gebhart/patrepeval huggingface dataset:
Proteomic analysis of anti‐Francisella tularensis LVS antibody response in murine model of tularemia (2005)

Francisella tularensis live vaccine strain infection of mice has been established as an experimental model of tularemia that is suitable for studies of immune mechanisms against the intracellular pathogen. In this study, the model was used to explore immunogenic repertoire of F. tularensis with the aim of identifying new molecules able to activate the host immune system, potential bacterial markers with vaccine, and diagnostic applications. Immunoproteomic approach based on the combination of two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry was applied. Globally, 36 different proteins were identified, which strongly reacted with sera from experimentally infected mice, including several putative virulence markers of intracellular pathogens as nucleoside diphosphate kinase, isocitrate dehydrogenase, RNA-binding protein Hfq, and molecular chaperone ClpB. Of them, 27 proteins are described for the first time as immunorelevant Francisella proteins. When comparing murine immunoproteome of F. tularensis with our previous data from human patients, 25 of the total of 50 identified murine sera immunoreactive spots were recognized by human sera collected from patients suffering from tularemia, as well. Immune sera from two Lps gene congenic strains of mice, C3H/HeN (Lpsn) and C3H/HeJ (Lpsd), represented murine immunoproteome in this study. The spectrum of immunoreactive spots detected by two-dimensional immunoblotting varied throughout the course of infection depending on murine strain. Nevertheless, the antibody patterns of the two strains showed significant homogeneity in being directed against almost identical subset of antigens.
Involvement of CRAF1, a relative of TRAF, in CD40 signaling (1995)

CD40 is a receptor on the surface of B lymphocytes, the activation of which leads to B cell survival, growth, and differentiation. A yeast two-hybrid screen identified a gene, CRAF1, encoding a protein that interacts directly with the CD40 cytoplasmic tail through a region of similarity to the tumor necrosis factor-alpha (TNF-alpha) receptor-associated factors. Overexpression of a truncated CRAF1 gene inhibited CD40-mediated up-regulation of CD23. A region of CRAF1 was similar to the TNF-alpha receptor-associated factors TRAF1 and TRAF2 and so defined a shared TRAF-C domain that was necessary and sufficient for CD40 binding and homodimerization. The CRAF1 sequence also predicted a long amphipathic helix, a pattern of five zinc fingers, and a zinc ring finger. It is likely that other members of the TNF receptor superfamily use CRAF-related proteins in their signal transduction processes.
Decreased Glutamate Receptor 2 Expression and Enhanced Epileptogenesis in Immature Rat Hippocampus after Perinatal Hypoxia-Induced Seizures (2001)

Hypoxic encephalopathy is the most common cause of neonatal seizures and can lead to chronic epilepsy. In rats at postnatal days 10-12 (P10-12), global hypoxia induces spontaneous seizures and chronically decreases seizure threshold, thus mimicking clinical aspects of neonatal hypoxia. We have shown previously that the acute and chronic epileptogenic effects of hypoxia are age-dependent and require AMPA receptor activation. In this study, we aimed to determine whether hypoxia-induced seizures and epileptogenesis are associated with maturational and seizure-induced changes in AMPA receptor composition and function. Northern and Western blots indicated that glutamate receptor 2 (GluR2) mRNA and protein expression were significantly lower in neocortex and hippocampus at P10-12 compared with adult. After hypoxia-induced seizures at P10, GluR2 mRNA was significantly decreased within 48 hr, and GluR2 protein was significantly decreased within 96 hr. AMPA-induced Co(2+) uptake by neurons in hippocampal slices indicated higher expression of Ca(2+)-permeable AMPA receptors in immature pyramidal neurons compared with adult. In slices obtained 96 hr after hypoxia-induced seizures, AMPA-induced Co(2+) uptake was significantly increased compared with age-matched controls, and field recordings revealed increased tetanus-induced afterdischarges that could be kindled in the absence of NMDA receptor activation. In situ end labeling showed no acute or delayed cell death after hypoxia-induced seizures. Our results indicate that susceptibility to hypoxia-induced seizures occurs during a developmental stage in which the expression of Ca(2+)-permeable AMPA receptors is relatively high. Furthermore, perinatal hypoxia-induced seizures induce increased expression of Ca(2+)-permeable AMPA receptors and an increased capacity for AMPA receptor-mediated epileptogenesis without inducing cell death.
Accessing Deep Reservoirs by Drilling Severely Depleted Formations (2003)

Abstract In many maturing prospect around the world, operators are facing the challenge of having to drill through highly pressure-depleted formations in order to access lower-lying hydrocarbon-bearing zones. New technologies such as expandable casing are now becoming available to allow for extensions to conventional well designs in order to deal with depletion. However, before one can case off depleted formations, one first has to successfully drill them. This paper highlights key aspects in the planning and execution of the Ursa A-11 well, which was drilled through a 5500 psi depleted sand to a deeper horizon. Drilling complications included risks of excessive mud loss, internal blowout and differential sticking on the depleted sand. Moreover, fracturing of the depleted sand carried the risk of jeopardizing production at a nearby horizontal well. Key factors in the successful drilling of the Ursa A-11 well included special drilling fluid design, rock mechanics study, pro-active use of borehole strengthening technology, integration of supplier and operator expertise, and excellent communication between all parties involved.
Separation and characterization of the neoplastic and stromal elements of the R3230AC mammary adenocarcinoma. (1981)

The purification of the various types of cells in solid tumors is necessary for study of their biochemical and immunological functions. The R3230AC adenocarcinoma contains both a variety of stromal cells and well-differentiated neoplastic cells that possess many of the biosynthetic capabilities of normal rat mammary cells. Suspensions of cells from tumors weighing less than 1.2 g consisted of 70.4 +/- 7.2% (S.D.) malignant cells by morphology, 6.8 +/- 3.0% lymphocytes, 6.3 +/- 3.2% macrophages, 15.2 +/- 5.2% red blood cells, 0.8 +/- 0.5% granulocytes, and 0.5 +/- 0.6% unidentified cells. Sedimentation of the cells from the R3230AC tumor in a previously described isokinetic gradient resulted in a 5- to 6-fold purification of lymphocytes and macrophages. The modal fraction of malignant cells contained 95.3 +/- 2.9% malignant cells. Detection of alpha-lactalbumin by the direct peroxidase conjugate technique gave vacuolar staining of malignant cells, in contrast to the indirect and peroxidase-antiperoxidase techniques which stained ducts from normal lactating mammary gland and a wide variety of cells without vacuoles in the tumor. The best fixative for frozen sections, paraffin-embedded tissue, and cell suspensions was 50% ethanol-50% acetone. The suspensions of tumor cells contained 14.4 +/- 9.4% cells with histochemically demonstrable alpha-lactalbumin. Squamous metaplasia was commonly observed in tumors than lactating rats.
The Antidepressant -like Effects of Delta-Opioid Receptor Agonists (2006)

Activation of the delta-opioid receptor (DOR) system produces an interesting behavioral profile distinct from that of other opioids. Unlike mu- and kappa-opioid agonists, delta-opioid agonists alone have limited pain-relieving qualities as measured in morphine-sensitive antinociceptive assays. Recent evidence, however, suggests that the DOR system may play a role in regulating mood and emotional states. For example, DOR activation stimulates robust antidepressant-like effects in preclinical assays, suggesting that these compounds may have therapeutic potential for treating human depression. This review discusses the role of the DORs in depression and the antidepressant-like effects of delta-opioid agonists as well as their limitations.
Using time-aware memory sensing to address resistance drift issue in multi-level phase change memory (2010)

Because of its great scalability potential and support of multi-level per cell storage, phase change memory has become a topic of great current interest. However, recent studies show that structural relaxation effect makes the resistance of phase change material drift over the time, which can severely degrade multi-level phase change memory storage reliability. This paper studies the potential of using a time-aware memory sensing strategy to address this challenge. The basic idea is to keep track of memory content lifetime and, when memory is being read, accordingly adjust the memory sensing configuration to minimize the negative impact of time-dependent resistance drift on memory storage reliability. Because multi-level phase change memory may demand the use of powerful error correction code (ECC) whose decoding can request either hard-decision or soft-decision log-likelihood (LLR) memory sensing, we discuss both hard-decision and soft-decision time-aware memory sensing in details. Using BCH code and LDPC code as ECC for 4-level/cell and 8-level/cell phase change memory, we carry out simulations and the results show that, compared with time-independent static memory sensing, time-aware memory sensing can increase allowable memory content lifetime by several orders of magnitude.
Ferroelectric liquid crystal on silicon spatial light modulator designed for high yield and low cost fabrication: The fast bitplane SLM (1998)

Abstract Ferroelectric liquid crystal on silicon spatial light modulators are increasing in pixel density and speed. This paper outlines a 320 × 240 pixel device which has been designed for high speed operation, with flexibility of addressing and maximum fill factor in an unplanarised device. Also outlined in this paper are new fabrication techniques which aim to greatly increase the yield of working finished devices per foundry wafer. The techniques outlined here have been specifically designed with the aim of producing a manufacturable product.
Explanation and Implication for Configuration Problems (2001)

In this work we explore the problem of generating explanations for configuration problems using the constraint satisfaction (CSP) framework. In addition, we are concerned with deriving implications from user choices in order to guide selection of later choices. We show that the consistency methods used in connection with constraint processing can be used to generate inferences that support both functions. In this work we use the Ò-queens problem as a testbed. The system we have developed is interactive and allows the user to make selections and perform arc consistency on the current problem, as well as retracting selections, a typical arrangement with current configurator systems. At the same time it generates explanations for value deletions and current choices as well as implications in terms of the amount of future domain reduction that will follow certain choices and whether these choices will lead to solutions or non-solutions. Explanations take the form of trees which show the basis in terms of previous choices for current choices and deletions. Together, these methods suggest ways in which the process of solving combinatorial problems can be made more perspicuous and more interactive.
Kinetic interactions of tazobactam with beta-lactamases from all major structural classes (1993)

Tazobactam was shown to be a potent inhibitor of group 1, 2a, 2b, and 2b' beta-lactamases. Extended kinetic studies with class A and C serine beta-lactamases showed that the PC1, TEM-2, and P99 enzymes all were reversibly inhibited prior to inactivation of the enzymes. The CcrA metallo-beta-lactamase was less well inhibited, with a 50% inhibitory concentration at least 3 orders of magnitude less favorable than those for most serine beta-lactamases. The numbers of hydrolytic turnovers of tazobactam before inactivation were 2 for PC1, 125 for TEM-2, 50 for P99, and 4,000 for the CcrA enzyme. In spectral studies, transient intermediates were formed after reaction of tazobactam with the PC1, TEM-2, and CcrA beta-lactamases, corresponding to enzyme-associated intermediates responsible for hydrolysis of tazobactam. Chromophores absorbing at 270 nm (CcrA) and 288 nm (TEM-2 and PC1) were observed for these reaction intermediates. The P99 cephalosporinase formed a stable complex with a UV maximum at 295 nm. Incubation of tazobactam with all of the enzymes resulted in accumulation of a tazobactam reaction product with a short-wavelength absorbance. This product has characteristics similar to those of the major eucaryotic metabolite of tazobactam. Possible reaction mechanisms are presented to explain the findings. In conclusion, both serine-based and metallo-beta-lactamases were irreversibly inactivated by tazobactam following an initial transient inhibition phase.
Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies (2016)

A subset of bovine antibodies have an exceptionally long third heavy-chain complementarity determining region (CDR H3) that is highly variable in sequence and includes multiple cysteines. These long CDR H3s (up to 69 residues) fold into a long stalk atop which sits a knob domain that is located far from the antibody surface. Three new bovine Fab crystal structures have been determined to decipher the conserved and variable features of ultralong CDR H3s that lead to diversity in antigen recognition. Despite high sequence variability, the stalks adopt a conserved β-ribbon structure, while the knob regions share a conserved β-sheet that serves as a scaffold for two connecting loops of variable length and conformation, as well as one conserved disulfide. Variation in patterns and connectivity of the remaining disulfides contribute to the knob structural diversity. The unusual architecture of these ultralong bovine CDR H3s for generating diversity is unique in adaptive immune systems.
Implications for the use of amnion and chorion in podiatric medicine and surgery. (1985)

The purpose of this article is to show the possibility of using fetal membranes as a biologic dressing for some of the pedal ulcerations that podiatrists encounter. There are as many treatment modalities for lower extremity ulcerations as there are types of ulcers. Through the following case histories, the authors demonstrate various types of ulcerations treated with amnion and chorion and the results achieved. The clinical application of fetal membranes has been under study for many years. The authors' efforts support the use of amnion and chorion by the medical community in treating some lower extremity ulcers.
Dominant Alleles of the Basic Helix-Loop-Helix Transcription Factor ATR2 Activate Stress-Responsive Genes in Arabidopsis (2002)

Members of the R/B basic helix-loop-helix (bHLH) family of plant transcription factors are involved in a variety of growth and differentiation processes. We isolated a dominant mutation in an R/B-related bHLH transcription factor in the course of studying Arabidopsis tryptophan pathway regulation. This mutant, atr2D, displayed increased expression of several tryptophan genes as well as a subset of other stress-responsive genes. The atr2D mutation creates an aspartate to asparagine change at a position that is highly conserved in R/B factors. Substitutions of other residues with uncharged side chains at this position also conferred dominant phenotypes. Moreover, overexpression of mutant atr2D, but not wild-type ATR2, conferred pleiotropic effects, including reduced size, dark pigmentation, and sterility. Therefore, atr2D is likely to be an altered-function allele that identifies a key regulatory site in the R/B factor coding sequence. Double-mutant analysis with atr1D, an overexpression allele of the ATR1 Myb factor previously isolated in tryptophan regulation screens, showed that atr2D and atr1D have additive effects on tryptophan regulation and are likely to act through distinct mechanisms to activate tryptophan genes. The dominant atr mutations thus provide tools for altering tryptophan metabolism in plants.
Host‐Enhanced π–π Interaction for Water‐Soluble Supramolecular Polymerization (2011)

Host-enhanced π-π interaction based on anthracene derivatives and cucurbit[8]uril can be used as the driving force for constructing water-soluble supramolecular polymers. For this purpose, two anthracene moieties were encapsulated into one cucurbit[8]uril cavity, forming a ternary complex. After encapsulation in the host, the distance between the two anthracene moieties was shortened, and the π-π interaction between them was enhanced significantly. To realize supramolecular polymerization, a bifunctional monomer consisting of two anthracene moieties and a short linker in between was carefully designed. Cyclization was avoided in this way. Thus, host-enhanced π-π interaction can function as a new driving force for supramolecular polymerization.
Synergistic Toughening in Ternary Silica/Hollow Glass Spheres/Epoxy Nanocomposites (2014)

Herein, the fracture toughness of ternary epoxy systems containing nanosilica and hollow glass microspheres (HGMS) is investigated. The experimental measurements reveal synergistic fracture toughness in some hybrid compositions: The incorporation of 10 phr of HGMS and nanosilica alone modify the fracture toughness of epoxy by 39% and 91%, respectively. However, use of 10 phr hybrid modifier can enhance the fracture toughness of the resin up to 120%. Observations reveal different toughening mechanisms for the blends i.e., plastic deformation for silica nanoparticles and crack bifurcation for HGMS. Both of these toughening mechanisms additively contribute to the synergism in ternary epoxies.
PTEN Loss Compromises Homologous Recombination Repair in Astrocytes: Implications for Glioblastoma Therapy with Temozolomide or Poly(ADP-Ribose) Polymerase Inhibitors (2010)

Glioblastomas (GBM) are lethal brain tumors that are highly resistant to therapy. The only meaningful improvement in therapeutic response came from use of the S(N)1-type alkylating agent temozolomide in combination with ionizing radiation. However, no genetic markers that might predict a better response to DNA alkylating agents have been identified in GBMs, except for loss of O(6-)methylguanine-DNA methyltransferase via promoter methylation. In this study, using genetically defined primary murine astrocytes as well as human glioma lines, we show that loss of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) confers sensitivity to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), a functional analogue of temozolomide. We find that MNNG induces replication-associated DNA double-strand breaks (DSB), which are inefficiently repaired in PTEN-deficient astrocytes and trigger apoptosis. Mechanistically, this is because PTEN-null astrocytes are compromised in homologous recombination (HR), which is important for the repair of replication-associated DSBs. Our results suggest that reduced levels of Rad51 paralogs in PTEN-null astrocytes might underlie the HR deficiency of these cells. Importantly, the HR deficiency of PTEN-null cells renders them sensitive to the poly(ADP-ribose) polymerase (PARP) inhibitor ABT-888 due to synthetic lethality. In sum, our results tentatively suggest that patients with PTEN-null GBMs (about 36%) may especially benefit from treatment with DNA alkylating agents such as temozolomide. Significantly, our results also provide a rational basis for treating the subgroup of patients who are PTEN deficient with PARP inhibitors in addition to the current treatment regimen of radiation and temozolomide.
Extracellular Maltase from Aspergillus flavus (1981)

SUMMARYAn extracellular maltase activity was induced in Aspergillus flavus during growth in liquid medium containing maltose as the sole carbon source. The enzyme was also detected in the mycelial extracts of the organism. Synthesis of this enzyme was repressed by the addition of glucose or lactose to maltose-metabolizing cells, and was induced in glucose- or lactose-containing cultures by addition of maltose. The enzyme was partially purified by ammonium sulphate precipitation followed by gel permeation and ion exchange chromatography. The purified enzyme has an approximate molecular weight of 63,000 Daltons and exhibited maximum activity at pH 6.0 and 35 C. Ion exchange chromatography resolved the enzyme complex into two components with apparent Km's of 10 mM and 29 mM, respectively, for maltose.
<title>Photobleaching of photosensitizers applied for photodynamic therapy</title> (2000)

It is well known that photosensitizers used for PDT are liable to photobleaching. This phenomenon should be taken into account when developing the appropriate tactics of treatment. The present paper deals with detailed investigation of photobleaching of two photosensitizers: ALA induced protoporphyrin IX (PPIX) and sulphonated aluminum phthalocyanines. The fluorescence decay curves during light irradiation in vivo and in vitro have been obtained and analyzed. The mathematical model taking into account both first and second order photobleaching as well as spatial inhomogeneity of light distribution in tissue is presented. The experimental data for fluorescence decay of ALA induced PPIX during light irradiation are fitted to this mode. As opposed to PPIX the photobleaching behavior for sulphonated aluminum phthalocyanines is rather complicated to be fitted by proposed mathematical mode. The fluorescence outburning and residual fluorescence for sulphonated aluminum phthalocyanines have been observe.d It has been shown that fluorescence maximum correlates with blood oxygen saturation decrease induced by PDT effect.
A single-pixel wireless contact lens display (2011)

We present the design, construction and in vivo rabbit testing of a wirelessly powered contact lens display. The display consists of an antenna, a 500 × 500 µm2 silicon power harvesting and radio integrated circuit, metal interconnects, insulation layers and a 750 × 750 µm2 transparent sapphire chip containing a custom-designed micro-light emitting diode with peak emission at 475 nm, all integrated onto a contact lens. The display can be powered wirelessly from ∼1 m in free space and ∼2 cm in vivo on a rabbit. The display was tested on live, anesthetized rabbits with no observed adverse effect. In order to extend display capabilities, design and fabrication of micro-Fresnel lenses on a contact lens are presented to move toward a multipixel display that can be worn in the form of a contact lens. Contact lenses with integrated micro-Fresnel lenses were also tested on live rabbits and showed no adverse effect.