gebhart/patrepeval huggingface dataset:
Potent Induction of Focused Th1‐Type Cellular and Humoral Immune Responses by RTS,S/SBAS2, a RecombinantPlasmodium falciparumMalaria Vaccine (1999)

The RTS,S/SBAS2 vaccine confers sterile protection against Plasmodium falciparum sporozoite challenge. The mechanisms underlying this are of great interest, yet little is known about the immune effector mechanisms induced by this vaccine. The immune responses induced by RTS,S/SBAS2 were characterized in 10 malaria-naive volunteers. Several epitopes in the circumsporozoite protein (CSP) were identified as targets of cultured interferon (IFN)-gamma-secreting CD4+ T cells. RTS,S-specific IFN-gamma-secreting effector T cells were induced in 8 subjects; this ex vivo response mapped to a single peptide in Th2R. CSP-specific CD8+ cytotoxic T lymphocytes were not detected. RTS, S-specific IFN-gamma production was universal, whereas interleukin-4 and -5 production was rare. RTS,S-specific lymphoproliferative responses and antibodies to CSP were strongly induced in all volunteers. Responses waned with time but were boostable. Thus, RTS, S/SBAS2 is a potent inducer of Th1-type cellular and humoral immunity. These results highlight possible immune mechanisms of protection and have important implications for vaccine design in general.
Structure and tensile behavior of irradiation-and peroxide-crosslinked polyethylenes (1987)

Abstract Three grades of polyethylene differing mainly in their molecular weight were irradiation and peroxide crosslinked. Their gel content, degree of swelling, melting temperature, degree of crystallinity, and tensile properties were determined. The irradiation and peroxide crosslinking of the same polymers makes it possible to properly compare the effects of the two crosslinking methods. Upon irradiation the competition between crosslinking and chain scission reactions determines the level of the critical dose required to form the first gel and the magnitude of maximum attainable gel content. Crosslinking causes trapping of entanglements which then contribute to the effective network density determined by solvent swelling. crystalline polyethylene enhances the degree of crystallinity and crystal perfection while subsequent crystallization from the melt is hindered by the presence of crosslinks. The homogeneity of the crosslinked network, or distribution of crosslinks, depends on the crosslinking method. Irradiation crosslinking is essentially a selective process taking place mainly in amorphous regions. The resulting structural changes by the two crosslinking methods significantly affect the polymers' tensile behavior.
The Internal Propeptide of the Ricin Precursor Carries a Sequence-Specific Determinant for Vacuolar Sorting (2001)

Ricin is a heterodimeric toxin that accumulates in the storage vacuoles of castor bean (Ricinus communis) endosperm. Proricin is synthesized as a single polypeptide precursor comprising the catalytic A chain and the Gal-binding B chain joined by a 12-amino acid linker propeptide. Upon arrival in the vacuole, the linker is removed. Here, we replicate these events in transfected tobacco (Nicotiana tabacum) leaf protoplasts. We show that the internal linker propeptide is responsible for vacuolar sorting and is sufficient to redirect the ricin heterodimer to the vacuole when fused to the A or the B chain. This internal peptide can also target two different secretory protein reporters to the vacuole. Moreover, mutation of the isoleucine residue within an NPIR-like motif of the propeptide affects vacuolar sorting in proricin and in the reconstituted A-B heterodimer. This is the first reported example of a sequence-specific vacuolar sorting signal located within an internal propeptide.
Dynamic modes of microcapsules in steady shear flow: Effects of bending and shear elasticities (2010)

The dynamics of microcapsules in steady shear flow were studied using a theoretical approach based on three variables: the Taylor deformation parameter αD , the inclination angle θ , and the phase angle ϕ of the membrane rotation. It is found that the dynamic phase diagram shows a remarkable change with an increase in the ratio of the membrane shear and bending elasticities. A fluid vesicle (no shear elasticity) exhibits three dynamic modes: (i) tank treading at low viscosity ηin of internal fluid (αD and θ relaxes to constant values), (ii) tumbling (TB) at high ηin (θ rotates), and (iii) swinging (SW) at middle ηin and high shear rates γ (θ oscillates). All of three modes are accompanied by a membrane (ϕ) rotation. For microcapsules with low shear elasticity, the TB phase with no ϕ rotation and the coexistence phase of SW and TB motions are induced by the energy barrier of ϕ rotation. Synchronization of ϕ rotation with TB rotation or SW oscillation occurs with integer ratios of rotational frequencies. At high shear elasticity, where a saddle point in the energy potential disappears, intermediate phases vanish and either ϕ or θ rotation occurs. This phase behavior agrees with recent simulation results of microcapsules with low bending elasticity.
Cancer Immunotherapy with Immunomodulatory Anti-CD137 and Anti–PD-1 Monoclonal Antibodies Requires BATF3-Dependent Dendritic Cells (2015)

Immunotherapy with immunostimulatory mAbs is currently achieving durable clinical responses in different types of cancer. We show that cross-priming of tumor antigens by BATF3-dependent DCs is a key limiting factor that can be exploited to enhance the antitumor efficacy of anti-PD-1 and anti-CD137 immunostimulatory mAbs.
Identification of a Surface Protein from Lactobacillus reuteri JCM1081 That Adheres to Porcine Gastric Mucin and Human Enterocyte-Like HT-29 Cells (2008)

Adhesion of lactobacilli to the host gastrointestinal (GI) tract is considered an important factor in health-promoting effects. However, studies addressing the molecular mechanisms of the adhesion of lactobacilli to the host GI tract have not yet been performed. The aim of this work was to identify Lactobacillus reuteri surface molecules mediating adhesion to intestinal epithelial cells and mucins. Nine strains of lactobacilli were tested for their ability to adhere to human enterocyte-like HT-29 cells. The cell surface proteins involved in the adhesion of Lactobacillus to HT-29 cells and gastric mucin were extracted. The active fractions were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting with horseradish peroxidase-labeled mucin and NHS-Biotin-labeled HT-29 cells. Furthermore, tandem mass spectrometry analysis was performed to identify the surface protein that participates in adhesion. It was shown that the ability of lactobacilli to adhere to HT-29 cells in vitro varied considerably among different strains. The most adhesive strain was the chicken intestinal tract isolate Lactobacillus reuteri JCM1081 (495.07 +/- 80.03 bacterial cells/100 HT-29 cells). The adhesion of L. reuteri JCM1081 to HT-29 cells appeared to be mediated by a cell surface protein, with an approximate molecular mass of 29 kDa. The peptides generated from the 29-kDa protein significantly matched the Lr0793 protein sequence of L. reuteri strain ATCC55730 (~71.1% identity) and displayed significant sequence similarity to the putative ATP-binding cassette transporter protein CnBP.
Structural requirements in the herpes simplex virus type 1 transactivator Vmw65 for interaction with the cellular octamer-binding protein and target TAATGARAT sequences (1990)

Herpes simplex virus type 1 virion protein Vmw65 forms a complex (TRF.C) with TAATGARAT sequences and the cellular transcription factor oct-1, which has been implicated as an intermediate in the activation of gene expression by Vmw65. To examine structural requirements within Vmw65 for this interaction, we analyzed extracts of transfected cells that express mutant Vmw65 proteins by gel retardation assay and identified two regions in the primary sequence of Vmw65 which are necessary for in vitro assembly of TRF.C. The amino-terminal boundary for complex assembly and trans activation mapped between residues 49 and 75. At the carboxyl terminus, deletion as far as residue 388 did not affect in vitro TRF.C assembly, although trans-activating activity was abolished. Deletion beyond residue 388 rapidly impaired the ability of the protein to participate in the TRF.C complex, such that a truncated mutant of 380 residues was completely inactive. These requirements towards the carboxyl terminus overlap a region of strong local sequence similarity between Vmw65 and terminal protein p3 of bacteriophage phi 29. Although substitution of corresponding p3 residues into Vmw65 failed to produce a functional chimera, site-directed mutagenesis within the region of similarity identified a number of single-point mutant proteins which were completely deficient for TRF.C formation. These mutant proteins were also unable to trans activate expression from immediate-early promoters, despite the integrity of the acidic carboxyl terminus. The extreme sensitivity of both TRF.C formation and trans activation to single-residue substitutions within this region of Vmw65 suggests that it is directly involved in the protein-protein or protein-DNA interactions required for assembly of a transcriptional complex containing oct-1.
Fast Gradient-Based Algorithms for Constrained Total Variation Image Denoising and Deblurring Problems (2009)

This paper studies gradient-based schemes for image denoising and deblurring problems based on the discretized total variation (TV) minimization model with constraints. We derive a fast algorithm for the constrained TV-based image deburring problem. To achieve this task, we combine an acceleration of the well known dual approach to the denoising problem with a novel monotone version of a fast iterative shrinkage/thresholding algorithm (FISTA) we have recently introduced. The resulting gradient-based algorithm shares a remarkable simplicity together with a proven global rate of convergence which is significantly better than currently known gradient projections-based methods. Our results are applicable to both the anisotropic and isotropic discretized TV functionals. Initial numerical results demonstrate the viability and efficiency of the proposed algorithms on image deblurring problems with box constraints.
Evaluation of Biotin−Dye Conjugates for Use in an HPLC Assay To Assess Relative Binding of Biotin Derivatives with Avidin and Streptavidin (2000)

In this investigation, studies were conducted to determine if size exclusion HPLC could be used to assess relative association rates (on-rates) and dissociation rates (off-rates) of biotin derivatives from avidin (Av) and streptavidin (SAv). For easy detection and quantification of biotin derivatives, molecules that can be detected by UV absorbance were conjugated to biotin. Concern that conjugation of the chromophoric moieties (dyes) might affect biotin binding with Av and SAv or might interact with the HPLC column led to evaluation of 10 biotin-dye conjugates. The dyes conjugated with biotin included dansyl, cyanocobalamin (CN-Cbl), coumarin 343, Lissamine-rhodamine, fluorescein, Cascade Blue, Lucifer Yellow, Oregon Green, tetramethylrhodamine, and Alexa Fluor 594. The biotin-dye conjugates were initially evaluated to determine their peak characteristics on two different size exclusion HPLC columns. Measurement of the percent of biotin-dye conjugate bound with Av in the presence of an equal quantity of biotin provided an association rate relative to biotin. All of the biotin-dyes tested had association rates within a factor of 3x (slower) that of biotin. The relative dissociation rate of biotin-dye conjugates was assessed by challenging the biotin conjugate bound to Av or SAv with a large excess of biotin. All of the initial biotin-dye conjugates tested bound Av and SAv tightly resulting in very slow dissociation rates. From the biotin-dye conjugates studied, biotin-CN-Cbl, 6b, was selected as the best conjugate for the HPLC assay. To test the HPLC assay, an iminobiotin-CN-Cbl conjugate, 13a, and a biotin-sarcosine-CN-Cbl conjugate, 13b, were synthesized. The fact that the iminobiotin does not bind with Av at physiological pH was easily detected in the size exclusion HPLC assay. The biotin-sarcosine-CN-Cbl conjugate was expected to have a more rapid dissociation rate than the other biotin-dye conjugates. This was confirmed in that HPLC assay. Although 13b bound tightly with Av in the absence of added biotin, it was completely released within 1 h when challenged by an excess of biotin. A slower dissociation of 13b was noted with SAv. The results obtained indicate that CN-Cbl conjugates of biotin derivatives can be used to determine relative on-rates and off-rates of biotin derivatives with Av and SAv. The studies also demonstrated that the biotin-CN-Cbl conjugate, 6b, can be used as a reference compound to compare on-rates and off-rates of nonchromophoric biotin derivatives.
A fundamental study of inter-area oscillations in power systems (1991)

A fundamental study of the nature of inter-area oscillations in power systems is presented. The effects of the system structure, generator modeling, excitation type, and system loads are discussed in detail. Both small signal and transient stability analyses are used to determine the characteristics of the system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid internalization and surface expression of a functional, fluorescently tagged G-protein-coupled glutamate receptor (1999)

l-Glutamate is the principal excitatory neurotransmitter in the vertebrate central nervous system, where it mediates many of its actions via G-protein-coupled metabotropic glutamate (mGlu) receptors. Since little is known about the dynamics of mGlu receptors at the plasma membrane, we have constructed a fusion protein comprising the mGlu receptor subtype 1alpha (mGlu1alpha) and green fluorescent protein (GFP). Using imaging of Ca2+ release from intracellular stores as a functional assay, the agonist pharmacology of this fluorescently tagged receptor was found to be similar to that of the wild-type receptor when expressed in HEK-293 cells. Receptor movement and function were measured simultaneously by combined imaging of Ca2+, using fura-red, and GFP fluorescence in single cells. Exposure to agonist induced a rapid loss of up to 30% of membrane-associated fluorescence, with a corresponding decrease in the functional response. Following removal of the agonist there was recovery of both the membrane fluorescence and the functional response. These data suggest that the surface expression of G-protein-coupled glutamate receptors might be rapidly regulated in response to agonist activation.
The homologous HD‐Zip I transcription factors HaHB1 and AtHB13 confer cold tolerance via the induction of pathogenesis‐related and glucanase proteins (2011)

Plants deal with cold temperatures via different signal transduction pathways. The HD-Zip I homologous transcription factors HaHB1 from sunflower and AtHB13 from Arabidopsis were identified as playing a key role in such cold response. The expression patterns of both genes were analyzed indicating an up-regulation by low temperatures. When these genes were constitutively expressed in Arabidopsis, the transgenic plants showed similar phenotypes including cell membrane stabilization under freezing treatments and cold tolerance. An exploratory transcriptomic analysis of HaHB1 transgenic plants indicated that several transcripts encoding glucanases and chitinases were induced. Moreover, under freezing conditions some proteins accumulated in HaHB1 plants apoplasts and these extracts exerted antifreeze activity in vitro. Three genes encoding two glucanases and a chitinase were overexpressed in Arabidopsis and these plants were able to tolerate freezing temperatures. All the obtained transgenic plants exhibited cell membrane stabilization after a short freezing treatment. Finally, HaHB1 and AtHB13 were used to transiently transform sunflower and soybean leading to the up-regulation of HaHB1/AtHB13-target homologues thus indicating the conservation of cold response pathways. We propose that HaHB1 and AtHB13 are involved in plant cold tolerance via the induction of proteins able to stabilize cell membranes and inhibit ice growth.
DeepStereo: Learning to Predict New Views from the World's Imagery (2015)

Deep networks have recently enjoyed enormous success when applied to recognition and classification problems in computer vision, but their use in graphics problems has been limited. In this work, we present a novel deep architecture that performs new view synthesis directly from pixels, trained from a large number of posed image sets. In contrast to traditional approaches which consist of multiple complex stages of processing, each of which require careful tuning and can fail in unexpected ways, our system is trained end-to-end. The pixels from neighboring views of a scene are presented to the network which then directly produces the pixels of the unseen view. The benefits of our approach include generality (we only require posed image sets and can easily apply our method to different domains), and high quality results on traditionally difficult scenes. We believe this is due to the end-to-end nature of our system which is able to plausibly generate pixels according to color, depth, and texture priors learnt automatically from the training data. To verify our method we show that it can convincingly reproduce known test views from nearby imagery. Additionally we show images rendered from novel viewpoints. To our knowledge, our work is the first to apply deep learning to the problem of new view synthesis from sets of real-world, natural imagery.
41.3: New LCD Modes for Wide‐Viewing‐Angle Applications (1998)

Abstract Two novel liquid crystal display modes are proposed for wide viewing angle applications. One is named as “electrically‐induced optical compensation (EOC) mode”. It adopts the homeotropic alignment, positive dielectric liquid crystal as well as self domain divided method. The other is named as “Reverse Twisted Hybrid Aligned Nematic(RT HAN) mode” in which the IPS panel structure plus the hybrid LC mode is used. The display principle as well as the performance measured from real displays will be presented.
The anti-microbial peptide LL-37 inhibits the activation of dendritic cells by TLR ligands (2006)

The endogenous anti-microbial peptide LL-37/hCAP-18 is an effector molecule of the innate host defense system at surfaces of the body. Besides its direct anti-microbial activity, the peptide interacts with different cell types. Dendritic cells (DCs) play a central role in mucosal host defense. It was the aim of the study to determine whether LL-37 modulates the response of DCs to pathogen-associated molecular patterns. Monocyte-derived DCs were stimulated with the Toll-like receptors (TLRs) ligands LPS, lipoteichoic acid and flagellin. We measured classical markers of DC maturation and assayed the ability of the DCs to activate T cell responses. Co-incubation with LL-37 resulted in suppressed activation of DCs. Levels of released IL-6, IL-12p70 and TNF-alpha and surface expression of HLA-DR, CD80, CD83, CD86 and the chemokine receptor CCR7 were decreased. Exposure of DCs to LL-37 during LPS exposure induced co-cultured naive T cells to produce less IL-2 and IFN-gamma and decreased their proliferation. The response of memory T cells to a recall antigen was also decreased. In conclusion, we demonstrate that the anti-microbial peptide LL-37 inhibits the activation of DCs by TLR ligands. We propose that LL-37 is a regulator of host defense responses at the intersection of innate and adaptive immune systems.
Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues (2016)

Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology.
Osteoclast-Like Cell Formation and its Regulation by Osteotropic Hormones in Mouse Bone Marrow Cultures* (1988)

We developed a mouse bone marrow culture system to examine the process of osteoclast-like multinucleated cell formation from its progenitors. When mouse marrow cells were cultured for 8 days with 1 alpha,25-dihydroxyvitamin D3 [1 alpha,25-(OH)2D3, 10(-10) to 10(-7) M] or human PTH (1-34) (25-100 ng/ml), tartrate-resistant acid phosphatase (TRACP)-positive multinucleated cells formed. No TRACP-positive multinucleated cells appeared in the absence of these hormones. 1 alpha,25-(OH)2D3 and PTH also increased the number of the clusters of TRACP-positive mononuclear cells. Time course studies showed that these TRACP-positive mononuclear cell clusters appeared before the formation of TRACP-positive multinucleated cells, suggesting that the TRACP-positive mononuclear cells are precursors of the multinucleated cells. Salmon calcitonin markedly inhibited the formation of TRACP-positive multinucleated cells but not TRACP-positive mononuclear cell clusters induced by 1 alpha,25-(OH)2D3 or PTH. TRACP-positive mononuclear cells and multinucleated cells were rarely stained for nonspecific esterase, but some mononuclear cells were positively stained for both nonspecific esterase and TRACP. More that 90% of the TRACP-positive mononuclear cell clusters and multinucleated cells were found near colonies of alkaline phosphatase-positive mononuclear cells (possibly osteoblasts). When marrow mononuclear cells were cultured on sperm whale dentine slices in the presence of 1 alpha,25-(OH)2D3 or PTH, numerous resorption lacunae were formed. These results suggest that 1) TRACP-positive multinucleated cells formed in response to osteotropic hormones in mouse marrow cultures satisfy most of the criteria of osteoclasts, and 2) osteoblasts may play an important role in osteoclast formation.