIV-1 therapeutics, including the IN strand-transfer-specific compounds. Herein we review the concept of allosteric IN inhibition, and the small molecules that have been investigated to bind non-active-site regions to inhibit IN function.
Automatic recovery of the atmospheric light in hazy images (2014)

Most image dehazing algorithms require, for their operation, the atmospheric light vector, A, which describes the ambient light in the scene. Existing methods either rely on user input or follow error-prone assumptions such as the gray-world assumption. In this paper we present a new automatic method for recovering the atmospheric light vector in hazy scenes given a single input image. The method first recovers the vector's orientation, Â = A/∥A∥, by exploiting the abundance of small image patches in which the scene transmission and surface albedo are approximately constant. We derive a reduced formation model that describes the distribution of the pixels inside such patches as lines in RGB space and show how these lines are used for robustly extracting Â. We show that the magnitude of the atmospheric light vector,∥A∥, cannot be recovered using patches of constant transmission. We also show that errors in its estimation results in dehazed images that suffer from brightness biases that depend on the transmission level. This dependency implies that the biases are highly-correlated with the scene and are therefore hard to detect via local image analysis. We address this challenging problem by exploiting a global regularity which we observe in hazy images where the intensity level of the brightest pixels is approximately independent of their transmission value. To exploit this property we derive an analytic expression for the dependence that a wrong magnitude introduces and recover ∥A∥ by minimizing this particular type of dependence. We validate the assumptions of our method through a number of experiments as well as evaluate the expected accuracy at which our procedure estimates A as function of the transmission in the scene. Results show a more successful recovery of the atmospheric light vector compared to existing procedures.
Molecular Regulation of B Lymphocyte Response (1988)

Antibodies are one of the key elements in the immune system. On the one hand, they play an essential role in protection against viral and bacterial infections; on the other hand, they are involved in certain autoimmune diseases and in immediate-type hypersensivity. B cells are the only euka­ ryotic cells that can produce antibody molecules. The regulated production of antibody molecules is one of the most complex examples of eukaryotic cell differentiation and one of those most. amenable to scientific in­ vestigation. Since the discovery of T and B cell interaction in the antibody response, the mechanism of the regulatory function(s) ofT cells in the B cell response has been one of the central issues in immunology. The existence ofT cell­ derived helper factors that promote B cell proliferation and antibody secretion was recognized in the early and mid 1970s. Dutton and his colleagues (1) as well as Schimpl & Wecker (2) demonstrated that culture supernatants of murine T cells stimulated by mixed lymphocyte reaction or by T cell mitogens could reconstitute the antibody response of T cell­ depleted splenic lymphocytes. Kishimoto and his colleagues (3) showed that anti-immunoglobulin (anti-Ig) and T cell--wnditioned medium could induce Ig secretion in rabbit B cells, indicating that two totally antigen­ nonspecific signals (i.e. cross-linking Ig-receptors and T cell-derived helper factors) could induce Ig production in B cells. Subsequently, the results obtained with rabbit B cells were confirmed in the murine system. Parker and his colleagues (4) could induce Ig secretion in murine B cells with in solubilized anti-Ig and culture supernatants of concanavalin A (Con A)­ stimulated T cells. All of these results indicated that the helper function of T cells in antibody response was mediated by soluble factors.
Management of sepsis (2013)

(sepsis) 2 30-50% . . >38C <36C, >90 /, >20 / PaCO 2 <32 mmHg, >12,000 cells/mm 3 <4,000 cells/mm 3 >10% 2 . , , . ( 90 mmHg 65 mmHg ) . , [1,2]. 2012 (2012 the surviving sepsis campaign guidelines) [3] (care bundles) Appendix 1 .
Identification of a tetrapeptide recognition sequence for the alpha 2 beta 1 integrin in collagen. (1991)

The alpha 2 beta 1 integrin serves as either a specific cell surface receptor for collagen or as both a collagen and laminin receptor depending upon the cell type. Recently we established that the alpha 2 beta 1 integrin binds to a site within the alpha 1 (I)-CB3 fragment of type I collagen (Staatz, W. D., Walsh, J. J., Pexton, T., and Santoro, S. A. (1990) J. Biol. Chem. 265, 4778-4781). To define the alpha 2 beta 1 recognition sequence further we have prepared an overlapping set of synthetic peptides which completely spans the 148-amino acid alpha 1(I)-CB3 fragment and tested the peptides for ability to inhibit cell adhesion to collagen and laminin substrates. The minimal active recognition sequence defined by these experiments is a tetrapeptide of the sequence Asp-Gly-Glu-Ala (DGEA) corresponding to residues 435-438 of the type I collagen sequence. The DGEA-containing peptides effectively inhibited alpha 2 beta 1-mediated Mg2(+)-dependent adhesion of platelets, which use the alpha 2 beta 1 integrin as a collagen-specific receptor, to collagen but had no effect on alpha 5 beta 1-mediated platelet adhesion to fibronectin or alpha 6 beta 1-mediated platelet adhesion to laminin. In contrast, with T47D breast adenocarcinoma cells, which use alpha 2 beta 1 as a collagen/lamin receptor, adhesion to both collagen and laminin was inhibited by DGEA-containing peptides. Deletion of the alanine residue or substitution of alanine for either the glutamic or aspartic acid residues in DGEA-containing peptides resulted in marked loss of inhibitory activity. These results indicate that the amino acid sequence DGEA serves as a recognition site for the alpha 2 beta 1 integrin complex on platelets and other cells.
Adaptive nonlinear control of a pH neutralization process (1994)

An adaptive nonlinear control strategy for a bench-scale pH neutralization system is developed and experimentally evaluated. The pH process exhibits severe nonlinear and time-varying behavior and therefore cannot be adequately controlled with a conventional PI controller. The nonlinear controller design is based on a modified input-output linearization approach which accounts for the implicit output equation in the reaction invariant model. Because the reaction invariants cannot be measured online and the linearized system is unobservable, a nonlinear output feedback controller is developed by combining the input-output linearizing controller with a reduced-order, open-loop observer. The adaptive nonlinear control strategy is obtained by augmenting the non-adaptive controller with an indirect parameter estimation scheme which accounts for unmeasured buffering changes. Experimental tests demonstrate the superior performance of the adaptive nonlinear controller as compared to a non-adaptive nonlinear controller and conventional PI controller.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Picture-Coding Algorithm for the Merli Scan (1973)

A method is proposed and evaluated for coding a notched scan that jumps back and forth between adjacent scan lines of a normal raster. Alternate points in the line are coded using the normal differential quantizer algorithm while the remaining points use a nonlinear predictor proposed by Graham. The advantage of the algorithm over normal differential quantization is that the prediction strategy is improved while the advantage over other two-dimensional strategies is that the effect of transmission errors is confined to the line pair being processed and does not spread vertically. For coarse coding there is a significant improvement in picture quality when compared with normal differential quantization while for high-quality pictures there is a small reduction in entropy. The effect of transmission errors is investigated and shown to be similar to the effect with normal differential quantization.
Induction of basal cell carcinomas and trichoepitheliomas in mice overexpressing GLI-1 (2000)

Basal cell carcinoma is the most prevalent cancer in the western world, showing a rapid increase in incidence. Activation of the Sonic hedgehog/Patched (PTCH) signaling pathway because of PTCH1 inactivation is a key event in sporadic and familial basal cell carcinoma development in humans and is associated with transcriptional activation of specific target genes, including PTCH1 itself. These changes are analogous to the situation in Drosophila where hedgehog activates the zinc-finger transcription factor Cubitus interruptus, leading to increased transcription of target genes. In the present study, we show that mice ectopically expressing the human Cubitus interruptus homolog GLI-1 in the skin develop tumors closely resembling human BCCs as well as other hair follicle-derived neoplasias, such as trichoepitheliomas, cylindromas, and trichoblastomas. Furthermore, examination of the tumors revealed wild-type p53 and Ha ras genes. These findings firmly establish that increased GLI-1 expression is central and probably sufficient for tumor development and suggest that GLI-1-induced tumor development does not depend on additional p53 or Ha ras mutations.
Coronary Artery Calcium Score and Risk Classification for Coronary Heart Disease Prediction (2010)

In this multi-ethnic cohort, addition of CACS to a prediction model based on traditional risk factors significantly improved the classification of risk and placed more individuals in the most extreme risk categories.
A new working formulation of non-Hodgkin's lymphomas a retrospective study of the new NCI classification proposal in comparison to the rappaport and kiel classifications (1983)

Two hundred thirty cases of malignant non-Hodgkin's lymphomas were reclassified in a retrospective study according to the New Working Formulation for Clinical Usage of the NCI as compared to the Rappaport and Kiel classifications. The reproducibility for the individual schemes this study was 81% (Rappaport), 79% (Kiel), and 85% (New Working Formulation). In keeping with the results of the NCI international study, all lymphomas were subdivided into 3 prognostic groups: (1) low-grade malignancy (6.0 years median survival); (2) intermediate-grade malignancy (3.5 years median survival); and (3) high-grade malignancy (1.4 years median survival). The NCI-proposed New Working Formulation for Clinical Usage is thus recommended as practical and unprejudicing classification scheme for general application; however, its usefulness as tool for translating one classification scheme into another appears limited.
Estimating divergence functionals and the likelihood ratio by penalized convex risk minimization (2007)

We develop and analyze an algorithm for nonparametric estimation of divergence functionals and the density ratio of two probability distributions. Our method is based on a variational characterization of f-divergences, which turns the estimation into a penalized convex risk minimization problem. We present a derivation of our kernel-based estimation algorithm and an analysis of convergence rates for the estimator. Our simulation results demonstrate the convergence behavior of the method, which compares favorably with existing methods in the literature.
Lattice-Based Skinning and Deformation for Real-Time Skeleton-Driven Animation (2011)

In this paper, we present an efficient framework to deform polygonal models for skeleton-driven animation. Standard solutions of skeleton-driven animation, such as linear blend skinning, require intensive artist intervention and focus on primary deformations. The proposed approach can generate both low- and high-frequency surface motions such as muscle deformation and vibrations with little user intervention. Given a surface mesh, we construct a lattice of cubic cells embracing the mesh and we apply lattice-based smooth skinning to drive the surface primary deformation with volume preservation. Lattice shape matching with dynamic particles, in the meantime, is utilized for secondary deformations. Due to the highly parallel lattice structure, the proposed method is liable to GPU computation. Our results show that it is adequate to vividly real-time animation.
Noncontact specular microscopy of human lens epithelium. (2000)

With the use of the corneal specular microscope excellent in vivo specular images of the LECs were obtained, the features in these images that correlated well with microscopic findings were classified, and cell density in vivo was estimated.
Neuroblastoma mRNAs Predict Outcome in Children With Stage 4 Neuroblastoma: A European HR-NBL1/SIOPEN Study (2014)

High levels of TH and PHOX2B mRNA in PB at diagnosis objectively identify children with ultrahigh-risk disease who may benefit from novel treatment approaches. The level of TH, PHOX2B, and DCX mRNA in BM and/or PB at diagnosis might contribute to an algorithm to improve stratification of children for treatment.