gebhart/patrepeval huggingface dataset:
Fuel Ethanol Production from Lignocellulose Using Genetically Engineered Bacteria (1997)

The technologies to convert carbohydrate components of lignocellulose into fuel ethanol are currently available. Today's challenge is to assemble these into a cost-effective process for commercial demonstration while mounting a vigorous research and development program to achieve incremental improvements. Bacteria such as Escherichia coli KO11 have been engineered to produce ethanol from all of the sugars present in lignocellulose by adding the genes (pdc, adhB) encoding the ethanol pathway from Zymomonas mobilis. These Z. mobilis genes have been integrated into the E. coli chromosome to produce a stable organism for industrial applications. The effectiveness of KO11 has been demonstrated at 150-L scale with hemicellulose syrups and at 10,000-L scale with laboratory sugars, producing over 40 g ethanol/L within 48 h (greater than 90% of theoretical yield). Additional organisms have been engineered for the fermentation of cellulose using an analogous approach. One of these, Klebsiella oxytoca P2, has been investigated in some detail. Cellulase enzymes represent a major cost associated with ethanol production from lignocellulose. K. oxytoca P2 contains native enzymes for the uptake and metabolism of cellobiose and cellotriose, eliminating the need for one of the major cellulase components, ß-glucosidase. Additional studies have shown that the cellulase requirement for ethanol production can be reduced by enzyme recycling during simultaneous saccharification and fermentation. With mixed waste office paper, projected cellulase costs (production on site) can be as low as $0.085 cents (U.S.)/L with a yield of 539 L/metric ton. Recent studies have identified inexpensive nutrients which can be used for industrial processes and opportunities for synergy between lignocellulose to ethanol plants and grain-based or cane-based ethanol plants.
Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions (2015)

We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion.
Generation of multiwatt, broadband continua in holey fibers (2002)

We demonstrate that 2-W average-fpower 310-nm-wide continua can be generated in holey fibers by use of a novel 6-W pump source at 770 nm. The pump source is demonstrated by use of the 64% efficient quasi-phase-matched second-harmonic generation of a seeded 10-W erbium fiber amplifier in periodically poled KTP. Nonlinear contributions to generation of high-power continua in holey fibers are identified and analyzed.
The role of T-cell interleukin-17 in conducting destructive arthritis: lessons from animal models. (2005)

Interleukin-17 (IL-17) is a T cell cytokine spontaneously produced by cultures of rheumatoid arthritis (RA) synovial membranes. High levels have been detected in the synovial fluid of patients with RA. The trigger for IL-17 is not fully identified; however, IL-23 promotes the production of IL-17 and a strong correlation between IL-15 and IL-17 levels in synovial fluid has been observed. IL-17 is a potent inducer of various cytokines such as tumor necrosis factor (TNF)-alpha, IL-1, and receptor activator of NF-kappaB ligand (RANKL). Additive or even synergistic effects with IL-1 and TNF-alpha in inducing cytokine expression and joint damage have been shown in vitro and in vivo. This review describes the role of IL-17 in the pathogenesis of destructive arthritis with a major focus on studies in vivo in arthritis models. From these studies in vivo it can be concluded that IL-17 becomes significant when T cells are a major element of the arthritis process. Moreover, IL-17 has the capacity to induce joint destruction in an IL-1-independent manner and can bypass TNF-dependent arthritis. Anti-IL-17 cytokine therapy is of interest as an additional new anti-rheumatic strategy for RA, in particular in situations in which elevated IL-17 might attenuate the response to anti-TNF/anti-IL-1 therapy.
Cyber-physical security using system-level PUFs (2011)

Cyber Physical Systems (CPS) is an emerging computing paradigm that is becoming prevalent in various technologies. Achieving a trustworthy CPS requires us to build mechanisms that ensure the integrity and authenticity of these systems. Fortunately with the new advancements in semi-conductor-based technologies, in particular Physical Unclonable Functions (PUFs), we have the potential to build secure couplings between cyber and physical substrates based on intrinsic physical material. In this paper, we share some thoughts on how to utilize the PUF technology for security in CPS. Based on a composition approach, we illustrate the benefits of combining multiple PUF elements, with some inherently bias factor, into one randomly secure and strong system-level PUF.
Cyclin B and E2F-1 expression in prostate carcinoma cells treated with the novel retinoid CD437 are regulated by the ubiquitin-mediated pathway. (2002)

E2F-1 and cyclin B are important regulators of the cell cycle, and their expressionand degradation are tightly regulated. Proteolysis of both molecules is mediated by the ubiquitin degradation pathway involving the activation of specific E3 ubiquitin ligases. Treatment of prostate carcinoma cells with the novel retinoid 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (CD437/AHPN) results in the enhanced expression of E2F-1 and rapid degradation of cyclin B in the absence of the modulation of mRNA levels; this is accompanied by the S phase arrest of the cells and subsequent apoptosis. The elevated level of E2F-1 is because of the enhanced stability of the molecule, as indicated by pulse-labeling studies, demonstrating a prolonged half-life. The enhanced E2F-1 stability is associated with the concomitant acetylation of E2F-1, the disassociation of E2F-1 from the E2F-1 E3 ligase p45(SKP2), and decreased E2F-1 ubiquitination, suggesting CD437 inhibition of E-3 E2F-1 ligase activity. Exposure of the cells to CD437 also results in the enhanced association of the cyclin B E3 ligase APC with cyclin B and the rapid proteolysis of cyclin B. The CD437-enhanced proteolysis of cyclin B is blocked in the presence of the ubiquitin proteolysis inhibitor N-acetyl-leu-leu-norleu-al. Thus, CD437 modulates the expression of E2F-1 and cyclin B through the simultaneous stimulation and inhibition of the cyclin B and E2F-1 E3 ligases, respectively.
Disrupted cardiac development but normal hematopoiesis in mice deficient in the second CXCL12/SDF-1 receptor, CXCR7 (2007)

Chemotactic cytokines (chemokines) attract immune cells, although their original evolutionary role may relate more closely with embryonic development. We noted differential expression of the chemokine receptor CXCR7 (RDC-1) on marginal zone B cells, a cell type associated with autoimmune diseases. We generated Cxcr7(-/-) mice but found that CXCR7 deficiency had little effect on B cell composition. However, most Cxcr7(-/-) mice died at birth with ventricular septal defects and semilunar heart valve malformation. Conditional deletion of Cxcr7 in endothelium, using Tie2-Cre transgenic mice, recapitulated this phenotype. Gene profiling of Cxcr7(-/-) heart valve leaflets revealed a defect in the expression of factors essential for valve formation, vessel protection, or endothelial cell growth and survival. We confirmed that the principal chemokine ligand for CXCR7 was CXCL12/SDF-1, which also binds CXCR4. CXCL12 did not induce signaling through CXCR7; however, CXCR7 formed functional heterodimers with CXCR4 and enhanced CXCL12-induced signaling. Our results reveal a specialized role for CXCR7 in endothelial biology and valve development and highlight the distinct developmental role of evolutionary conserved chemokine receptors such as CXCR7 and CXCR4.
Purification to apparent homogeneity of murine interleukin 1. (1981)

Interleukin 1 was purified to apparent homogeneity from the culture fluid of P388D1 cell line macrophages by a procedure involving ammonium sulfate fractionation, phenyl Sepharose and Ultrogel AcA54 chromatographies, and preparative isoelectrofocusing. The interleukin 1 was purified more than 300-fold to a specific activity of approximately 1 X 10(6) U/mg protein. The purified interleukin 1 exhibited microheterogeneity. Three charge species, which we have termed alpha, beta, gamma, were resolved by Tris-glycinate discontinuous polyacrylamide gel electrophoresis. The partial amino acid content of the alpha species of interleukin 1 was determined. On the basis of the purification data, it appears that interleukin 1 is biologically active within the 10(-11) to 10(-10) M concentration range. The success of the purification was due in part to the use of a superinduction protocol that resulted in the production of interleukin 1 at a rate of approximately 1 microgram/24 hr/4 X 10(6) P388D1 cells.
A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. (1989)

We describe the construction of six strains of Escherichia coli with different mutations at the same coding position in the lacZ gene, which specifies the active site glutamic acid residue at position 461 in beta'-galactosidase. Each strain is Lac- and reverts to Lac+ only by restoring the glutamic acid codon. The strains have been designed so that each reverts via one of the six base substitutions. The set of strains allows detection of each transition and transversion simply by monitoring the Lac- to Lac+ frequency, as demonstrated here with characterized mutagens and mutator alleles. These strains are useful for rapidly determining the mutagenic specificity of mutagens at a single site, for detecting low levels of stimulation of certain base substitutions, for monitoring specific base changes in response to various experimental conditions or strain backgrounds, and for isolating new mutator strains.
Photo‐aligned anisotropic optical thin films (2004)

Abstract— Photo‐alignment of anisotropic optical thin films enables realization of novel optical elements, which were not feasible up until now. Photo‐aligned anisotropic thin films can be applied to rigid or flexible substrates, which may be flat or curved. The optical performance of such films can be tailored to application‐specific requirements by introducing tilt profiles of the optical axis and/or generate patterned retarders with continuous or periodical in‐plane variation of the optical axis.
Phase-matched excitation of whispering-gallery-mode resonances by a fiber taper (1997)

We show that high-Q whispering-gallery modes in fused-silica microspheres can be efficiently excited by an optical fiber taper. By adjusting the taper diameter to match the ropagation constant of the mode in the taper with that of the resonant mode of interest, one can couple more than 90% of the light into the sphere. This represents a significant improvement in excitation efficiency compared with other methods and is, we believe, the most efficient excitation of a high- Q microcavity resonance by a monomode optical fiber yet demonstrated.
A Proliferation‐inducing Ligand (APRIL) is Expressed by Astrocytes and is Increased in Multiple Sclerosis (2006)

A proliferation-inducing ligand (APRIL) is a newly described member of the tumour necrosis factor (TNF) superfamily that was first identified as a factor favouring tumorigenesis. APRIL is also important for several immune functions, including B-cell survival. Multiple sclerosis (MS) is an inflammatory, demyelinating disease of the central nervous system (CNS) that is commonly diagnosed in early adulthood. Several TNF superfamily members have been identified in brains of patients with MS, although their exact function within the CNS is presently unknown. To investigate whether APRIL is expressed in the CNS, we studied APRIL protein expression by immunohistochemistry in MS patients and controls. Morphologically, APRIL-positive cells appeared to be astrocytes. A two-colour immunohistochemistry revealed that APRIL expression was cytoplasmic, granular and restricted to GFAP-positive cells. Conversely, HLA class II-positive microglial cells were negative for APRIL expression. APRIL-positive cells were fewer in brains of controls compared with those with MS. We further corroborated our findings by studying APRIL protein expression in several glioblastoma cell lines, and found APRIL to be expressed by most cell lines analysed. APRIL's binding partner syndecan-1 (CD138) was detected in brains of neither MS nor control patients. Furthermore, B cells were detectable in the brain of one of five patients with MS. We conclude that APRIL is expressed by reactive astrocytes in MS and may be of relevance in gliotic scar formation.
Effect of Subconjunctival Bevacizumab (Avastin) on Experimental Corneal Neovascularization in Guinea Pigs (2008)

Subconjunctival injection of bevacizumab decreases the extent of chemically induced corneal neovascularization in guinea pigs. The antineovascular effect of bevacizumab is higher if the injection is performed simultaneously with the chemical cauterization.
Preparation of Biodegradable Thermo-responsive Polyaspartamides with N-Isopropylamine Pendent Groups (I) (2006)

Novel amphiphilic, thermo-responsive polyaspartamides which showed both LCST (lower critical solution temperature), and sol-gel transition were prepared and characterized. The polyaspartamide derivatives were synthesized from polysuccinimide, the polycondensate of aspartic acid monomer, via successive nucleophilic ring-opening reaction by using dodecylamine and N-isopropylethylenediamine (NIPEDA). At the intermediate composition ranges, the dilute aqueous solution exhibited a thermally responsive phase separation due to the presence of LCST. The phase transition temperature was controllable by changing the content of pendent groups. In addition, a physical gelation, i.e. the sol-gel transition was observed from the concentrated solutions, which was elucidated by dynamic viscoelastic measurements. These novel injectable and thermo-responsive hydrogels have potential for various biomedical applications such as tissue engineering and current drug delivery system.
Sensitization of IL-2 Signaling through TLR-7 Enhances B Lymphoma Cell Immunogenicity (2006)

The innate ability of B lymphoma cells to escape control by tumor-reactive T cells must be overcome to develop effective immunotherapies for these diseases. Because signals from both the innate and adaptive immune systems direct the acquisition of strong immunogenicity by professional APCs, the effects of IL-2 and the TLR-7 agonist, S28690, on the immunogenic properties of chronic lymphocytic leukemia (CLL) B cells were studied. IL-2 with S28690 caused CLL cells to proliferate and increased their expression of B7-family members, production of TNF-alpha and IL-10, and levels of tyrosine-phosphorylated STAT-1 and STAT-3 proteins. S28690 increased CD25 expression on CLL cells and sensitized them to IL-2 signaling. However, IL-2 did not change TLR-7 expression or signaling in CLL cells. The ability to stimulate T cell proliferation required additional activation of protein kinase C, which inhibited tumor cell proliferation, "switched off" IL-10 production, and caused essentially all CLL cells (regardless of clinical stage) to acquire a CD83(high)CD80(high)CD86(high)CD54(high) surface phenotype marked by the activation of STAT-1 without STAT-3. These findings suggest that TLR-7 "licenses" human B cells to respond to cytokines of the adaptive immune system (such as IL-2) and provide a strategy to increase the immunogenicity of lymphoma cells for therapeutic purposes.
Smooth muscle dynamics and maximal expiratory flow in asthma (2005)

A computational model for maximal expiratory flow in constricted lungs is presented. The model was constructed by combining a previous computational model for maximal expiratory flow in normal lungs and a previous mathematical model for smooth muscle dynamics. Maximal expiratory flow-volume curves were computed for different levels of smooth muscle activation. The computed maximal expiratory flow-volume curves agree with data in the literature on flow in constricted nonasthmatic subjects. In the model, muscle force during expiration depends on the balance between the decrease in force that accompanies muscle shortening and the recovery of force that occurs during the time course of expiration, and the computed increase in residual volume (RV) depends on the magnitude of force recovery. The model was also used to calculate RV for a vital capacity maneuver with a slow rate of expiration, and RV was found to be further increased for this maneuver. We propose that the measurement of RV for a vital capacity maneuver with a slow rate of expiration would provide a more sensitive test of smooth muscle activation than the measurement of maximal expiratory flow.
Regulation of Clusterin Gene Expression by Transforming Growth Factor β (1997)

Transforming growth factor beta (TGFbeta) induces the expression of a wide variety of genes in many cell types. Our previous studies have shown that TGFbeta stimulates both clusterin mRNA and protein levels, and induces its accumulation in the nucleus of CCL64 cells. To further investigate the molecular mechanism of clusterin mRNA induction by TGFbeta, we created a 1.3-kilobase rat clusterin promoter/luciferase reporter construct. We demonstrate that TGFbeta enhances luciferase activity 2.5-6-fold in transient transfection assays of epithelial, endothelial, and fibroblast cell lines. Deletional analysis reveals that an AP-1-binding site (5'-TGAGTCA) in the minimal promoter region is necessary for initiating transactivation by TGFbeta. A single T to G base mutation in the AP-1 site (5'-TGAGGCA) abolishes TGFbeta-induced clusterin promoter transactivation. In transcription factor decoy experiments, 23-mer oligonucleotides of wild type AP-1 reduce TGFbeta induction of clusterin mRNA levels and promoter transactivation, while an oligonucleotide containing the mutated AP-1 site has no effect. Two specific protein kinase C inhibitors, GF109203X and calphostin C, block TGFbeta-induced clusterin mRNA levels and promoter transactivation. Together these results indicate that TGFbeta regulates clusterin gene expression through an AP-1 site and its cognate transcription factor AP-1, and requires the involvement of protein kinase C.
Exploiting Intrinsic Variability of Filamentary Resistive Memory for Extreme Learning Machine Architectures (2015)

In this paper, we show for the first time how unavoidable device variability of emerging nonvolatile resistive memory devices can be exploited to design efficient low-power, low-footprint extreme learning machine (ELM) architectures. In particular, we utilize the uncontrollable off-state resistance (Roff/HRS) spreads, of nanoscale filamentary-resistive memory devices, to realize random input weights and random hidden neuron biases; a characteristic requirement of ELM. We propose a novel RRAM-ELM architecture. To validate our approach, experimental data from different filamentary-resistive switching devices (CBRAM, OXRAM) are used for full-network simulations. Learning capability of our RRAM-ELM architecture is illustrated with the help of two real-world applications: 1) diabetes diagnosis test (classification) and 2) SinC curve fitting (regression).
Nomenclature of the Human Immunoglobulin Kappa (IGK) Genes (2001)

'Nomenclature of the Human Immunoglobulin Kappa (IGK) Genes', the 17th report of the 'IMGT Locus in Focus' section, provides the first complete list of all the human IGK genes. In the most frequent haplotypes, the human IGK locus spans 1,820 kb and the IGKV genes are organized in two clusters separated by 800 kb. In those haplotypes where both the proximal and distal IGKV clusters are present, the total number of human IGK genes per haploid genome is 82 (107 genes if the orphons are included) of which 37-41 are functional. If only the proximal IGKV cluster is present, which is found in a rare haplotype, the total number of genes per haploid genome is 46 (71 genes if the orphons are included) of which 23-25 genes are functional. IMGT/HUGO gene names and definitions of the human IGK genes on chromosome 2p11.2, and IGK orphons on chromosomes 1, 2, 15, and 22 are provided with the gene functionality and the number of alleles according to the rules of the IMGT Scientific chart, with the accession numbers of the IMGT reference sequences, and the accession ID of the Genome Database GDB and NCBI LocusLink databases in which all the IMGT human IGK genes have been entered. The tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr:8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.
Characterization of Recombinant Shrimp Allergen Pen a 1 (Tropomyosin) (1997)

Tropomyosin (Pen a 1) from brown shrimp, Penaeus aztecus, has been identified as the only major shrimp allergen. Since beef, pork and chicken are other tropomyosin-containing foods that are not very allergenic, tropomyosins can serve to investigate the contribution of the structural properties of a protein to its allergenicity. The aim of this study was to determine the primary structure of Pen a 1 and to identify IgE-binding epitopes. The screening of a unidirectional expression cDNA library from shrimp tail muscle with the Pen-a-1-specific monoclonal antibody 4.9.5 resulted in 4 positive Escherichia coli clones. Immunoblot analysis with human sera from shrimp-allergic subjects demonstrated IgE binding of all 4 recombinant shrimp proteins. Three of 4 expressed recombinant proteins have a molecular weight of approximately 36 kD, consistent with the molecular weight of natural Pen a 1. The DNA sequence analysis identified these recombinant shrimp proteins as tropomyosin and could be aligned with the sequence of greasyback shrimp (Metapenaeus ensis) tropomyosin (Met e 1). In order to characterize contiguous IgE-binding epitopes of Pen a 1, a peptide library (Novagen epitope mapping system) expressing 10-30 amino-acid-residue-long recombinant Pen a 1 peptides was constructed and screened with human IgE. Four recombinant, IgE-reactive Pen a 1 peptides were selected and sequenced. They show various degrees of sequence identity with tropomyosins of other arthropods, such as fruitfly and house dust mite, helminths and vertebrates.
Nucleoside Analogues as Chemotherapeutic Agents: A Review (1992)

Abstract The importance of nucleoside analogues in chemotherapy and in other potential therapeutic approaches as immunomodulation or regulation of gene expression, is reviewed.