gebhart/patrepeval huggingface dataset:
Effector mechanisms in transplant rejection (2003)

Antigens, provided by the allograft, trigger the activation and proliferation of allospecific T cells. As a consequence of this response, effector elements are generated that mediate graft injury and are responsible for the clinical manifestations of allograft rejection. Donor-specific CD8+ cytotoxic T lymphocytes play a major role in this process. Likewise, CD4+ T cells mediate delayed-type hypersensitivity responses via the production of soluble mediators that function to further activate and guide immune cells to the site of injury. In addition, these mediators may directly alter graft function by modulating vascular tone and permeability or by promoting platelet aggregation. Allospecific CD4+ T cells also promote B-cell maturation and differentiation into antibody-secreting plasma cells via CD40-CD40 ligand interactions. Alloantibodies that are produced by these B cells exert most of their detrimental effects on the graft by activating the complement cascade. Alternatively, antibodies can bind Fc receptors on natural killer cells or macrophages and cause target cell lysis via antibody-dependent cell-mediated cytotoxicity. In this review, we discuss these major effector pathways, focusing on their role in the pathogenesis of allograft rejection.
PZT thin-film actuator driven micro optical scanning sensor by 3D integration of optical and mechanical devices (1999)

In this paper, a novel functional element integration method is proposed and demonstrated by highly miniaturized micro optical scanning sensor with dimensions of W2.0/spl times/L4.0/spl times/H2.8 mm/sup 3/. In the sensor as small as a wheat grain, the functional elements such as a laser diode (LD), photo detectors (PDs), a beam splitter, a ball lens, and a PZT thin-film actuator integrated optical scanner are integrated on separate substrates each consisting a functional module and the substrates are stacked. And the sensor is capable of multi-optical sensing: the 2D object shape recognition (+/- 10 degs scanning area for two direction) and the range measurement (50 mm +/- 10 mm with 0.5 mm resolution).
Recognition of DNA Topology in Reactions between Plasmid DNA and Cationic Copolymers (2000)

This study for the first time demonstrates phenomenon of recognition of DNA tertiary structure by the synthetic polycationic molecules. Effects of DNA topology were evaluated using supercoiled and linearized forms of plasmid DNA (scDNA and lDNA). Recognition is achieved by using relatively simple chemical structures interacting with the DNA. Two polycations modified with water-soluble poly(ethylene glycol) (PEG) chains, PEG−block−poly(N-methyl-4-vinylpyridinium sulfate) (PEG−b−PVP) and PEG−graft−polyethyleneimine (PEG−g−PEI) were used. When added to the mixtures of lDNA and scDNA, PEO−b−PVP selectively bound to scDNA, while lDNA remained free. In contrast, PEO−g−PEI interacted with both forms of the DNA present in the mixture. Distinct behavior of two copolymers was attributed to the differences in their structure, particularly, charge density of the polycation blocks. Relatively small variation in the polycation ionization state can result in drastic changes in its behavior upon interaction with DNA. Particularly, the change of pH from 7.0 to 5.0, increasing the charge density of PEI block in PEO−g−PEI, was also accompanied by the appearance of recognition phenomena. These findings uncover possibilities for the control of the processes of DNA incorporation in the complexes with cationic species by altering the DNA topology, which may have practical significance in using these complexes for gene delivery.
Bit-interleaved coded modulation with iterative decoding using constellation shaping (2006)

We investigate the association between constellation shaping and bit-interleaved coded modulation with iterative decoding (BICM-ID). To this end, we consider a technique which consists of inserting shaping block codes between mapping and channel coding functions in order to achieve constellation shaping. By assuming the example of a 2-bit/s/Hz 16-QAM BICM-ID, it is demonstrated using computer simulations that this technique can improve the performance of BICM-ID schemes by a few tenths of decibels.
Identification of T Cell-Restricted Genes, and Signatures for Different T Cell Responses, Using a Comprehensive Collection of Microarray Datasets (2005)

We used a comprehensive collection of Affymetrix microarray datasets to ascertain which genes or molecules distinguish the known major subsets of human T cells. Our strategy allowed us to identify the genes expressed in most T cell subsets: TCR alphabeta+ and gammadelta+, three effector subsets (Th1, Th2, and T follicular helper cells), T central memory, T effector memory, activated T cells, and others. Our genechip dataset also allowed for identification of genes preferentially or exclusively expressed by T cells, compared with numerous non-T cell leukocyte subsets profiled. Cross-comparisons between microarray datasets revealed important features of certain subsets. For instance, blood gammadelta T cells expressed no unique gene transcripts, but did differ from alphabeta T cells in numerous genes that were down-regulated. Hierarchical clustering of all the genes differentially expressed between T cell subsets enabled the identification of precise signatures. Moreover, the different T cell subsets could be distinguished at the level of gene expression by a smaller subset of predictor genes, most of which have not previously been associated directly with any of the individual subsets. T cell activation had the greatest influence on gene regulation, whereas central and effector memory T cells displayed surprisingly similar gene expression profiles. Knowledge of the patterns of gene expression that underlie fundamental T cell activities, such as activation, various effector functions, and immunological memory, provide the basis for a better understanding of T cells and their role in immune defense.
Recombinant Bifunctional Molecule FV/IFN-γ Possesses the Anti-Tumor FV as Well as the Gamma Interferon Activities (1993)

Recombinant DNA techniques were used to clone, construct and express the bifunctional molecule FV/IFN-gamma. The FV/IFN-gamma is a single-chain 42KD fusion protein expressed in E. coli under control of the strong T7 bacteriophage promoter in the expression vector pT7-7-FV-IFN-gamma. The fused gene fragment FV-IFN-gamma containing a single-chain anti-TAG72 FV gene fragment as well as the human recombinant cDNA fragment of IFN-gamma molecule. The renatured soluble form of FV/IFN-gamma was purified from E. coli inclusion bodies using HTPT chromatography. The yield of this fusion protein was estimated at 10mg/L. Our data showed that the FV/IFN-gamma molecule retained the TAG72 antigen-binding specificity and the IFN-gamma activity as measured in ELISA, Western blotting and up-regulation of CEA expression by IFN-gamma. Therefore, it may prove to be useful in targeting the biological effect of IFN-gamma to tumor cells and stimulating its immune destruction.
Site-specific one-pot triple click labeling for DNA and RNA (2018)

We report site-specific triple click labeling for DNA and RNA in a one-pot setup by performing inverse electron demand Diels-Alder reaction and strain-promoted and copper catalyzed click reactions sequentially. Our methodology can be applied to long and short nucleic acids alike, and could have broader potential for labeling other (bio-)molecules.
Biosynthesis and Post-translational Processing of the Precursor to Brain-derived Neurotrophic Factor (2001)

We examined the biosynthesis and post-translational processing of the brain-derived neurotrophic factor precursor (pro-BDNF) in cells infected with a pro-BDNF-encoding vaccinia virus. Metabolic labeling, immunoprecipitation, and SDS-polyacrylamide gel electrophoresis reveal that pro-BDNF is generated as a 32-kDa precursor that is N-glycosylated and glycosulfated on a site, within the pro-domain. Some pro-BDNF is released extracellularly and is biologically active as demonstrated by its ability to mediate TrkB phosphorylation. The precursor undergoes N-terminal cleavage within the trans-Golgi network and/or immature secretory vesicles to generate mature BDNF (14 kDa). Small amounts of a 28-kDa protein that is immunoprecipitated with BDNF antibodies is also evident. This protein is generated in the endoplasmic reticulum through N-terminal cleavage of pro-BDNF at the Arg-Gly-Leu-Thr(57)- downward arrow-Ser-Leu site. Cleavage is abolished when Arg(54) is changed to Ala (R54A) by in vitro mutagenesis. Blocking generation of 28-kDa BDNF has no effect on the level of mature BDNF and blocking generation of mature BDNF with alpha(1)-PDX, an inhibitor of furin-like enzymes, does not lead to accumulation of the 28-kDa form. These data suggest that 28-kDa pro-BDNF is not an obligatory intermediate in the formation of the 14-kDa form in the constitutive secretory pathway.
THE IMPACT OF NATIONAL CANCER ACT (1991)

Taxol, an antimicrotubule agent, has shown promise for efficacy in treatment of breast cancer, but severe hypersensitivity reactions led to cessation of many phase I clinical trials. Consequently, investigators and the National Cancer Institute recommended that phase I and II studies of this agent use 24-hour infusions and antiallergic medications. Using a premedication regimen effective in preventing hypersensitivity reactions, we have performed a phase II trial of taxol in patients with metastatic breast cancer. Taxol was administered to 25 patients at a dose of 250 mg/m2 by 24-hour infusion every 21 days. These patients had received only one prior chemotherapy regimen, either adjuvant to surgery or for metastatic disease; all but two had received doxorubicin. In 60% of the patients, the dominant site of disease was the viscera. All patients were assessable. In April 1991, at a median time on study of 9 months (range, 5-13+ months), the objective response rate was 56% (12% complete and 44% partial; 95% confidence interval, 35%-76%). Disease progressed in only 8% of the patients. The median number of courses of therapy was 11. Granulocytopenia was the dose-limiting toxic effect, but neutropenia with fever occurred in only 5% of 232 courses. A chronic glove-and-stocking neuropathy developed in most patients, but no allergic reactions occurred. We conclude that taxol is an active agent in the treatment of metastatic breast cancer and that it warrants continued study. Currently, we are conducting a phase I trial of taxol plus doxorubicin. Future trials should address the optimal effective dose, the optimal sequencing of combinations, mechanisms of drug resistance in tumors, and dose-limiting toxic effects (particularly cardiac toxic effects of taxol given as a single agent or in drug combinations).
Relative malignant potential of human breast carcinoma cell lines established from pleural effusions and a brain metastasis. (1991)

Three human breast cancer cell lines from pleural effusions (MDA-MB-435, MDA-MB-231, MDA-MB-468) and one from a brain metastasis (MDA-MB-361) were tested for growth potential in vitro (minimum serum requirements, growth in semisolid agarose), for tumorigenicity and metastasis in nude mice following injection into the mammary fatpad (m.f.p.) and intravenously (i.v.), and for formation of experimental brain metastasis following injection into the carotid artery (i.a.). Colony-forming efficiency of the breast cancer cells in dense agarose corresponded with metastatic potential of the m.f.p. tumors. The results consistently ranked the 4 cell lines as follows: MDA-MB-435 greater than MDA-MB-231 greater than MDA-MB-468 greater than MDA-MB-361, from the most to the least aggressive. The exception was for tumor growth in the brain after i.a. injection of cells, where MDA-MB-361 cells were ranked as second highest for tumor take, but with the slowest growth rate. These results indicate that in this series of breast carcinomas, the cells from a brain metastasis (MDA-MB-361) have a lower malignant potential than cells from visceral metastases.
Blocking the effects of IL-1 in rheumatoid arthritis protects bone and cartilage (2002)

Destruction of articular joints occurs progressively in patients with rheumatoid arthritis (RA). Although the exact aetiology of RA has not been fully elucidated, a large body of evidence supports a role for interleukin-1 (IL-1) in cartilage and bone erosion. In vitro studies suggest that IL-1 can cause cartilage destruction by stimulating the release of matrix metalloproteinases and other degradative products, and it can increase bone resorption by stimulating osteoclast differentiation and activation. In animal models of RA, blocking the effects of IL-1 with either IL-1 receptor antagonist (IL-1Ra; endogenous), anti-IL-1 monoclonal antibodies, or soluble IL-1 type II receptors significantly reduced cartilage destruction and bone erosion. Gene therapy with IL-1Ra was also effective in reducing joint destruction in experimental RA and osteoarthritis (OA) models. In clinical studies, anakinra, a human recombinant IL-1 receptor antagonist (IL-1ra; exogenous), significantly slowed radiographic progression of RA relative to placebo and significantly reduced clinical symptoms when used as monotherapy or in addition to existing methotrexate therapy. These results demonstrate that blocking IL-1 protects bone and cartilage from progressive destruction in RA.
Carbohydrate protein interactions. Syntheses of agglutination inhibitors of wheat germ agglutinin by phase transfer catalysis (1991)

Starting from chloride 1, a series of para-substituted aryl 2-acetamido-2-deoxy-β-D-glucopyranosides were prepared using phase transfer catalysis conditions with tetrabutylammonium hydrogen sulfate in 1 M sodium hydroxide and methylene chloride at room temperature. Zemplén de-O-acetylation afforded the unprotected glycosides. Optimization of reaction conditions was evaluated. Several functional group manipulations were effected to widen the number and nature of the para-substituents. Key words: phase transfer catalysis, aryl 2-acetamido-2-deoxy-β-D-glucopyranosides.
Cloning and characterization of AKAP 95, a nuclear protein that associates with the regulatory subunit of type II cAMP-dependent protein kinase. (1994)

The subcellular location of the type II cAMP-dependent protein kinase is dictated by the interaction of the regulatory subunit (RII) with A-kinase anchor proteins (AKAPs). Using an interaction cloning strategy with RII alpha as a probe, we have isolated cDNAs encoding a novel 761-amino acid protein (named AKAP 95) that contains both RII- and DNA-binding domains. Deletion analysis and peptide studies revealed that the RII-binding domain of AKAP 95 is located between residues 642 and 659 and includes a predicted amphipathic helix. Zinc overlay and DNA binding studies suggest that the DNA-binding domain is composed of two CC/HH-type zinc fingers between residues 464 and 486 and residues 553 and 576. The AKAP was detected in a nuclear matrix fraction, and immunofluorescence using purified anti-AKAP 95 antibodies revealed a distinct nuclear staining in a variety of cell types. Direct overlay of fluorescein isothiocyanate-labeled RII alpha onto fixed rat embryo fibroblasts showed that high-affinity binding sites for RII exist in the nucleus and that these sites are blocked by an anchoring inhibitor peptide. Furthermore, AKAP 95 was detected in preparations of RII that were purified from cellular extracts using cAMP-agarose. The results suggest that AKAP 95 could play a role in targeting type II cAMP-dependent protein kinase for cAMP-responsive nuclear events.
Origins of High Mobility and Low Operation Voltage of Amorphous Oxide TFTs: Electronic Structure, Electron Transport, Defects and Doping (2009)

Amorphous oxide semiconductors (AOSs) are expected as new channel materials in thin-film transistors (TFTs) for large-area and/or flexible flat-panel displays and other giant-microelectronics devices. So far, many prototype displays have been demonstrated in these four years since the first report of AOS TFT. The most prominent feature of AOS TFTs is that they operate with good performances even if they are fabricated at low temperatures without a defect passivation treatment. The TFT mobilities exceed 10 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /(V ldr s), which are more than ten times larger than those of conventional amorphous semiconductor devices. In addition, they operate at low voltages, e.g., <5V owing to their small subthreshold voltage swings. These features indicate that electron transport in oxide semiconductors are insensitive to random structures and these oxides do not form high-density defects that affect electron transport and TFT operation. In this paper, we discuss the origins of the prominent features of AOS devices from the viewpoint of materials science of AOS.
Regiospecific Vinyl Phosphate/β-Keto Phosphonate Rearrangements Initiated by Halogen−Metal Exchange (1998)

A new strategy has been developed for preparation of β-keto phosphonates via a halogen−metal exchange induced 1,3-phosphorus migration of 2-bromovinyl phosphates. These intermediates can be prepared through conversion of an α-bromo ketone to the appropriate enolate by reaction with strong base, or through conjugate addition to an α-bromo α,β-unsaturated ketone. In either case, trapping the resulting enolate by reaction with a dialkyl phosphorochloridate gives the 2-bromovinyl phosphate. Metalation can be accomplished upon treatment with n-BuLi, and rearrangement is facile once metalation has been achieved. Studies with isotopically labeled substrates have shown that this rearrangement is regiospecific, in contrast to vinyl phosphate/β-keto phosphonate rearrangements induced by strong base where regioisomeric products are sometimes obtained.
Desorption-Limited Mechanism of Release from Polymer Nanofibers (2007)

This work examines the release of a model water-soluble compound from electrospun polymer nanofiber assemblies. Such release attracts attention in relation to biomedical applications, such as controlled drug delivery. It is also important for stem cell attachment and differentiation on biocompatible electrospun nanofiber scaffolds containing growth factors, which have been encapsulated by means of electrospinning. Typically, the release mechanism has been attributed to solid-state diffusion of the encapsulated compound from the fibers into the surrounding aqueous bath. Under this assumption, a 100% release of the encapsulated compound is expected in a certain (long) time. The present work focuses on certain cases where complete release does not happen, which suggests that solid-state diffusion may not be the primary mechanism at play. We show that in such cases the release rate can be explained by desorption of the embedded compound from nanopores in the fibers or from the outer surface of the fibers in contact with the water bath. After release, the water-soluble compound rapidly diffuses in water, whereas the release rate is determined by the limiting desorption stage. A model system of Rhodamine 610 chloride fluorescent dye embedded in electrospun monolithic poly(methylmethacrylate) (PMMA) or poly(caprolactone) (PCL) nanofibers, in nanofibers electrospun from PMMA/PCL blends, or in core-shell PMMA/PCL nanofibers is studied. Both the experimental results and theory point at the above mentioned desorption-related mechanism, and the predicted characteristic time, release rate, and effective diffusion coefficient agree fairly well with the experimental data. A practically important outcome of this surface release mechanism is that only the compound on the fiber and pore surfaces can be released, whereas the material encapsulated in the bulk cannot be freed within the time scales characteristic of the present experiments (days to months). Consequently, in such cases, complete release is impossible. We also demonstrate how the release rate can be manipulated by the polymer content and molecular weight affecting nanoporosity and the desorption enthalpy, as well as by the nanofiber structure (monolithic fibers, fibers from polymer blends, and core-shell fibers). In particular, it is shown that, by manipulating the above parameters, release times from tens of hours to months can be attained.
Amyloid &#946; Conformation in Aqueous Environment (2008)

Amyloid β peptide (Aβ), 42-residue peptide and its variations, is known to form amyloid fibrils in Alzheimers disease. Solid-state NMR study reveals a parallel β-sheet structure in the Aβ fibrils. The atomic level structure of Aβ in aqueous environment, however, has not been determined, because of its tendency to aggregate. There are several reports that soluble forms of Aβ possess intrinsic neurotoxicity. It has recently become possible to determine the crystal structure of Aβ fragments in an aqueous solution without organic solvents and detergents using a fusion technique with a hyperthermophile protein. Aβ28-42 forms a β-conformation. This fusion technique enables us to obtain structural information at atomic resolution for amyloidogenic peptides in aqueous environments. This review describes our current knowledge on the Aβ conformation in aqueous environments and some viewpoints based on the knowledge. Keywords: Alzheimer's disease, amyloid, monomer, structure, fusion technique
A Stronger DNA Damage-Induced G2 Checkpoint Due to Over-Activated CHK1 in the Absence of PARP-1 (2006)

Poly(ADP-ribose) polymerase 1 (PARP-1) is involved in multi-pathways to respond to DNA damage. Lack of or inhibition of PARP-1 activity leads to slow progress of cell cycle and sensitization of cells to different stresses. Recently, it was reported that besides the Ku dependent main nonhomologous end joining (NHEJ) pathway, there is a PARP-1 dependent complementary NHEJ pathway to repair DNA double strand break (DSB). Here we show that compared with PARP-1+/+ cells, PARP-1-/- cells display a much stronger G2 checkpoint response following ionizing radiation (IR). Treatment with Chk1 siRNA abolishes the stronger G2 checkpoint response and sensitizes PARP-1-/- cells to IR. These data indicate that the stronger G2 checkpoint response in PARP-1-/- cells is CHK1 dependent, which protects cells from IR induced killing. We also show that 4-Amino-1,8-naphthalimide (4-AN, inhibitor of PARP) but not methoxyamine (inhibitor of base excision repair (BER)), affects IR induced G2 arrest and cell sensitivity in PARP-1+/+ cells, resulting in the phenotypes similar to those of PARP-1-/- cells. These results indicate that DSB repair from the complementary NHEJ pathway of PARP-1, but not single strand break (SSB) repair from the BER function of PARP-1, may play an essential role in the over-activated CHK1 regulated G2 checkpoint response and radiosensitivity in PARP-1-/- cells.
Preservation of Membranes in Anhydrobiotic Organisms: The Role of Trehalose (1984)

Trehalose is a nonreducing disaccharide of glucose commonly found at high concentrations in anhydrobiotic organisms. In the presence of trehalose, dry dipalmitoyl phosphatidylcholine (DPPC) had a transition temperature similar to that of the fully hydrated lipid, whereas DPPC dried without trehalose had a transition temperature about 30 degrees Kelvin higher. Results obtained with infrared spectroscopy indicate that trehalose and DPPC interact by hydrogen bonding between the OH groups in the carbohydrate and the polar head groups of DPPC. These and previous results show that this hydrogen bonding alters the spacing of the polar head groups and may thereby decrease van der Waals interactions in the hydrocarbon chains of the DPPC. This interaction between trehalose and DPPC is specific to trehalose. Hence this specificity may be an important factor in the ability of this molecule to stabilize dry membranes in anhydrobiotic organisms.