gebhart/patrepeval huggingface dataset:
TRANCE (Tumor Necrosis Factor [TNF]-related Activation-induced Cytokine), a New TNF Family Member Predominantly Expressed in T cells, Is a Dendritic Cell–specific Survival Factor (1997)

TRANCE (tumor necrosis factor [TNF]-related activation-induced cytokine) is a new member of the TNF family that is induced upon T cell receptor engagement and activates c-Jun N-terminal kinase (JNK) after interaction with its putative receptor (TRANCE-R). In addition, TRANCE expression is restricted to lymphoid organs and T cells. Here, we show that high levels of TRANCE-R are detected on mature dendritic cells (DCs) but not on freshly isolated B cells, T cells, or macrophages. Signaling by TRANCE-R appears to be dependent on TNF receptor-associated factor 2 (TRAF2), since JNK induction is impaired in cells from transgenic mice overexpressing a dominant negative TRAF2 protein. TRANCE inhibits apoptosis of mouse bone marrow-derived DCs and human monocyte-derived DCs in vitro. The resulting increase in DC survival is accompanied by a proportional increase in DC-mediated T cell proliferation in a mixed leukocyte reaction. TRANCE upregulates Bcl-xL expression, suggesting a potential mechanism for enhanced DC survival. TRANCE does not induce the proliferation of or increase the survival of T or B cells. Therefore, TRANCE is a new DC-restricted survival factor that mediates T cell-DC communication and may provide a tool to selectively enhance DC activity.
High levels of (24S)-24-hydroxycholesterol 3-sulfate, 24-glucuronide in the serum and urine of children with severe cholestatic liver disease (1997)

Extracts of urine and serum from children with cholestatic liver disease were analyzed by fast atom bombardment (FAB) mass spectrometry. About half of all spectra showed a peak at m/z 657, compatible with the presence of a glucuronidated cholestenediol sulfate. Separation by ion exchange chromatography before and after solvolysis and treatment with beta-glucuronidase, combined with analyses by gas chromatography-mass spectrometry and FAB mass spectrometry with collision-induced dissociation, showed that the major compound responsible for the peak at m/z 657 was (24S)-24-hydroxycholesterol 3-sulfate, 24-glucuronide. The double conjugate of 27-hydroxycholesterol was also identified and double conjugates of cholestene- and cholestanetriols were also present. Semiquantitative analyses of the double conjugate of 24-hydroxycholesterol in patients whose FAB spectra showed a peak at m/z 657 indicated serum levels of 2-18 microM and a daily urinary excretion of 0.1-2.7 mumol/24 h. Eleven of 13 studied patients with a prominent peak at m/z 657 in the FAB spectra of their serum or urine either underwent liver transplantation or died. It is concluded that double conjugation of hydroxysterols with sulfuric and glucuronic acids can be an important metabolic pathway, particularly for (24S)-24-hydroxycholesterol. It is speculated that serious cholestatic liver disease may induce an increased formation and release of (24S)-24-hydroxycholesterol from brain (Lütjohann et al. 1996, Proc. Nutl. Acad. Sci. USA. 93: 9799-9804) with subsequent extracerebral conjugation with sulfuric and glucuronic acids.
Cavity-Assisted Quantum Bath Engineering (2012)

We demonstrate quantum bath engineering for a superconducting artificial atom coupled to a microwave cavity. By tailoring the spectrum of microwave photon shot noise in the cavity, we create a dissipative environment that autonomously relaxes the atom to an arbitrarily specified coherent superposition of the ground and excited states. In the presence of background thermal excitations, this mechanism increases state purity and effectively cools the dressed atom state to a low temperature.
Synergistic multi-doping effects on the Li7La3Zr2O12 solid electrolyte for fast lithium ion conduction (2015)

Here, we investigate the doping effects on the lithium ion transport behavior in garnet Li7La3Zr2O12 (LLZO) from the combined experimental and theoretical approach. The concentration of Li ion vacancy generated by the inclusion of aliovalent dopants such as Al(3+) plays a key role in stabilizing the cubic LLZO. However, it is found that the site preference of Al in 24d position hinders the three dimensionally connected Li ion movement when heavily doped according to the structural refinement and the DFT calculations. In this report, we demonstrate that the multi-doping using additional Ta dopants into the Al-doped LLZO shifts the most energetically favorable sites of Al in the crystal structure from 24d to 96 h Li site, thereby providing more open space for Li ion transport. As a result of these synergistic effects, the multi-doped LLZO shows about three times higher ionic conductivity of 6.14 × 10(-4) S cm(-1) than that of the singly-doped LLZO with a much less efforts in stabilizing cubic phases in the synthetic condition.
73-GHz self-aligned SiGe-base bipolar transistors with phosphorus-doped polysilicon emitters (1992)

The authors report a thermal-cycle emitter process using phosphorus for the fabrication of self-aligned SiGe-base heterojunction bipolar transistors. The low thermal cycle results in extremely, narrow basewidths and preservation of lightly doped spacers in both the emitter-base and base-collector junctions for improved breakdown. Transistors with 35-nm basewidths were obtained with low emitter-base reverse leakage and a peak cutoff frequency of 73 GHz for an intrinsic base sheet resistance of 16 k Omega / Square Operator . Minimum NTL (nonthreshold logic) and ECL (emitter-coupled logic) gate delays of 28 and 34 ps, respectively were obtained with these devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Serum anti-glycan antibodies predict complicated Crohnʼs disease behavior (2009)

This is the first study showing the clinical value of serum antiglycan antibodies for prediction of a more complicated disease course in adult patients with CD.
The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer (2009)

The natural history of cancers associated with virus exposure is intriguing, since only a minority of human tissues infected with these viruses inevitably progress to cancer. However, the molecular reasons why the infection is controlled or instead progresses to subsequent stages of tumorigenesis are largely unknown. In this article, we provide the first complete DNA methylomes of double-stranded DNA viruses associated with human cancer that might provide important clues to help us understand the described process. Using bisulfite genomic sequencing of multiple clones, we have obtained the DNA methylation status of every CpG dinucleotide in the genome of the Human Papilloma Viruses 16 and 18 and Human Hepatitis B Virus, and in all the transcription start sites of the Epstein-Barr Virus. These viruses are associated with infectious diseases (such as hepatitis B and infectious mononucleosis) and the development of human tumors (cervical, hepatic, and nasopharyngeal cancers, and lymphoma), and are responsible for 1 million deaths worldwide every year. The DNA methylomes presented provide evidence of the dynamic nature of the epigenome in contrast to the genome. We observed that the DNA methylome of these viruses evolves from an unmethylated to a highly methylated genome in association with the progression of the disease, from asymptomatic healthy carriers, through chronically infected tissues and pre-malignant lesions, to the full-blown invasive tumor. The observed DNA methylation changes have a major functional impact on the biological behavior of the viruses.
A CMOS contact imager for locating individual cells (2006)

We describe the design of a contact imager for applications in lab-on-a-chip systems, such as sample preparation and manipulation and monitoring of cells. This is a challenging task because most cells are nearly transparent, so the contrast between the presence and absence of a cell is small. Thus additional image processing is necessary to locate cells. To enhance the image contrast and facilitate object recognition, the contact imager implements on-chip one bit quantization with a dynamic threshold that adapts to the background illumination. The imager is capable of locating dark objects in a bright background or bright objects in a dark background. The locations of recognized cells are generated as outputs to alleviate computational requirements for generating control signals in closed-loop systems.
Visualizations of binding and internalization of two nonlinked protein components of botulinum C2 toxin in tissue culture cells (1992)

Binding and internalization of two nonlinked components of botulinum C2 toxin were visualized in tissue culture cells with components directly labeled with fluorescence. The binding of both untrypsinized and trypsinized component II (UT-II and T-II, respectively) to common specific sites on the cell membrane was evidenced by competitive binding between fluorescence-labeled and unlabeled components. The distribution patterns of fluorescence-labeled T-II and UT-II after binding to cells at 37 degrees C were different; T-II clustered on the cell membrane and entered the cells in endosomes, whereas UT-II entered the cells inefficiently and not in vesicles and was distributed on the nuclear surface. The difference may be due to the multivalent property of T-II, which is not shared with UT-II. Fluorescence-labeled component I, which binds only to cells bound with T-II, entered cells by the same route as T-II did; both colocated on the same clusters on the cell membrane and also in the same vesicles in the cytoplasm. The present results suggest that component I of C2 toxin, which ADP-ribosylates cytoplasmic actin, directly binds to T-II but not to UT-II on the cell membrane and is internalized into cells together with T-II in the same endosomes.
Plasmon-resonant gold nanorods provide spectroscopic OCT contrast in excised human breast tumors (2008)

Plasmon-resonant gold nanorods have been demonstrated recently as contrast agents for optical coherence tomography (OCT). To evaluate their ability to produce contrast in a structurally heterogeneous environment, nanorods were injected at discrete locations into an excised sample of human breast invasive ductal carcinoma. The distribution of nanorods within the tissue was revealed using spectroscopic OCT imaging techniques, by analyzing the evolution of the backscattered light spectrum over tissue depth. We compare a variety of signal processing methods including spatial averaging and least-squares fitting to the <i>a priori</i> extinction spectrum of the nanorods, with the goal of optimizing the detection sensitivity to the nanorods in these tissues. Because nanorods can be conjugated with proteins specific to biomolecular targets, they may potentially be used with these imaging methods to provide molecular contrast in human tissues.
Thalidomide Costimulates Primary Human T Lymphocytes, Preferentially Inducing Proliferation, Cytokine Production, and Cytotoxic Responses in the CD8+ Subset (1998)

The efficacy of thalidomide (alpha-phthalimido-glutarimide) therapy in leprosy patients with erythema nodosum leprosum is thought to be due to inhibition of tumor necrosis factor alpha. In other diseases reported to respond to thalidomide, the mechanism of action of the drug is unclear. We show that thalidomide is a potent costimulator of primary human T cells in vitro, synergizing with stimulation via the T cell receptor complex to increase interleukin 2-mediated T cell proliferation and interferon gamma production. The costimulatory effect is greater on the CD8+ than the CD4+ T cell subset. The drug also increases the primary CD8+ cytotoxic T cell response induced by allogeneic dendritic cells in the absence of CD4+ T cells. Therefore, human T cell costimulation can be achieved pharmacologically with thalidomide, and preferentially in the CD8+ T cell subset.
Silicon and silicon dioxide thermal bonding for silicon-on-insulator applications (1988)

There has been a good deal of interest recently in the applicability of thermal bonding to silicon-on-insultator (SOI) technology. Thermal bonding (also called direct bonding) is accomplished by mating polished, properly hydrolyzed silicon and/or silicon dioxide surfaces, which are then annealed to promote diffusion bonding. In order to produce high-quality SOI layers it must be demonstrated that the interface betweeen the wafers is void-free over the entire surface of the wafer (4-in. wafers in our study). We have found that the standard annealing step which has been used by other groups to form the wafer bond must be followed by a hyperbaric, high-temperature annealing cycle in order to produce interfaces which are completely void-free. In addition, we have found that mating the wafers in a controlled atmosphere is necessary to insure that voids do not remain after the thermal processing is complete. We shall present transmission electron micrographs which reveal the morphology of the bonded interface on an atomic scale. We shall submit C-scan acoustic micrographs and infrared transmission thermographs which display the areal nature of the bonding voids.
Donor–Acceptor Conjugated Polymer Based on Naphtho[1,2-c:5,6-c]bis[1,2,5]thiadiazole for High-Performance Polymer Solar Cells (2011)

Donor-acceptor conjugated polymers PBDT-DTBT and PBDT-DTNT, based on 2,1,3-benzothiadiazole (BT) and naphtho[1,2-c:5,6-c]bis[1,2,5]thiadiazole (NT), have been designed and synthesized for polymer solar cells. NT contains two fused 1,2,5-thiadiazole rings that lower the band gap, enhance the interchain packing, and improve the charge mobility of the resulting polymer. Consequently, the NT-based polymer PBDT-DTNT exhibited considerably better photovoltaic performance with a power conversion efficiency (PCE) of 6.00% when compared with the BT-based polymer PBDT-DTBT, which gave a PCE of 2.11% under identical device configurations.
Identification and Characterization of l-Arabonate Dehydratase, l-2-Keto-3-deoxyarabonate Dehydratase, and l-Arabinolactonase Involved in an Alternative Pathway of l-Arabinose Metabolism (2006)

Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L-KDA dehydratase, which may be a candidate for such a natural mutation.
Basic Fibroblast Growth Factor Is Neither Necessary nor Sufficient for the Development of Retinal Neovascularization (1998)

Basic fibroblast growth factor (FGF2) is constitutively expressed in the retina and its expression is increased by a number of insults, but its role in the retina is still uncertain. This study was designed to test the hypothesis that altered expression of FGF2 in the retina affects the development of retinal neovascularization. Mice with targeted disruption of the Fgf2 gene had no detectable expression of FGF2 in the retina by Western blot, but retinal vessels were not different in appearance or total area from wild-type mice. When FGF2-deficient mice were compared with wild-type mice in a murine model of oxygen-induced ischemic retinopathy, they developed the same amount of retinal neovascularization. Transgenic mice with a rhodopsin promoter/Fgf2 gene fusion expressed high levels of FGF2 in retinal photoreceptors but developed no retinal neovascularization or other abnormalities of retinal vessels; in the ischemic retinopathy model, they showed no significant difference in the amount of retinal neovascularization compared with wild-type mice. These data indicate that FGF2 expression is not necessary nor sufficient for the development of retinal neovascularization. This suggests that agents that specifically antagonize FGF2 are not likely to be useful adjuncts in the treatment of retinal neovascularization and therapies designed to increase FGF2 expression are not likely to be complicated by retinal neovascularization.
Efficient and stable perovskite solar cells prepared in ambient air irrespective of the humidity (2016)

Poor stability of organic-inorganic halide perovskite materials in humid condition has hindered the success of perovskite solar cells in real applications since controlled atmosphere is required for device fabrication and operation, and there is a lack of effective solutions to this problem until now. Here we report the use of lead (II) thiocyanate (Pb(SCN)2) precursor in preparing perovskite solar cells in ambient air. High-quality CH3NH3PbI3-x(SCN)x perovskite films can be readily prepared even when the relative humidity exceeds 70%. Under optimized processing conditions, we obtain devices with an average power conversion efficiency of 13.49% and the maximum efficiency over 15%. In comparison with typical CH3NH3PbI3-based devices, these solar cells without encapsulation show greatly improved stability in humid air, which is attributed to the incorporation of thiocyanate ions in the crystal lattice. The findings pave a way for realizing efficient and stable perovskite solar cells in ambient atmosphere.
Protocols to differentiate embryonic stem cells into insulin-producing cells (2008)

Embryonic stem cells represent an interesting alternative to treat diabetes due to their two main properties: self-renewal by symmetric divisions, and the potential for cell differentiation into insulin-expressing cells under certain culture conditions. Achieving the latter implies the modification of the culture medium adding specific growth factors and/or reprogramming the cells by transfecting specific DNA constructs. Several laboratories have used one or a combination of such strategies in order to obtain insulin-positive cells with different degrees of success. The main obstacles posed in the different protocols concern the amounts of intracellular insulin stored and secreted in response to different stimuli, the correct processing of the hormone, the risk of forming teratomas and the immune rejection once cells are transplanted. Promising results have been obtained from protocols which try to recapitulate the pancreas ontogeny in the culture dish. To this end, it is instrumental to understand the embryonic development process of the human pancreas from definitive endoderm to the adult, as well as its molecular markers and the functional traits of the obtained cells in order to achieve a transplantable product to cure diabetes. This manuscript explores published protocols following this objective, analyzing the main features that could contribute to elaborate a more definitive strategy. The final protocol must be universal, easily transferable to the clinical practice and, most importantly, liberate patients from the insulin injections without the development of secondary complications.
Chlamydial Heat Shock Protein 60 Activates Macrophages and Endothelial Cells Through Toll-Like Receptor 4 and MD2 in a MyD88-Dependent Pathway (2002)

Active inflammation and NF-kappaB activation contribute fundamentally to atherogenesis and plaque disruption. Accumulating evidence has implicated specific infectious agents including Chlamydia pneumoniae in the progression of atherogenesis. Chlamydial heat shock protein 60 (cHSP60) has been implicated in the induction of deleterious immune responses in human chlamydial infections and has been found to colocalize with infiltrating macrophages in atheroma lesions. cHSP60 might stimulate, enhance, and maintain innate immune and inflammatory responses and contribute to atherogenesis. In this study, we investigated the signaling mechanism of cHSP60. Recombinant cHSP60 rapidly activated NF-kappaB in human microvascular endothelial cells (EC) and in mouse macrophages, and induced human IL-8 promoter activity in EC. The inflammatory effect of cHSP60 was heat labile, thus excluding a role of contaminating LPS, and was blocked by specific anti-chlamydial HSP60 mAb. In human vascular EC which express Toll-like receptor 4 (TLR4) mRNA and protein, nonsignaling TLR4 constructs that act as dominant negative blocked cHSP60-mediated NF-kappaB activation. Furthermore, an anti-TLR4 Ab abolished cHSP60-induced cellular activation, whereas a control Ab had no effect. In 293 cells, cHSP60-mediated NF-kappaB activation required both TLR4 and MD2. A dominant-negative MyD88 construct also inhibited cHSP60-induced NF-kappaB activation. Collectively, our results indicate that cHSP60 is a potent inducer of vascular EC and macrophage inflammatory responses, which are very relevant to atherogenesis. The inflammatory effects are mediated through the innate immune receptor complex TLR4-MD2 and proceeds via the MyD88-dependent signaling pathway. These findings may help elucidate the mechanisms by which chronic asymptomatic chlamydial infection contribute to atherogenesis.
Immunization of fucose-containing polysaccharides from Reishi mushroom induces antibodies to tumor-associated Globo H-series epitopes (2013)

Carbohydrate-based vaccines have shown therapeutic efficacy for infectious disease and cancer. The mushroom Ganoderma lucidum (Reishi) containing complex polysaccharides has been used as antitumor supplement, but the mechanism of immune response has rarely been studied. Here, we show that the mice immunized with a l-fucose (Fuc)-enriched Reishi polysaccharide fraction (designated as FMS) induce antibodies against murine Lewis lung carcinoma cells, with increased antibody-mediated cytotoxicity and reduced production of tumor-associated inflammatory mediators (in particular, monocyte chemoattractant protein-1). The mice showed a significant increase in the peritoneal B1 B-cell population, suggesting FMS-mediated anti-glycan IgM production. Furthermore, the glycan microarray analysis of FMS-induced antisera displayed a high specificity toward tumor-associated glycans, with the antigenic structure located in the nonreducing termini (i.e., Fucα1-2Galβ1-3GalNAc-R, where Gal, GalNAc, and R represent, respectively, D-galactose, D-N-acetyl galactosamine, and reducing end), typically found in Globo H and related tumor antigens. The composition of FMS contains mainly the backbone of 1,4-mannan and 1,6-α-galactan and through the Fucα1-2Gal, Fucα1-3/4Man, Fucα1-4Xyl, and Fucα1-2Fuc linkages (where Man and Xyl represent d-mannose and d-xylose, respectively), underlying the molecular basis of the FMS-induced IgM antibodies against tumor-specific glycans.