gebhart/patrepeval huggingface dataset:
Resistance to the Cytotoxic Effects of Tumor Necrosis Factor α Can Be Overcome by Inhibition of a FADD/Caspase-dependent Signaling Pathway (1999)

Tumor necrosis factor (TNF) alpha initiates the activation of a pro-apoptotic pathway involving the recruitment of the death domain containing protein FADD and the subsequent activation of specific proteases (caspases). Many cells are resistant, however, to the cytotoxic effects of TNFalpha due to the concurrent activation of pro-survival pathways involving the transcription factor NFkappaB and TRAF2. Here we show that the TNFalpha-activated FADD/caspase pathway can also exert an unexpected pro-survival effect. Inhibition of this pathway in NIH3T3 fibroblasts or U937 leukemic cells by peptide caspase inhibitors or expression of dominant-negative FADD leads to rapid death following treatment with TNFalpha, whereas control cells are TNFalpha-resistant. FADD/caspase-inhibited cells die by a non-apoptotic mechanism caused by increased production of reactive oxygen species which precedes loss of the mitochondrial membrane potential. Cytotoxicity can be prevented by preincubation with antioxidants including reduced glutathione or by expression of a dominant-negative Rac GTP-binding protein. These results indicate that caspase activation in response to TNFalpha has anti-necrotic as well as pro-apoptotic effects and extend our understanding of the biological role of these proteases.
Role of Nonesterified Fatty Acids in Necrotizing Pancreatitis: An In Vivo Experimental Study in Rats (2001)

This in vivo study does not confirm the hypothetical role of NEFA produced by pancreatic lipase in the necrotic process and its systemic complications, up to now mainly suggested on the basis of ex vivo experiments.
Convectively Driven Polymerase Chain Reaction Thermal Cycler (2004)

We have fabricated a low-cost disposable polymerase chain reaction thermal chamber that uses buoyancy forces to move the sample solution between the different temperatures necessary for amplification. Three-dimensional, unsteady finite element modeling and a simpler 1-D steady-state model are used together with digital particle image velocimetry data to characterize the flow within the device. Biological samples have been amplified using this novel thermal chamber. Time for amplification is less than 30 min. More importantly, an analysis of the energy consumption shows significant improvements over current technology.
Practical uses of botanicals in skin care. (2009)

Cosmeceuticals are the fastest growing sector of the cosmetic industry, and the future of antiaging cosmeceuticals in particular is very promising. Botanical extracts that support the health, texture, and integrity of the skin, hair, and nails are widely used in cosmetic formulations. They form the largest category of cosmeceutical additives found in the marketplace today due to the rising consumer interest and demand for natural products. Various plant extracts that formed the basis of medical treatments in ancient civilizations and many traditional cultures are still used today in cleansers, moisturizers, astringents, and many other skin care products. New botanical skin care treatments are emerging, presenting dermatologists and their patients the challenge of understanding the science behind these cosmeceuticals. Thus, dermatologists must have a working knowledge of these botanicals and keep up with how they evolve to provide optimal medical care and answer patient questions. The most popular botanicals commonly incorporated into skin care protocols are discussed.
Extending the computational reach of a noisy superconducting quantum processor (2018)

Quantum computation, a completely different paradigm of computing, benefits from theoretically proven speed-ups for certain problems and opens up the possibility of exactly studying the properties of quantum systems. Yet, because of the inherent fragile nature of the physical computing elements, qubits, achieving quantum advantages over classical computation requires extremely low error rates for qubit operations as well as a significant overhead of physical qubits, in order to realize fault-tolerance via quantum error correction. However, recent theoretical work has shown that the accuracy of computation based off expectation values of quantum observables can be enhanced through an extrapolation of results from a collection of varying noisy experiments. Here, we demonstrate this error mitigation protocol on a superconducting quantum processor, enhancing its computational capability, with no additional hardware modifications. We apply the protocol to mitigate errors on canonical single- and two-qubit experiments and then extend its application to the variational optimization of Hamiltonians for quantum chemistry and magnetism. We effectively demonstrate that the suppression of incoherent errors helps unearth otherwise inaccessible accuracies to the variational solutions using our noisy processor. These results demonstrate that error mitigation techniques will be critical to significantly enhance the capabilities of near-term quantum computing hardware.
New Construct Approaches for Efficient Gene Silencing in Plants (2006)

An important component of conventional sense, antisense, and double-strand RNA-based gene silencing constructs is the transcriptional terminator. Here, we show that this regulatory element becomes obsolete when gene fragments are positioned between two oppositely oriented and functionally active promoters. The resulting convergent transcription triggers gene silencing that is at least as effective as unidirectional promoter-to-terminator transcription. In addition to short, variably sized, and nonpolyadenylated RNAs, terminator-free cassette produced rare, longer transcripts that reach into the flanking promoter. These read-through products did not influence the efficacy and expression levels of the neighboring hygromycin phosphotransferase gene. Replacement of gene fragments by promoter-derived sequences further increased the extent of gene silencing. This finding indicates that genomic DNA may be a more efficient target for gene silencing than gene transcripts.
The thermal stability of oligonucleotide duplexes is sequence independent in tetraalkylammonium salt solutions: application to identifying recombinant DNA clones (1988)

In solutions of tetraalkylammonium salts the melting temperature of oligonucleotide duplexes is independent of nucleotide sequence and thus GC content. Data quantitating the destabilizing effects of various mismatches in these solvents are also presented. The results are in accord with theories on DNA melting and establish conditions under which oligonucleotides can be used as hybridization probes with predictable and controllable specificity.
Dexamethasone regulates the program of secretory glycoprotein synthesis in hepatoma tissue culture cells (1980)

The secretory glycoproteins synthesized by hepatoma tissue culture (HTC) cells were resolved by two-dimensional polyacrylamide gel electrophoresis of media from cells that were grown in the presence of [(3)H]fucose. These cells synthesize and secrete a complex set of fucose-containing glycoproteins. These secretory glycoproteins are distinct from those glycoproteins present in the plasma membrane of HTC cells. Incubation of HTC cells with dexamethasone has a pronounced effect on the quality and quantity (denoted here as the program) of secretory protein synthesis, as assayed by the short-term incorporation of labeled mannose, fucose, or methionine. The synthesis of two mannose- and fucose- containing glycoprotein series, one of 50,000 mol wt and a more heterogeneous series with mol wt of 35,000-50,000, is increased to a high level by the hormone; conversely, the synthesis of other secretory proteins, particularly one with mol wt of 70,000, is decreased or stopped completely. The synthesis of some major secretory proteins is not affected by the hormone. Dexamethasone has less of an effect on the composition of either total cell membrane glycoprotein or plasma membrane glycoprotein. But there is a decrease in the synthesis of a major membrane glycoprotein series with mol wt of 140,000. These effects of dexamethasone are relatively specific to HTC cells. Neither Reuber H-35 cells nor primary cultures of rat hepatocytes show the same response to the steroid. Two variant HTC cell lines, which were selected for their resistance to dexamethasone inhibition of extracellular plasminogen activator activity, respond only partially to the steroid-induced regulation of the secretory and membrane glycoproteins.
Bloom’s syndrome protein, BLM, colocalizes with replication protein A in meiotic prophase nuclei of mammalian spermatocytes (1999)

Bloom's syndrome (BS) is a rare autosomal recessive disorder of humans characterized by severe pre- and postnatal growth deficiency, immunodeficiency, genomic instability, and a predisposition to a wide variety of neoplasms. The genomic instability is evidenced in BS somatic cells as a high incidence of gaps and breaks, chromatid exchanges, chromosome rearrangements, and locus-specific mutations. BS arises from a mutation in BLM, a gene encoding a protein with homology to the RecQ helicase family. Men with BS are sterile; women have reduced fertility and a shortened reproductive span. The current immunocytological study on mouse spermatocytes shows that the BLM protein is first evident as discrete foci along the synaptonemal complexes (SCs) of homologously synapsed autosomal bivalents in late zygonema of meiotic prophase. BLM foci progressively dissociate from the synapsed autosomal axes during early pachynema and are no longer seen in mid-pachynema. BLM colocalizes with the single-stranded DNA binding replication protein A, which has been shown to be involved in meiotic synapsis. However, there is a temporal delay in the appearance of BLM protein along the SCs relative to replication protein A, suggesting that BLM is required for a late step in processing of a subset of genomic DNA involved in establishment of interhomologue interactions in early meiotic prophase. In late pachynema and into diplonema, BLM is more dispersed in the nucleoplasm, especially over the chromatin most intimately associated with the SCs, suggesting a possible involvement of BLM in resolution of interlocks in preparation for homologous chromosome disjunction during anaphase I.
Mutant subtilisin E with enhanced protease activity obtained by site-directed mutagenesis. (1988)

The specific activity of subtilisin E, an alkaline serine protease of Bacillus subtilis, was substantially increased by optimizing the amino acid residue at position 31 (Ile in the wild-type enzyme) in the vicinity of the catalytic triad of the enzyme. Eight uncharged amino acids (Cys, Ser, Thr, Gly, Ala, Val, Leu, and Phe) were introduced at this site, which is next to catalytic Asp32, using site-directed mutagenesis. Mutant enzymes were expressed in Escherichia coli and were prepared from the periplasmic space. Only the Val and Leu substitutions gave active enzyme, and the Leu31 mutant was found to have a greatly increased activity compared to the wild-type enzyme. The other six mutant enzymes showed a marked decrease in activity. This result indicates that a branched-chain amino acid at position 31 is essential for the expression of subtilisin activity and that the level of the activity depends on side chain structure. The purified Leu31 mutant enzyme was analyzed with respect to substrate specificity, heat stability, and optimal temperature. It was found that the Leu31 replacement caused a prominent 2-6-fold increase in catalytic efficiency (kcat/Km) due to a larger kcat for peptide substrates.
Evidence for the Covalent Binding of SHAP, Heavy Chains of Inter-α-Trypsin Inhibitor, to Hyaluronan (1995)

We previously showed that serum-derived 85-kDa proteins (SHAPs, serum-derived hyaluronan associated proteins) are firmly bound to hyaluronan (HA) synthesized by cultured fibroblasts. SHAPs were then identified to be the heavy chains of inter-alpha-trypsin inhibitor (ITI) (Huang, L., Yoneda, M., and Kimata, K. (1993) J. Biol. Chem. 268, 26725-26730). In this study, the SHAP.HA complex was isolated from pathological synovial fluid from human arthritis patients. The SHAP.HA complex was digested with thermolysin, followed by CsCl gradient centrifugation. The HA-containing fragments thus obtained were further digested with chondroitinase AC II and subjected to TSK gel high performance liquid chromatography (HPLC). Peptide-HA disaccharide-containing fractions (the SHAP.HA binding regions) were further purified by reverse phase HPLC. Major peaks were analyzed by protein sequencing and mass spectrometry (electrospray ionization mass spectrometry and collision induced dissociation-MS/MS). By comparison with the reported C-terminal sequences of the human ITI family, the peptides were found to correspond to tetrapeptides derived from the C termini of heavy chains 1 of and 2 of inter-alpha-trypsin inhibitor (HC1 and HC2), and heavy chain 3 of pre-alpha-trypsin inhibitor (HC3), respectively, and a heptapeptide from HC1. Mass spectrometric analyses suggested that the C-terminal Asp of each heavy chain was esterified to the C6-hydroxyl group of an internal N-acetylglucosamine of HA chain. This report is the first demonstration to give evidence for the covalent binding of proteins to HA.
Cardiovascular Failure in Mouse Embryos Deficient in VEGF Receptor-3 (1998)

Vascular endothelial growth factor (VEGF) is a key regulator of blood vessel development in embryos and angiogenesis in adult tissues. Unlike VEGF, the related VEGF-C stimulates the growth of lymphatic vessels through its specific lymphatic endothelial receptor VEGFR-3. Here it is shown that targeted inactivation of the gene encoding VEGFR-3 resulted in defective blood vessel development in early mouse embryos. Vasculogenesis and angiogenesis occurred, but large vessels became abnormally organized with defective lumens, leading to fluid accumulation in the pericardial cavity and cardiovascular failure at embryonic day 9.5. Thus, VEGFR-3 has an essential role in the development of the embryonic cardiovascular system before the emergence of the lymphatic vessels.
Spectroellipsometric characterization of plasma-deposited Au/SiO2 nanocomposite films (2000)

Nanocomposite films consisting of metal nanoparticles embedded in a dielectric matrix were fabricated by simultaneous sputtering of a gold target and plasma-enhanced chemical vapor deposition of hydrogenated SiO2. The optical constants of the films were determined from spectroscopic ellipsometry measurements and were modeled using the Maxwell–Garnett effective medium theory. The particle size dependence of the free electron absorption was included according to the limited electron mean free path effect using a broadening parameter A=0.16 determined from the comparison of the measured spectra with transmission electron microscopy micrographs. Using bulk interband optical constants for gold, very good agreement was obtained between the model and the measured spectra but only in the narrow particle size range ∼10–20 nm, the latter of which marks the onset of phase retardation effects. For smaller particles, the energy of the surface plasmon resonance was progressively blueshifted with respect to the predicted value. This was interpreted by a size dependence of the interband transitions as a result of strain-induced variation of the lattice constant within the particle.
Use of single and combined antithrombotic therapy and risk of serious upper gastrointestinal bleeding: population based case-control study (2006)

Antithrombotic treatment is becoming increasingly aggressive. Combined antithrombotic treatment confers particular risk and is associated with high incidence of gastrointestinal bleeding.
Structure and specificities of anti-ganglioside autoantibodies associated with motor neuropathies (1992)

Autoantibodies that bind to GM1 ganglioside and asialo GM1 (GA1) have been implicated in the pathogenesis of motor neuropathies. To investigate the structure and specificity of these autoantibodies, peripheral blood B cells from patients with motor neuron diseases and from normal individuals were immortalized by EBV, and B cells secreting anti-GM1 or GA1 antibodies were cloned. We report an analysis of the structure and specificities of eight autoantibodies from patients with motor neuropathy, and two from normal individuals. Four antibodies were IgM, six were IgG, and all bound predominantly to GA1. The sequences of V domains of H and L chains were determined by a reverse transcription-polymerase chain reaction procedure. A variety of V genes were used to encode these antibodies: four VH1, two VH3, three VH4, one VH5, two V kappa I, two V kappa II, three V kappa III, and two V lambda II. Most V genes (13/19) exhibited less than 95% similarity to known germ-line genes, which suggests that somatic mutation was required to generate these autoantibodies, or that the relevant germ-line genes have not been identified. The average length of the H chain CDR3 was 16 amino acids, and in three antibodies this segment contained more than 20 amino acids. It was not possible to identify amino acid sequences that were encoded by germ-line D segments by conventional alignment of sequences. Partial analogies could be identified by introducing gaps, allowing mismatches and searching for D-D fusions and inversions. These results indicate that anti-GA1 antibodies can be encoded by a variety of VH-VL pairs, that the antibodies exhibit extensive somatic mutation, and that the CDR3 segments are generated by a number of nonconventional mechanisms.
Remote progressive firmware update for flash-based networked embedded systems (2009)

Firmware update over a network connection is an essential but expensive feature for many embedded systems due to the relatively high power consumption and limited bandwidth. This work proposes a page-level, link-time technique that minimizes not only the size of patching scripts but also perturbation to the firmware memory, over the entire sequence of updates in the system's lifetime. Experimental results show our technique to reduce the energy consumption of firmware update by 38--42% over the state-of-the-art.
Electrokinetic-flow-induced viscous drag on a tethered DNA inside a nanopore (2007)

Recent work has shown that the resistive force arising from viscous effects within the pore region could explain observed translocation times in certain experiments involving voltage-driven translocations of DNA through nanopores [Ghosal, Phys. Rev. E 71, 051904 (2006); Phys. Rev. Lett. 98, 238104 (2007)]. The electrokinetic flow inside the pore and the accompanying viscous effects also play a crucial role in the interpretation of experiments where the DNA is immobilized inside a nanopore [Keyser, Nat. Phys. 2, 473 (2006)]. In this paper the viscous force is explicitly calculated for a nanopore of cylindrical geometry. It is found that the reductions of the tether force due to viscous drag and due to charge reduction by Manning condensation are of similar size. The result is of importance in the interpretation of experimental data on tethered DNA.
Si/C Composites for High Capacity Lithium Storage Materials (2003)

Thermal pyrolysis of polyvinyl chloride dispersed with nanosized silicon and fine graphite particles at 900°C produces a novel Si/C composite for lithium storage material. Incorporated silicon provides major capacity for lithium insertion, while the introduction of graphite component suppresses the initial irreversibility and hysteresis between charge and discharge caused by pyrolyzed carbon. The first cycle efficiency of the composite is about 85%. The large reversible capacity of ca. 700 mAh/g and good cyclability indicates that such Si/C composite may be a useful alternative to conventional graphite-based anode materials for lithium-ion cells. © 2003 The Electrochemical Society. All rights reserved.
Yeast KEX2 Protease Has the Properties of a Human Proalbumin Converting Enzyme (1987)

Several classes of proteolytic enzymes have been proposed to have a role in the processing of precursor forms of proproteins at paired basic amino acid residues. In higher eukaryotes, a single endopeptidase has yet to fulfill the necessary criteria as the physiologically relevant convertase. The observation of proalbumin circulating in a child with a bleeding disorder caused by an unusual alpha 1-antitrypsin mutation led to speculation that the presence of this alpha 1-antitrypsin mutant was inhibitory to the convertase. This provided an additional means of characterizing the processing enzyme. In this study the yeast KEX2 enzyme, a calcium-dependent thiol protease, was found to have all the properties expected for this processing enzyme. KEX2 correctly recognized and cleaved the prosequence in proalbumin. In addition, KEX2 was specifically inhibited by the mutant alpha 1-antitrypsin but not by other serine protease inhibitors.
Pharmacokinetics of BAY 59-7939 – an oral, direct Factor Xa inhibitor – in rats and dogs (2005)

The pharmacokinetics of BAY 59-7939 - a novel, oral, direct Factor Xa inhibitor - were investigated in rats and dogs in support of preclinical safety studies and clinical development. BAY 59-7939 was rapidly absorbed after oral dosing, with an absolute bioavailability of 57-66% in rats, and 60-86% in dogs. Plasma pharmacokinetics of BAY 59-7939 were linear across the investigated dose range (1-10 mg kg(-1) in rats, 0.3-3 mg kg(-1) in dogs). Plasma clearance was low: 0.4 l kg(-1) h(-1) in rats and 0.3 l kg(-1) h(-1) in dogs; volume of distribution (V(ss)) was moderate: 0.3 l kg(-1) in rats, and 0.4 l kg(-1) in dogs. The elimination half-life after oral administration was short in both species (0.9-2.3 h). Whole-body autoradiography showed moderate tissue affinity. No retention or small volume enrichments of BAY 59-7939-related radioactivity were observed. The plasma-protein binding of BAY 59-7939 was high, species dependent and fully reversible. BAY 59-7939 was rapidly excreted in rats and dogs, and was not irreversibly retained. A dual mode of excretion (biliary/faecal and renal) was observed. In summary, BAY 59-7939 had a favourable, predictable pharmacokinetic profile, with high oral bioavailability and a dual route of excretion.
Minimizing Shape Change at Zn Sponge Anodes in Rechargeable Ni–Zn Cells: Impact of Electrolyte Formulation (2015)

The historically poor electrochemical rechargeability of Zn in alkaline electrolyte has hindered the commercial viability of Ni–Zn batteries, a system otherwise of interest because of high specific energy (up to 140 Wh kg–1). We have redesigned the Zn anode as a three-dimensional (3D), monolithic porous architecture ("sponge") that exhibits unprecedented Zn specific capacity and dendrite-free cycling. Maintaining the integrity of the 3D Zn sponge architecture throughout charge–discharge is required to ultimately achieve technologically relevant performance in terms of cycle life and capacity. En route to this goal, we systematically evaluated a series of electrolyte and electrode additives used in conjunction with our Zn sponge anode in order to down-select formulations that minimize electrode shape change with cycling in prototype Ni–3D Zn cells. The classes of additives chosen for this study include those that either inhibit ZnO passivation during discharge (Type I: LiOH, K2SiO3) or promote it (Type II/III: KF, K2CO3, ZnO, Ca(OH)2), as well as combinations thereof. We find that the second class of additives effectively retains the cycled Zn sponge in its pre-cycled condition.