gebhart/patrepeval huggingface dataset:
Human B cell proliferation and Ig secretion induced by recombinant CD40 ligand are modulated by soluble cytokines (1993)

Recombinant human CD40 ligand (hCD40L) was expressed on the surface of CV1/EBNA cells and examined for its ability to induce proliferation and Ig secretion from human B cells in the presence or absence of soluble cytokines. hCD40L was directly mitogenic in a dose-dependent fashion for purified tonsil B cells with maximal proliferation occurring at days 5 to 7. Proliferation induced by CD40L was significantly enhanced in the presence of IL-2, IL-4, or IL-10 and strongly suppressed by transforming growth factor-beta. Although IL-5, TNF-alpha, and IFN-gamma had no stimulatory effect in the presence of hCD40L alone, if IL-4 was also present in cultures, these cytokines enhanced the proliferative response above that seen with IL-4 alone. Interestingly, in the absence of IL-4, IFN gamma had an inhibitory effect on hCD40L-induced proliferation. Although CD40L alone did not enhance Ig secretion, addition of IL-2 or IL-10 to the cultures significantly elevated the levels of IgM, IgG1, and IgA that were observed. Addition of IL-4 to the cultures did not enhance secretion of these isotypes but had a weak inhibitory effect. However, CD40L-mediated induction of IgG4 and IgE was dependent on the presence of IL-4. Of the cytokines examined, only IL-10 enhanced IgE secretion under these conditions. Although transforming growth factor-beta only partially inhibited secretion of IgM, IgG1, and IgA, it was strongly suppressive for IgG4 and IgE production. Our data demonstrate that proliferation and Ig secretion induced in the presence of CD40L can be modulated in a positive and negative fashion by soluble cytokines. IL-2 and IL-10 specifically enhance IgM, IgG1, and IgA production although IL-4, despite costimulating B cell proliferation, does not augment secretion of these isotypes but provided an essential cosignal with CD40L for the production of IgG4 and IgE.
Predictive monitoring for early detection of subacute potentially catastrophic illnesses in critical care (2011)

We wish to save lives of patients admitted to ICUs. Their mortality is high enough based simply on the severity of the original injury or illness, but is further raised by events during their stay. We target those events that are subacute but potentially catastrophic, such as infection. Sepsis, for example, is a bacterial infection of the bloodstream, that is common in ICU patients and has a >25% risk of death. Logically, early detection and treatment with antibiotics should improve outcomes. Our fundamental precepts are (1) some potentially catastrophic medical and surgical illnesses have subclinical phases during which early diagnosis and treatment might have life-saving effects, (2) these phases are characterized by changes in the normal highly complex but highly adaptive regulation and interaction of the nervous system and other organs such as the heart and lungs, (3) teams of clinicians and quantitative scientists can work together to identify clinically important abnormalities of monitoring data, to develop algorithms that match the clinicians' eye in detecting abnormalities, and to undertake the clinical trials to test their impact on outcomes.
Modulation of Cell Death byM. tuberculosisas a Strategy for Pathogen Survival (2011)

It has been clearly demonstrated that in vitro, virulent M. tuberculosis can favor necrosis over apoptosis in infected macrophages, and this has been suggested as a mechanism for evading the host immune response. We recently reported that an effect consistent with this hypothesis could be observed in cells from the blood of TB patients, and in this paper, we review what is known about evasion strategies employed by M. tuberculosis and in particular consider the possible interaction of the apoptosis-inhibiting effects of M. tuberculosis infection with another factor (IL-4) whose expression is thought to play a role in the failure to control M. tuberculosis infection. It has been noted that IL-4 may exacerbate TNF-α-induced pathology, though the mechanism remains unexplained. Since pathology in TB typically involves inflammatory aggregates around infected cells, where TNF-α plays an important role, we predicted that IL-4 would inhibit the ability of cells to remove M. tuberculosis by apoptosis of infected cells, through the extrinsic pathway, which is activated by TNF-α. Infection of human monocytic cells with mycobacteria in vitro, in the presence of IL-4, appears to promote necrosis over apoptosis in infected cells-a finding consistent with its suggested role as a factor in pathology during M. tuberculosis infection.
Bevacizumab, Capecitabine, and Oxaliplatin As Neoadjuvant Therapy for Patients With Potentially Curable Metastatic Colorectal Cancer (2008)

These data suggest that bevacizumab can be safely administered until 5 weeks before liver resection in patients with metastatic CRC without increasing the rate of surgical or wound healing complications or severity of bleeding. To our knowledge, they are also the first to show that neoadjuvant bevacizumab does not affect liver regeneration after resection.
Specific inhibition of the T-cell response to myelin basic protein by the synthetic copolymer Cop 1. (1988)

Cop 1 is a synthetic basic random copolymer of L-alanine, L-glutamic acid, L-lysine, and L-tyrosine in a residue molar ratio of 6.0:1.9:4.7:1.0 and with a molecular weight of 21,000 which proved to be effective in specific suppression of experimental allergic encephalomyelitis and has been proposed as a candidate drug against multiple sclerosis. In the present study we further investigated the mechanism of Cop 1 suppressive activity and tested whether Cop 1 could inhibit the specific T-cell response to myelin basic protein (BP). Eight BP-specific T-cell lines and clones with various H-2 restrictions and antigenic specificities were used. The responses of all these lines and clones to BP, as followed by both cell proliferation and interleukin 2 secretion assays, were affected by Cop 1. For one line, a direct cross proliferation with Cop 1 was observed, whereas in the other seven lines and clones, Cop 1 specifically inhibited the responses to BP in a competitive dose-dependent manner. The inhibition of the response to BP is specific to Cop 1, as D-Cop 1 and another random acidic polymer, poly(Tyr,Glu,Ala) (TGA), both of which were previously demonstrated to be ineffective in suppression of experimental allergic encephalomyelitis, did not inhibit the response to BP. Furthermore, Cop 1 specifically inhibited only the response of the T-cell lines and clones to BP. It did not inhibit their response to the mitogen Con A, nor did it inhibit the responses of the purified protein derivative-specific T-cell line and clone. These results suggest that Cop 1 may be effective in suppression of experimental allergic encephalomyelitis, not only because of the selective stimulation of suppressor T cells, as we have previously demonstrated, but also by specific inhibition of BP-specific effector T cells.
Formation of specific receptor–ligand bonds between liquid interfaces (2011)

Bi-dimensional (2D) specific interactions are crucial in numerous biological processes. Attachment of molecules to a surface provides several distinct properties absent in a three-dimensional (3D) configuration, such as type of surface molecular anchorage, nature of the surface and sensitivity to local mechanical stress. While rules governing formation and stability of specific molecular interactions in 3D have been extensively described, much less is known about 2D. Here, we devised a model experiment seeking to clarify the main features of these interactions when molecules are attached to liquid interfaces. We prepared two complementary micrometric liquid droplet populations exhibiting either streptavidin as the receptor or biotin as the ligand. We brought the grafted interfaces into contact under different experimental configurations and analyzed the molecular interfacial contact formed. We measured contact formation characteristic time, molecular density, molecular dynamics and geometry. We observed formation of an irreversible liquid film concentrated in ligands and receptors and driven by specific molecular interactions. Molecular contact, although sterically saturated, was not frozen and the bonds themselves were capable of lateral diffusion in the confined space of interdroplet film. While bond diffusion was limited to the interfacial contact zone, unbound molecules were free to be exchanged between droplet contact and contour. We concluded that formation of specific receptor–ligand bonds between liquid interfaces resulted from the subtle interplay of universal surface forces and specific molecular interactions. This shed light on an interesting system of functional colloidal interactions in which molecular composition and physical properties of interfacial contact could be independently tuned.
Daptomycin: a rapidly bactericidal lipopeptide for the treatment of Gram-positive infections (2007)

Antimicrobial resistance among Gram-positive organisms continues to increase and has reached epidemic proportions in a number of countries and within medical centers worldwide. Daptomycin is a new lipopeptide antibiotic with rapid bactericidal activity against Staphylococcus aureus. It is also active against coagulase-negative staphylococci, enterococci and streptococci. It exerts its effect through cell membrane disruption that results in dissipation of the membrane potential. Daptomycin exhibits a prolonged postantibiotic effect and is well tolerated. In Phase III clinical trials, daptomycin was found to be similar in efficacy to standard therapy in complicated skin and skin structure infections. More recently, it was approved for the treatment of S. aureus bacteremia and right-sided endocarditis. Daptomycin is not indicated for pulmonary infections. Preliminary data suggest that daptomycin may be effective in urinary tract, bone and joint infections. However, randomized clinical trials are needed to confirm these findings. Daptomycin is an effective antimicrobial agent for the treatment of various serious Gram-positive infections, especially those caused by methicillin-resistant S. aureus.
Desorption Electrospray Ionization (DESI) Analysis of Tryptic Digests/Peptides (2008)

INTRODUCTIONThe analytical utility of desorption electrospray ionization (DESI) is such that it can be applied to qualitative proteomics research in the same way as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) methods, although little work has yet been reported in this regard. Because DESI is a surface analysis technique and easily automated, it can be implemented for high-throughput applications, which include the analysis of chromatographic fractions of digested proteins. The analysis of tryptic peptides follows the same protocols as in typical MALDI or ESI methods, except that the mixture is spotted directly onto an insulating surface, allowed to dry, and analyzed directly without adding matrix compounds (as in the case of MALDI methods). The spectral characteristics are similar to those of ESI in that both singly and multiply charged analyte ions are detected. Spectra are highly similar to electrospray spectra of tryptic digests with regard to the overwhelming presence of multiply charged ions of peptides. DESI-mass spectrometry (DESI-MS) is an emerging technique with great promise, but its application range is still being investigated. Therefore, the protocol for DESI-MS analysis of tryptic digests/peptides presented here provides general procedures used for the applications that have been investigated so far. Optimal ion source parameters and surface types may vary, depending on the application.
Smoothing an overlay grid to minimize linear distortion in texture mapping (2002)

Texture is an essential component of computer generated models. For a texture mapping procedure to be effective it has to generate continuous textures and cause only small mapping distortion. The Angle Based Flattening (ABF) parameterization method is guaranteed to provide a continuous (no foldovers) mapping. It also minimizes the angular distortion of the parameterization, including locating the optimal planar domain boundary. However, since it concentrates on minimizing the angular distortion of the mapping, it can introduce relatively large linear distortion.In this paper we introduce a new procedure for reducing length distortion of an existing parameterization and apply it to ABF results. The linear distortion reduction is added as a second step in a texture mapping computation. The new method is based on computing a mapping from the plane to itself which has length distortion very similar to that of the ABF parameterization. By applying the inverse mapping to the result of the initial parameterization, we obtain a new parameterization with low length distortion. We notice that the procedure for computing the inverse mapping can be applied to any other (convenient) mapping from the three-dimensional surface to the plane in order to improve it.The mapping in the plane is computed by applying weighted Laplacian smoothing to a Cartesian grid covering the planar domain of the initial mapping. Both the mapping and its inverse are provably continuous. Since angle preserving (conformal) mappings, such as ABF, locally preserve distances as well, the planar mapping has small local deformation. As a result, the inverse mapping does not significantly increase the angular distortion.The combined texture mapping procedure provides a mapping with low distance and angular distortion, which is guaranteed to be continuous.
Mobility Support Using MPLS and MP-BGP Signaling (2008)

This document describes a new approach to handling user mobility at
the network layer in the context of Multi-Protocol Label Switched
Networks (MPLS). This approach does not rely on the existing IP
mobility management protocols such as Mobile IP, and is instead based
on the combination of Multi-Protocol BGP (MP-BGP) and MPLS. This
document proposes to introduce new protocol elements to MP-BGP to
achieve Mobility Label distribution at the network control plane and
the optimal packet delivery to the mobile node by the network
forwarding plane using MPLS.
Measuring and Modeling the Conductivity of Highly Insulating Materials (2017)

A. Conductivity Theory and HDIMConductivity is the measure of how charge moves through a material under the influence of an electric field.Often this is determined by measuring the current resulting from a voltage applied to the material, using (1) to calculate the material's conductivity.To understand the macroscopic behavior of materials, it is necessary first to understand how the materials behave at the microscopic level.To this end, materials can generally be classified as conductors, semiconductors, and insulators.This classification is based on how charge moves through the material, which is determined by the size of the given material's band gap, or the energy gap between the conduction and valence bands (Figure 2).In insulators, the band gap is large, compared with the thermal energy, so that electrons cannot easily be excited from the valence to the conduction band.Disordered materials have an amorphous or even semi-crystalline structure, instead of a pure crystalline lattice [3].Thus, many of the assumptions and resulting properties for crystalline materials (such as long-range order, periodicity, and welldefined band gaps and density of states (DOS)) cannot be directly applied to disordered materials.Disorder can result from many different causes, "including concentrations of impurity atoms, geometric irregularities, the geometry of polymer chains, and their impurities" [4].Disorder in materials creates a DOS in the band gap, which means it produces localized, or "trap," states of varied energy levels within the gap [4].So, in disordered materials, electrons can move in the forbidden energy range within the band gap by hopping between these localized states (Figure 2).This movement takes place by primarily two methods: thermally assisted hopping and variable range hopping, or tunneling.This hopping motion of electrons is primarily how charge moves in HDIM [4].Equation 2 models the timedependent conductivity in the polymers concerned, with each term modeling a different physical process that dominates in different time intervals [1]
Calibration of low-cost measurement system by using a consumer digital stereo camera (2011)

The consumer digital stereo camera FinePix REAL 3D W1, which was designed to take a pair of stereo images for stereo viewing, was released in August 2009. The aim of our study is to evaluate camera calibration methods for a low-cost and easy-operation system to measure dimensions of an object on a sub-meter scale only by using a pair of stereo images acquired by the camera without any controls such as control points whose spatial locations are known or a ruler which provides the scale of the object. Three camera calibration methods were evaluated by estimation errors of lengths of line segments measured without any controls. The experiment results indicate that the best calibration method would be the method that ordinary camera calibration is first executed for each imaging unit in order to estimate its image distortion model, and then alignment between two imaging units is estimated by using two sets of the exterior orientation parameters of both imaging units obtained in the ordinary camera calibration executed previously. The experiment results indicate that the suitable calibration method would be able to provide sufficiently accurate measurement results less than 0.4 pixels on an image as well.
Remarkable Transglycosylation Activity of Glycosynthase Mutants of Endo-D, an Endo-β-N-acetylglucosaminidase from Streptococcus pneumoniae (2012)

Endo-β-N-acetylglucosaminidase from Streptococcus pneumoniae (Endo-D) is an endoglycosidase capable of hydrolyzing the Fc N-glycan of intact IgG antibodies after sequential removal of the sialic acid, galactose, and internal GlcNAc residues in the N-glycan. Endo-D also possesses transglycosylation activity with sugar oxazoline as the donor substrate, but the transglycosylation yield is low due to enzymatic hydrolysis of the donor substrate and the product. We report here our study on the hydrolytic and transglycosylation activity of recombinant Endo-D and its selected mutants. We found that Endo-D preferred core-fucosylated N-glycan for hydrolysis but favored nonfucosylated GlcNAc acceptor for transglycosylation. Several mutants showed significantly enhanced transglycosylation efficiency over the wild type enzyme. Two mutants (N322Q and N322A) were identified as typical glycosynthases that demonstrated remarkable transglycosylation activity with only marginal or no product hydrolysis activity. Kinetic studies revealed that the N322Q [corrected]and N322A glycosynthases had much higher catalytic efficiency for glycosylating the nonfucosylated GlcNAc acceptor. In comparison, the N322Q was much more efficient than N322A for transglycosylation. However, N322Q and N322A [corrected] could not take more complex N-glycan oxazoline as substrate for transglycosylation, indicating their strict substrate specificity. The usefulness of the N322Q glycosynthase was exemplified by its application for efficient glycosylation remodeling of IgG-Fc domain.
Retrovirus-Mediated Gene Transfer into T Cells: 95% Transduction Efficiency without Further in Vitro Selection (2000)

This study was designed to retrovirally transduce T cells by a protocol that would be simple, short, cost effective, applicable for clinical use, and efficient enough to avoid further selection of transduced T cells. Because retrovirally mediated infection is depending on the cell cycle, we first optimized the conditions for activating T cells in the presence of immobilized CD3 monoclonal antibodies and recombinant interleukin 2. Cell cycle analysis indicated that CD8+ and total T cells reach a maximum of cycling within 4 days whereas CD4+ T cells attain their maximum of cycling only by day 6. Taking into account these data, CD4+, CD8+, and total T cells were preactivated for 5 and 3 days, respectively, and then infected for 24 hr with supernatant containing retrovirus pseudotyped with gibbon-ape leukemia virus envelope, using a cell centrifugation protocol. Results show that approximately 95% of CD4+, CD8+, and total T cells can be transduced, this transduction efficiency being significantly higher than that obtained with amphotropic retrovirus vectors. Furthermore, under permanent growth stimulation, transduced T cells can be expanded approximately 1,000-fold in 4 weeks of culture with maintenance of transgene expression. However, Immunoscope analysis revealed alterations of T cell repertoire diversity after 2-3 weeks in culture that was not due to retroviral transduction per se. Overall, these data provide evidence that T cells can be transduced at levels that may alleviate the need for both further selection of transduced cells and in vitro expansion, thereby preserving the repertoire diversity of the transduced T cells to be reinfused.
Root-Specific Reduction of Cytokinin Causes Enhanced Root Growth, Drought Tolerance, and Leaf Mineral Enrichment inArabidopsisand Tobacco (2010)

Optimizing root system architecture can overcome yield limitations in crop plants caused by water or nutrient shortages. Classic breeding approaches are difficult because the trait is governed by many genes and is difficult to score. We generated transgenic Arabidopsis thaliana and tobacco (Nicotiana tabacum) plants with enhanced root-specific degradation of the hormone cytokinin, a negative regulator of root growth. These transgenic plants form a larger root system, whereas growth and development of the shoot are similar. Elongation of the primary root, root branching, and root biomass formation were increased by up to 60% in transgenic lines, increasing the root-to-shoot ratio. We thus demonstrated that a single dominant gene could regulate a complex trait, root growth. Moreover, we showed that cytokinin regulates root growth in a largely organ-autonomous fashion that is consistent with its dual role as a hormone with both paracrine and long-distance activities. Transgenic plants had a higher survival rate after severe drought treatment. The accumulation of several elements, including S, P, Mn, Mg, Zn, as well as Cd from a contaminated soil, was significantly increased in shoots. Under conditions of sulfur or magnesium deficiency, leaf chlorophyll content was less affected in transgenic plants, demonstrating the physiological relevance of shoot element accumulation. Our approach might contribute to improve drought tolerance, nutrient efficiency, and nutrient content of crop plants.
INVITED REVIEW POLYMERIC DELIVERY SYSTEMS FOR CONTROLLED DRUG RELEASE (1980)

The use of polymers to provide controlled long-term delivery of drugs and other chemicals is a rapidly emerging field. This review focuses primarily on the applications of these polymeric systems, and their release mechanisms. Examples of applications include clinical, pharmaceutical, biological, agricultural, environmental, and household uses. Release mechanisms considered are diffusive (reservoirs, matrices), chemical (biocrosion, pendent chain), swelling, and magnetic control of drug release from polymers. Advantages and disadvantages of controlled-release technology, and approaches for developing and testing effective polymeric delivery systems arediscussed.