gebhart/patrepeval huggingface dataset:
Bacterial silver resistance: molecular biology and uses and misuses of silver compounds (2003)

Resistance to silver compounds as determined by bacterial plasmids and genes has been defined by molecular genetics. Silver resistance conferred by the Salmonella plasmid pMGH100 involves nine genes in three transcription units. A sensor/responder (SilRS) two-component transcriptional regulatory system governs synthesis of a periplasmic Ag(I)-binding protein (SilE) and two efflux pumps (a P-type ATPase (SilP) plus a three-protein chemiosmotic RND Ag(I)/H+ exchange system (SilCBA)). The same genes were identified on five of 19 additional IncH incompatibility class plasmids but thus far not on other plasmids. Of 70 random enteric isolates from a local hospital, isolates from catheters and other Ag-exposed sites, and total genomes of enteric bacteria, 10 have recognizable sil genes. The centrally located six genes are found and functional in the chromosome of Escherichia coli K-12, and also occur on the genome of E. coli O157:H7. The use of molecular epidemiological tools will establish the range and diversity of such resistance systems in clinical and non-clinical sources. Silver compounds are used widely as effective antimicrobial agents to combat pathogens (bacteria, viruses and eukaryotic microorganisms) in the clinic and for public health hygiene. Silver cations (Ag+) are microcidal at low concentrations and used to treat burns, wounds and ulcers. Ag is used to coat catheters to retard microbial biofilm development. Ag is used in hygiene products including face creams, "alternative medicine" health supplements, supermarket products for washing vegetables, and water filtration cartridges. Ag is generally without adverse effects for humans, and argyria (irreversible discoloration of the skin resulting from subepithelial silver deposits) is rare and mostly of cosmetic concern.
Functional analysis of pAL5000, a plasmid from Mycobacterium fortuitum: construction of a "mini" mycobacterium-Escherichia coli shuttle vector (1990)

Functional domains of pAL5000 were determined by gene disruption and deletion analysis. Of the five plasmid open reading frames (ORFs), ORF1 to ORF5, and a putative origin of replication previously identified (J. Rauzier, J. Moniz-Pereira, and B. Gicquel-Sanzey, Gene 71:315-321), two of the ORFs (ORF3 and ORF4) were deemed dispensable for plasmid replication. A "mini" mycobacterium-Escherichia coli shuttle plasmid applicable for general recombinant DNA studies in mycobacteria was constructed by using the gene for Kanr (Tn903) as a selective marker. Heterologous expression of the gene for Kanr was confirmed by Western blotting (immunoblotting) analysis.
Increased production of reactive oxygen species in hyperglycemic conditions requires dynamic change of mitochondrial morphology (2006)

Increased production of mitochondrial reactive oxygen species (ROS) by hyperglycemia is recognized as a major cause of the clinical complications associated with diabetes and obesity [Brownlee, M. (2001) Nature 414, 813-820]. We observed that dynamic changes in mitochondrial morphology are associated with high glucose-induced overproduction of ROS. Mitochondria undergo rapid fragmentation with a concomitant increase in ROS formation after exposure to high glucose concentrations. Neither ROS increase nor mitochondrial fragmentation was observed after incubation of cells with the nonmetabolizable stereoisomer L-glucose. However, inhibition of mitochondrial pyruvate uptake that blocked ROS increase did not prevent mitochondrial fragmentation in high glucose conditions. Importantly, we found that mitochondrial fragmentation mediated by the fission process is a necessary component for high glucose-induced respiration increase and ROS overproduction. Extended exposure to high glucose conditions, which may mimic untreated diabetic conditions, provoked a periodic and prolonged increase in ROS production concomitant with mitochondrial morphology change. Inhibition of mitochondrial fission prevented periodic fluctuation of ROS production during high glucose exposure. These results indicate that the dynamic change of mitochondrial morphology in high glucose conditions contributes to ROS overproduction and that mitochondrial fission/fusion machinery can be a previously unrecognized target to control acute and chronic production of ROS in hyperglycemia-associated disorders.
Delivering optical power to subcutaneous implanted devices (2011)

In this paper, a new, easy-to-implement, and MRI-compatible approach for delivering power to implantable devices is presented. The idea is to harvest the energy of light within the therapeutic window wavelengths, where the optical absorption is small, by using subcutaneous photovoltaic (PV) cells. Depending on the application, this energy can then be used to directly drive the embedded electronics of an implanted device or recharge its battery. To show the feasibility of this system, a CMOS chip based on this concept has been implemented and tested. The experimental results demonstrate that μW's of power in ambient light conditions can be harvested using mm(2)-size PV cells. This amount of power is sufficient to address the needs of many low-power applications.
Influence of Oxygen on Proline Utilization During the Wine Fermentation (1987)

In order to overcome sluggish or stuck fermentations, it may be necessary to utilize oxygen and yeast-utilizable nitrogen sources found in some yeast foods. Government regulations in the US preclude the use of large amounts of yeast foods — even those derived from yeast or proteins often employed as food ingredients. The present work describes the conditions under which proline, an amino acid naturally present in high concentrations in musts, can be utilized fully as a source of nitrogen. Oxygen is required for proline degradation; it is also a requirement to ensure sufficient yeast growth and to avoid sluggish fermentations.
Linear Plasmids of the Bacterium Borrelia burgdorferi Have Covalently Closed Ends (1987)

The genetics of spirochetes, a division of eubacteria, has been little studied. Double-stranded linear plasmids were found in Borrelia burgdorferi, the agent of Lyme disease. A 49-kilobase linear plasmid contained the ospA and ospB genes, which encode the major outer membrane proteins of strain B31. Molecules of the 49-kilobase plasmid rapidly reannealed after alkaline denaturation; rapid renaturation was prevented if the 49-kilobase plasmids were first treated with S1 nuclease. When denatured plasmid molecules were examined directly, single-stranded circles of approximately 100-kilobase circumference were seen. These studies provide direct visual evidence that the linear plasmids have covalently closed ends. This form of DNA occurs in some animal viruses, but it has not heretofore been described in prokaryotic organisms.
Demonstration of vacuum field emission from a self-assembling biomolecular microstructure composite (1992)

We report the first demonstration of vacuum field emission from an electron source fabricated from self-assembling biomolecular composite microstructures. Diacetylenic lipid DC8,9PC is used to form hollow, 0.5 μm diam, ≳50 μm long, tubelike structures that are subsequently plated with metal and formed into an aligned composite in an epoxy matrix. The composite material is thin-sectioned across the axis of alignment and then etched to expose the plated tubules. The sharp edges of the exposed metal tubules produce a very large local electric field enhancement, allowing for the vacuum field emission of significant current densities at relatively low applied macroscopic fields (≤60–80 kV/cm).
Commercialization of Honeywell's VCSEL technology: further developments (2001)

Each year, more VCSEL technologies make the transition from research curiosities to commercially available products. In this paper we describe several such technologies at Honeywell, each at a different stage of that transition. Oxide-confined devices are already past the transition stage. We describe the generally excellent reliability of oxide-confined devices already in high-volume production, and compare it to results of the most recent-and possibly last-long-term reliability study of proton-implanted VCSELs. We report on detailed package-VCSEL interaction modeling, which is being used to improve performance and extend the life of common form-factor packages. We also note Honeywell's progress toward commercialization of VCSELs and allied products at wavelengths other than 850 nm.
c-Jun N-terminal kinase has a key role in Alzheimer disease synaptic dysfunction in vivo (2014)

Altered synaptic function is considered one of the first features of Alzheimer disease (AD). Currently, no treatment is available to prevent the dysfunction of excitatory synapses in AD. Identification of the key modulators of synaptopathy is of particular significance in the treatment of AD. We here characterized the pathways leading to synaptopathy in TgCRND8 mice and showed that c-Jun N-terminal kinase (JNK) is activated at the spine prior to the onset of cognitive impairment. The specific inhibition of JNK, with its specific inhibiting peptide D-JNKI1, prevented synaptic dysfunction in TgCRND8 mice. D-JNKI1 avoided both the loss of postsynaptic proteins and glutamate receptors from the postsynaptic density and the reduction in size of excitatory synapses, reverting their dysfunction. This set of data reveals that JNK is a key signaling pathway in AD synaptic injury and that its specific inhibition offers an innovative therapeutic strategy to prevent spine degeneration in AD.
Purification and characterization of M3 protein expressed on the surface of group A streptococcal type 3 strain C203 (1995)

Monoclonal antibodies (mAbs) have been produced by immunizing BALB/C mice with whole M+ bacteria in incomplete Freund adjuvant and the resulting mAbs for M3 protein have been selected by an indirect immuno-fluorescent technique using formaldehyde-fixed M+ and M- bacteria. Four mAbs reacted with a 65 kDa protein in an extract obtained from the cell wall of M+ bacteria after treatment with N-acetyl muramidase and lysozyme. The purified 65 kDa protein neutralized the phagocytic activity of rabbit anti-M3 antibody. The N-terminal amino acid sequence of the 65 kDa protein was identical with that of protein generated by the M3 gene which has been previously cloned and sequenced. The evidence indicates that the 65 kDa protein is M3 protein. The M3 protein bound not only human fibrinogen but also human serum albumin (HSA). When the M3 protein was purified by gel-filtration and ion-exchange chromatography in the absence of phenylmethyl sulfonyl fluoride (PMSF), four fragments (35 kDa, 32 kDa, 30 kDa, and 25 kDa) in addition to the intact molecule appeared. N-terminal amino acid sequence analysis showed that 35 kDa and 25 kDa fragments were ANAAD and DARSV, respectively, being identical at positions 1-5 and 198-202 to the M3 gene derived protein. Therefore, the 35 kDa and 25 kDa fragments, which were presumed to be cleavage products, may be derived from the C-terminal part and N-terminal part of the intact molecule, respectively. When the effect of purified M3 protein in the bactericidal activity of normal human blood in the presence of M- bacteria was investigated, the M3 protein was responsible for the organism's resistance to attack by phagocytic cells.
Chemical Modification of Surface Active Poly(ethylene oxide)−Poly(propylene oxide) Triblock Copolymers (1996)

A general route has been developed to chemically modify a series of poly(ethylene oxide)-poly(propylene oxide) triblock copolymers with molecular weights from 6500 to 14600. It is initiated by the introduction of p-nitrophenyl groups; such nitrophenyl conjugated copolymers are stable in an organic milieu and in a dry state but are seen to react easily with amino-containing molecules including small peptides. Among them, introduction of 2-pyridyl disulfide groups after coupling with 2-(2-pyridyldithio)ethylamine enables the selective attachment of thiol-containing molecules. The released thiopyridone in such thiol-disulfide reactions can be used to quantify the content of 2-pyridyl disulfide groups. In addition, a new type of modified copolymers was developed for the radioisotope (125I) labeling purpose that consists of a reaction of nitrophenyl conjugated copolymers with hydrazine and a subsequent coupling with N-succinimidyl 3-(4-hydroxyphenyl)propionate (Bolton-Hunter reagent). Adsorption studies of 125I-labeled and 2-pyridyl disulfide conjugated copolymers on polystyrene particles are consistent with previous determinations of surface coverage using other technologies, in turn indicating that this new chemical modification does not alter their surfactant properties on hydrophobic solid phase. The coating of common hydrophobic surfaces with 2-pyridyl disulfide conjugated copolymers has been demonstrated as a general and robust immobilization method to generate a high-sensitivity bioactive surface with low nonspecific binding. The optimal space between immobilized ligands can also be controlled by incubating the solid phase with solutions containing mixtures with different ratios of unmodified and modified copolymers.
Harnessing Regulatory T Cells for the Therapy of Lupus and Other Autoimmune Diseases (2009)

Regulatory T cells (Tregs) maintain immunological homeostasis and prevent autoimmunity. The depletion or functional alteration of Tregs may lead to the development of autoimmune diseases. Tregs consist of different subpopulations of cells, of which CD4(+)CD25(+)Foxp3(+) cells are the most well characterized. However, CD8 Tregs also constitute a major cell population that has been shown to play an important role in autoimmune diseases. This review will discuss the role of Tregs in autoimmune diseases in general and specifically in systemic lupus erythematosus (SLE). SLE is a multisystem autoimmune disease characterized by the production of autoantibodies against nuclear components and by the deposition of immune complexes in the kidneys as well as in other organs. Abnormalities in Tregs were reported in SLE patients and in animal models of the disease. Current treatment of SLE is based on immunosuppressive drugs that are nonspecific and may cause adverse effects. Therefore, the development of novel, specific, side effect-free therapeutic means that will induce functional Tregs is a most desirable goal. Our group and others have designed and utilized tolerogenic peptides that ameliorate SLE manifestations in murine models. Here, we demonstrate the role of CD4 and CD8 Tregs, as well as the interaction between the two subsets of cells and the mechanism of action of the tolerogenic peptides. We also discuss their therapeutic potential for the treatment of SLE.
Functional Comparison of Engineered T Cells Carrying a Native TCR versus TCR-like Antibody–Based Chimeric Antigen Receptors Indicates Affinity/Avidity Thresholds (2014)

Adoptive transfer of Ag-specific T lymphocytes is an attractive form of immunotherapy for cancers. However, acquiring sufficient numbers of host-derived tumor-specific T lymphocytes by selection and expansion is challenging, as these cells may be rare or anergic. Using engineered T cells can overcome this difficulty. Such engineered cells can be generated using a chimeric Ag receptor based on common formats composed from Ag-recognition elements such as αβ-TCR genes with the desired specificity, or Ab variable domain fragments fused with T cell-signaling moieties. Combining these recognition elements are Abs that recognize peptide-MHC. Such TCR-like Abs mimic the fine specificity of TCRs and exhibit both the binding properties and kinetics of high-affinity Abs. In this study, we compared the functional properties of engineered T cells expressing a native low affinity αβ-TCR chains or high affinity TCR-like Ab-based CAR targeting the same specificity. We isolated high-affinity TCR-like Abs recognizing HLA-A2-WT1Db126 complexes and constructed CAR that was transduced into T cells. Comparative analysis revealed major differences in function and specificity of such CAR-T cells or native TCR toward the same antigenic complex. Whereas the native low-affinity αβ-TCR maintained potent cytotoxic activity and specificity, the high-affinity TCR-like Ab CAR exhibited reduced activity and loss of specificity. These results suggest an upper affinity threshold for TCR-based recognition to mediate effective functional outcomes of engineered T cells. The rational design of TCRs and TCR-based constructs may need to be optimized up to a given affinity threshold to achieve optimal T cell function.
Drilling and completing a horizontal well in fractured carbonate (1989)

Proco, Inc., recently completed a horizontal oil well in the Austin chalk, a vertically fractured carbonate reservoir, in Pearsall field, Texas. The horizontal technique was used to tap multiple major fracture systems in the chalk matrix indicated by seismic and, hence, substantially increase productivity over a vertical hole which may or may not intersect a fracture system. This article discusses drilling, completion and production procedures used on the well and problems encountered in all three phases. Lessons learned are reviewed, and recommendations are made for improving future operations.
Repressor- and Activator-Type Ethylene Response Factors Functioning in Jasmonate Signaling and Disease Resistance Identified via a Genome-Wide Screen of Arabidopsis Transcription Factor Gene Expression (2005)

Abstract To identify transcription factors (TFs) involved in jasmonate (JA) signaling and plant defense, we screened 1,534 Arabidopsis (Arabidopsis thaliana) TFs by real-time quantitative reverse transcription-PCR for their altered transcript at 6 h following either methyl JA treatment or inoculation with the incompatible pathogen Alternaria brassicicola. We identified 134 TFs that showed a significant change in expression, including many APETALA2/ethylene response factor (AP2/ERF), MYB, WRKY, and NAC TF genes with unknown functions. Twenty TF genes were induced by both the pathogen and methyl JA and these included 10 members of the AP2/ERF TF family, primarily from the B1a and B3 subclusters. Functional analysis of the B1a TF AtERF4 revealed that AtERF4 acts as a novel negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. In contrast, functional analysis of the B3 TF AtERF2 showed that AtERF2 is a positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. Our results suggest that plants coordinately express multiple repressor- and activator-type AP2/ERFs during pathogen challenge to modulate defense gene expression and disease resistance.
Identification and characterization of hematopoietic stem cells from the yolk sac of the early mouse embryo. (1993)

The yolk sac is the first site of hematopoiesis in the mammalian embryo. However, little is known about the initial stem cells in the yolk sac. We have isolated hematopoietic stem cells from early mouse embryonic yolk sac by using a sequential protocol of nonadherence to plastic, density gradient centrifugation, immunocytoadherence, and cell sorting. Isolated, nonadherent, density &lt; 1.077-g/cm3, surface antigen AA4.1+, wheat germ agglutinin bright (WGAbright) cells give rise to multiple lineages, including T cells, B cells, and myeloid cells, as detected by using fetal thymus organ culture, S17 stromal feeder layers, or methylcellulose culture colony-forming cells, respectively. AA4.1+, WGAbright cells expressed high levels of heat-stable antigen (HSA) and CD45 (Ly-5) but did not significantly express major histocompatibility complex antigens, CD44, or Sca-1. Peak stem cell concentration is reached by day 11, before stem cells can be found in the liver, omentum, or thymus. In vivo long-term reconstitution of lethally irradiated mice was effected by as few as 720 AA4.1+, WGAbright yolk sac cells, but it required addition of a subset of bone marrow cells capable of providing immediate (short-term) radiation protection. Yolk sac donor-derived T cells, B cells, and macrophages were readily identified 6 months after transfer of yolk sac-derived stem cells. We suggest that, because of their cell surface phenotype as well as their capacity to differentiate in vitro and in vivo, the cells isolated from the mouse embryonic yolk sac may include the most primitive hematopoietic pluripotential stem cells yet identified.
Activation of anti-hepatitis C virus responses via Toll-like receptor 7 (2006)

IFN-alpha is used to suppress the replication of hepatitis C virus (HCV) in chronically infected patients with partial success. Here we present evidence showing that a ligand of Toll-like receptor 7 (TLR7) can induce anti-HCV immunity not only by IFN induction, but also through an IFN-independent mechanism. Human hepatocyte line Huh-7 carrying an HCV replicon expressed TLR7, and activation of the receptor induced several antiviral genes including IFN regulatory factor-7. Inhibitors of the enzyme inosine monophosphate dehydrogenase augmented both IFN-dependent and -independent antiviral effect. Prolonged exposure of Huh-7 cells to a TLR7 ligand [SM360320 (9-benzyl-8-hydroxy-2-(2-methoxyethoxy)adenine)], alone or in combination with an inosine monophosphate dehydrogenase inhibitor, reduced HCV levels dose dependently. Immunohistochemical analysis of livers shows that TLR7 is expressed in hepatocytes of normal or HCV-infected people. Because TLR7 agonists can impede HCV infection both via type I IFN and independently of IFN, they may be considered as an alternative treatment of chronic HCV infection, especially in IFN-alpha-resistant patients.
Sequence-Controlled Polymers (2013)

Sequence-controlled polymers are macromolecules in which monomer units of different chemical nature are arranged in an ordered fashion. The most prominent examples are biological and have been studied and used primarily by molecular biologists and biochemists. However, recent progress in protein- and DNA-based nanotechnologies has shown the relevance of sequence-controlled polymers to nonbiological applications, including data storage, nanoelectronics, and catalysis. In addition, synthetic polymer chemistry has provided interesting routes for preparing nonnatural sequence-controlled polymers. Although these synthetic macromolecules do not yet compare in functional scope with their natural counterparts, they open up opportunities for controlling the structure, self-assembly, and macroscopic properties of polymer materials.
A robust system for natural spoken dialogue (1996)

This paper describes a system that leads us to believe in the feasibility of constructing natural spoken dialogue systems in task-oriented domains. It specifically addresses the issue of robust interpretation of speech in the presence of recognition errors. Robustness is achieved by a combination of statistical error post-correction, syntactically- and semantically-driven robust parsing, and extensive use of the dialogue context. We present an evaluation of the system using time-to-completion and the quality of the final solution that suggests that most native speakers of English can use the system successfully with virtually no training.