gebhart/patrepeval huggingface dataset:
Comparison of cytotoxic and inflammatory responses of photoluminescent silicon nanoparticles with silicon micron‐sized particles in RAW 264.7 macrophages (2008)

Photoluminescent silicon nanoparticles have a bright and stable fluorescence and are promising candidates for bio-imaging, cell staining and drug delivery. With increasing development of nanotechnology applications for biomedicine, an understanding of the potential toxicity of nanoparticles is needed to assess safety concerns for clinical applications. The objective of this study was to compare biological responses of silicon nanoparticles (SNs, 3 nm diameter) with silicon microparticles (SMs, approximately 100-3000 nm diameter) in cultured murine macrophages (RAW 264.7) using standard protocols for assessing cytotoxicity/cell viability and inflammatory responses developed for micron-sized particles. SNs and SMs were exposed to macrophages with and without addition of endotoxin lipopolysaccharide (LPS), a positive inducer of tumor necrosis factor-alpha (TNF-alpha), interleukin 6 (IL-6), and nitric oxide (NO). Cytotoxicity was assayed using the dye exclusion and MTT assays. Cell supernatants were assayed for production TNF-alpha, IL-6 and NO. SNs at concentrations < or = 20 microg ml(-1) exhibited no cytotoxicity or inflammatory responses; however, SNs and SMs >20 and 200 microg ml(-1), respectively, increased cytotoxicity compared with controls. SMs induced concentration-related increases in TNF-alpha and IL-6 production; in contrast, the production of these cytokines was shown to decrease with increasing concentrations of SNs. NO production was not induced by SNs or SMs alone. Fluorescence microscopy demonstrated that SNs were associated with the macrophages, either internalized or attached to cell membranes. In conclusion, evaluating differences in biological responses for nanoparticles compared with microparticles of the same material may help improve tests to assess biological responses of nanoparticles that may be used in biomedical applications.
Coarse Time Navigation: Equivalence of Algorithms and Reliability of Time Estimates (2012)

Methods that rely on estimating time-of-week (TOW) information, in addition to user position and receiver clock bias, rather than decoding TOW from live signals are commonly referred to as coarse time navigation algorithms. A priori information required for these algorithms include valid ephemeris, an approximate user position and TOW. Inputs to these algorithms are sub-ms pseudorange measurements. When sub-ms pseudorange measurements are used to resolve unknowns, integer-millisecond errors across measurements can lead to potential blunders. Two possible solutions are found in the literature to address this issue: Lannelongue & Pablos (1998) and van Diggelen (2002). One of the novel contributions of this paper is to clearly show that, under most practical conditions (range error less than 75 km), these two methods collapse down to be identical, through clear mathematical models. Further, this paper also evaluates the possibility of starting with coarse time parameters to resolve time within fine time standards (10 ms or better) by excluding degraded solutions through integrity checks. The analysis is presented using statistics gathered under different signal power and satellite geometry conditions. Results indicate that the proposed integrity checks are reliable in detecting solutions with a time error of 10 ms or more under nominal signal conditions. However, under weak signal conditions (25 dB-Hz) 5-15% of the filtered solutions still had an error larger than the desired 10 ms.
First isolation and further characterization of enteropathogenic Escherichia coli (EPEC) O157:H45 strains from cattle (2004)

This study reports the first isolation of typical O157:H45 EPEC strains from cattle. Furthermore, our findings emphasize the fact that E. coli with the O157 antigen are not always STEC but may belong to other pathotypes. Cattle seem also to be a reservoir of O157:H45 EPEC strains, which are described in association with human diseases. Therefore, these strains appear to play a role as food borne pathogens and have to be considered and evaluated in view of food safety aspects.
A comparison of bioimpedance methods for detection of body cell mass change in HIV infection (2000)

The maintenance of body cell mass (BCM) is critical for survival in human immunodeficiency virus (HIV) infection. Accuracy of bioimpedance for measuring change (Delta) in intracellular water (ICW), which defines BCM, is uncertain. To evaluate bioimpedance-estimated DeltaBCM, the ICW of 21 weight-losing HIV patients was measured before and after anabolic steroid therapy by dilution (total body water by deuterium - extracellular water by bromide) and bioimpedance. Multiple-frequency modeling- and dilution-determined DeltaICW did not differ. The DeltaICW was predicted poorly by 50-kHz parallel reactance, 50-kHz impedance, and 200 - 5-kHz impedance. The DeltaICW predicted by 500 - 5-kHz impedance was closer to, but statistically different from, dilution-determined DeltaICW. However, the effect of random error on the measurement of systematic error in the 500 - 5-kHz method was 12-13% of the average measured DeltaICW; this was nearly twice the percent difference between obtained and threshold statistics. Although the 500 - 5-kHz method cannot be fully rejected, these results support the conclusion that only the multiple-frequency modeling approach accurately monitors DeltaBCM in HIV infection.
Electrically directed assembly and detection of nanowire bridges in aqueous media (2006)

Although dielectrophoresis has been used previously to manipulate a variety of nanoscale materials, manipulation in ionic solutions is more difficult due to the high dielectric constant of water and the formation of electrical double-layers. Here, we report experiments aimed at the manipulation of nanowires in aqueous media and real-time detection of nanowire bridging events. Real-time video images demonstrate the ability to manipulate individual nanowires in aqueous media by capturing them along the edges of electrodes, and using a slow fluid flow to transport them until they bridge across micron-sized electrode gaps. By using special cancellation schemes, we demonstrate that it is possible to eliminate the effects of background currents through the electrolyte, and to electrically detect the bridging of electrodes by individual nanowires and nanowire bundles. These results have been obtained using gold nanowires with diameters ranging from ∼50 to 250 nm, ∼50 nm diameter silicon nanowires, and ∼70 nm diameter carbon nanofibres.
Efficient Lightweight Compression Alongside Fast Scans (2015)

The increasing main-memory capacity has allowed query execution to occur primarily in main memory. Database systems employ compression, not only to fit the data in main memory, but also to address the memory bandwidth bottleneck. Lightweight compression schemes focus on efficiency over compression rate and allow query operators to process the data in compressed form. For instance, dictionary compression keeps the distinct column values in a sorted dictionary and stores the values as index codes with the minimum number of bits. Packing the bits of each code contiguously, namely horizontal bit packing, has been optimized by using SIMD instructions for unpacking and by evaluating predicates in parallel per processor word for selection scans. Interleaving the bits of codes, namely vertical bit packing, provides faster scans, but incurs prohibitive costs for packing and unpacking. Here, we improve packing and unpacking for vertical bit packing using SIMD instructions, achieving more than an order of magnitude speedup. Also, we optimize horizontal bit packing on the latest CPUs and compare all approaches. While no single variant is better in all cases, vertical bit packing offers a good trade-off by combining the fastest scans with comparably fast packing and unpacking.
Design and Synthesis of Oligoamide‐Based Double α‐Helix Mimetics (2013)

Abstract An extensive series of bis‐oligobenzamides and bis‐oligopyridylamides have been efficiently prepared and studied by X‐ray analysis and computational methods. A modular synthesis led to double α‐helix mimics bearing between two and ten branched side‐chains. The inter‐helix angle and distance can be tuned by varying the length and rigidity of the spacer, thereby reproducing the recognition domains of a range of super‐secondary structures.
Survival of lactic acid bacteria in simulated gastrointestinal juice protected by a DNA-based complex gel (2003)

Salmon milt DNA was utilized in the approach to protect functional materials, proteins, microorganisms, drugs, etc., by forming a DNA-based complex gel with gelatin and kappa-carrageenan. The multiplier effect of the combination of DNA, gelatin and kappa-carrageenan was examined by measuring the release of methyl orange from the gel after being incubated in simulated gastric juice. The results indicated that the hydrogel made of DNA, gelatin and kappa-carrageenan can efficiently maintain the functional materials. Furthermore, a complex gel was developed and optimized by applying an emulsion of lactic acid bacteria and cacao oil onto the already prepared hydrogel. The existence of the lactic acid bacteria in the oil emulsion particles was confirmed by scanning electron microscopy. The protection capabilities in the simulated gastrointestinal juice, which had a viability of 1.50 x 10(6) CFU/g gel after 2 h incubation in the simulated gastric juice and 2.53 x 10(7) CFU/g gel after 6 h continued incubation in the simulated intestinal juice, were measured, in contrast to 2.58 x 10(7) CPU/g in the original gel before treatment.
The Second Intracellular Loop of the m5 Muscarinic Receptor Is the Switch Which Enables G-protein Coupling (1998)

We have completed a systematic search of the intracellular loops of a muscarinic acetylcholine receptor for domains that govern G-protein coupling. A unique feature of the second intracellular (i2) loop was an ordered cluster of residues where diverse substitutions cause constitutive activation. A second group of residues in i2 was identified where mutations compromised receptor/G-protein coupling. The residues of each group alternate and are spaced three to four positions apart, suggesting an alpha-helical structure where these groups form opposing faces of the helix. We propose that the constitutively activating face normally constrains the receptor in the "off-state," while the other face couples G-proteins in the "on-state." Therefore, the i2 loop functions as the switch enabling G-protein activation.
The Staphylococcal Enterotoxins and Their Relatives (1990)

In the article "The staphylococcal enterotoxins and their relatives" by Philippa Marrack and John Kappler (11 May, p. 705), figures 1, 2, and 3 were incorrectly printed. The color portions of figures 2 and 3 should have been included in figure 1. The correct figure 1 is printed below. See image in PDF file
One-pot Synthesis of Novel Polysubstituted Pyrazole and Pyrrolo[2,1-b]benzothiazole Derivatives† (1998)

K. Mohammed Dawood, J. Chem. Res. (S), 1998, 128 DOI: 10.1039/A706107B
Highly Active Dizinc Catalyst for the Copolymerization of Carbon Dioxide and Cyclohexene Oxide at One Atmosphere Pressure (2008)

Low-pressure catalyst: A novel dizinc complex (1) having a macrocyclic ancillary ligand shows remarkable activity for the copolymerization of carbon dioxide and cyclohexene oxide, at only one atmosphere of CO2. TON=turnover number; TOF=turnover frequency. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A p38 MAPK inhibitor, FR-167653, ameliorates murine bleomycin-induced pulmonary fibrosis (2002)

To elucidate the pathophysiology of pulmonary fibrosis, we investigated the involvement of p38 mitogen-activated protein kinase (MAPK), which is one of the major signal transduction pathways of proinflammatory cytokines, in a murine model of bleomycin-induced lung fibrosis. p38 MAPK and its substrate, activating transcription factor (ATF)-2, in bronchoalveolar lavage fluid cells were phosphorylated by intratracheal exposure of bleomycin, and the phosphorylation of ATF-2 was inhibited by subcutaneous administration of a specific inhibitor of p38 MAPK, FR-167653. FR-167653 also inhibited augmented expression of tumor necrosis factor -alpha, connective tissue growth factor, and apoptosis of lung cells induced by bleomycin administration. Moreover, daily subcutaneous administration of FR-167653 (from 1 day before to 14 days after bleomycin administration) ameliorated pulmonary fibrosis and pulmonary cachexia induced by bleomycin. These findings demonstrated that p38 MAPK is involved in bleomycin-induced pulmonary fibrosis, and its inhibitor, FR-167653, may be a feasible therapeutic agent.
Enzymatic preparation of enantiomerically pure sn‐2,3‐diacylglycerols: A stereoselective ethanolysis approach (2006)

Abstract Stereoselective ethanolysis of monoacid TAG by immobilized Rhizomucor miehei lipase (RML) was studied for preparation of optically pure sn ‐2,3‐DAG. Trioctanoylglycerol (TO) was used as a model substrate. The enantiomeric purity of the product, sn ‐2,3‐dioctanoylglycerol ( sn ‐2,3‐DO), was very high (percent enantiomeric excess &gt;99%) when an excess of ethanol was used. The result indicated that RML was highly stereoselective toward the sn ‐1 position of TO under conditions of excess ethanol. The stereoselectivity of RML depended on the amount of ethanol. The larger the amount of ethanol was, the higher the stereoselectivity became. After optimizing the parameters such as reactant molar ratio, water content, and temperature, (ethanol/TO molar ratio =31∶1 and water content =7.5 wt% of the reactants at 25°C), optically pure sn ‐2,3‐DO was obtained at 61.1 mol% in the glyceride fraction in 20 min. The above conditions were further applied for ethanolysis of monoacid TAG with different acyl groups such as tridecanoylglycerol (C10∶0), tridodecanoylglycerol (C12∶0), tritetradecanoylglycerol (C14∶0) and trioctadecenoylglycerol [triolein, (C18∶1)]. The yields and enantiomeric purities of 1,2(2,3)‐DAG were dramatically reduced when TAG with FA longer than decanoic acid were used.
New role for 15-hydroxyeicosatetraenoic acid. Activator of leukotriene biosynthesis in PT-18 mast/basophil cells. (1982)

Leukotrienes are vasoactive arachidonic acid metabolites which are released by mast cells during hypersensitivity reactions. The mechanisms for regulating leukotriene biosynthesis are not well understood. A murine mast/basophil cell line (PT-18) was used to investigate this problem. Exogenously supplied [14C]arachidonic acid is not appreciably converted to leukotrienes by untreated PT-18 cells. However, when the cells were preincubated with the lymphocyte product 15-hydroxyeicosatetraenoic acid (15-HETE), addition of [14C]arachidonic acid consistently resulted in a dose-dependent synthesis of large amounts of both [14C]leukotriene B4 and [14C]5-HETE. These metabolites were isolated by high pressure liquid chromatography, converted to the methyl ester trimethylsilyl ether derivatives, and the structures confirmed by gas chromatography-mass spectrometry. These findings indicate that 15-HETE induces a direct activation of a cryptic 5-lipoxygenase in these cells. The closely related 12-HETE was ineffective. The activation phenomenon occurs rapidly and is reversible. Furthermore, the activation appears to be highly cell- and enzyme-specific, since lipoxygenases in three primary cell types including one that contains a 5-lipoxygenase and six other cell lines did not show this specific induction of leukotriene biosynthesis by 15-HETE. This report is the first evidence that 15-HETE, a major arachidonate metabolite in lymphocytes, can act as a signal to activate leukotriene production by susceptible mast cells.
Treatment of common cutaneous herpes simplex virus infections. (2000)

Herpes simplex virus infection is increasingly common in the United States. New antiviral medications have expanded treatment options for the two most common cutaneous manifestations, orolabial and genital herpes. Acyclovir therapy remains an effective and often less expensive option. Famciclovir and valacyclovir offer improved oral bioavailability and convenient oral dosing schedules but are more expensive than acyclovir. Patients who have six or more recurrences of genital herpes per year can be treated with one of the following regimens: acyclovir, 400 mg twice daily; valacyclovir, 1 g daily; or famciclovir, 250 mg twice daily. These regimens are effective in suppressing 70 to 80 percent of symptomatic recurrences. Episodic treatment of recurrent genital herpes is of questionable benefit, but it may be helpful in appropriately selected patients. There is little evidence indicating benefit from treatment of recurrent orolabial herpes, which tends to be mild and infrequent.
Intestinal absorption and excretion of octapeptidescomposed of D amino acids. (1994)

Octapeptides synthesized from D amino acids were absorbed from the intestine and excreted in urine of normal rats drinking 5% glucose/1% creatinine containing the 125I-labeled peptides at 0.1-25 mg/dl. The rats ingested fluid at the rate of about 20 ml/hr and produced urine at 15 ml/hr for several hours during the nocturnal feeding period. Sixty-one +/- 4% of the ingested creatinine and 50 +/- 3% of a lipid-insoluble D octapeptide (EASASYSA, 784 Da) were excreted intact in the urine. The steady-state molar rate of absorption-excretion of creatinine equaled or exceeded the maximum rate of carrier-mediated intestinal transport of glucose, suggesting that both the creatinine and the D octapeptide were transported paracellularly by solvent drag through absorptive cell junctions that were dilated by the glucose. More than 70% of the ingested glucose was also absorbed paracellularly. The results demonstrate that intact oligopeptides can be absorbed efficiently from the intestine when they are not hydrolyzed by membrane-bound peptidases of the brush border. The results also provide support for recent theories proposing that coupling of membrane digestion with paracellular solvent drag accounts for a major fraction of normal intestinal absorption of nutrients.
A Partition-Based Match Making Algorithm for Dynamic Ridesharing (2015)

Ridesharing offers the opportunity to make more efficient use of vehicles while preserving the benefits of individual mobility. Presenting ridesharing as a viable option for commuters, however, requires minimizing certain inconvenience factors. One of these factors includes detours which result from picking up and dropping off additional passengers. This paper proposes a method which aims to best utilize ridesharing potential while keeping detours below a specific limit. The method specifically targets ridesharing systems on a very large scale and with a high degree of dynamics which are difficult to address using classical approaches known from operations research. For this purpose, the road network is divided into distinct partitions which define the search space for ride matches. The size and shape of the partitions depend on the topology of the road network as well as on two free parameters. This allows optimizing the partitioning with regard to sharing potential utilization and inconvenience minimization. Match making is ultimately performed using an agent-based approach. As a case study, the algorithm is applied to investigate the potential for taxi sharing in Singapore. This is done by considering about 110 000 daily trips and allowing up to two sharing partners. The outcome shows that the number of trips could be reduced by 42% resulting in a daily mileage savings of 230 000 km. It is further shown that the presented approach exceeds the mileage savings achieved by a greedy heuristic by 6% while requiring 30% lower computational efforts.
Isolation and structure of an untriakontapeptide with opiate activity from camel pituitary glands. (1976)

The isolation of an untriakontapeptide from camel pituitary extracts has been described. Its structure has been determined and shown to be identical to the sequence of carboxyl-terminal 31 amino acids of ovine beta-lipotropin. The peptide possesses very low lipotropic activity but significant opiate activity.
Human immunodeficiency virus type 1 Vpr protein binds to the uracil DNA glycosylase DNA repair enzyme (1996)

The role of the accessory gene product Vpr during human immunodeficiency virus type 1 infection remains unclear. We have used the yeast two-hybrid system to identify cellular proteins that interact with Vpr and could be involved in its function. A cDNA clone which encodes the human uracil DNA glycosylase (UNG), a DNA repair enzyme involved in removal of uracil in DNA, has been isolated. Interaction between Vpr and UNG has been demonstrated by in vitro protein-protein binding assays using translated, radiolabeled Vpr and UNG recombinant proteins expressed as a glutathione S-transferase fusion protein. Conversely, purified UNG has been demonstrated to interact with Vpr recombinant protein expressed as a glutathione S-transferase fusion protein. Coimmunoprecipitation experiments confirmed that Vpr and UNG are associated within cells expressing Vpr. By using a panel of C- and N-terminally deleted Vpr mutants, we have determined that the core protein of Vpr, spanning amino acids 15 to 77, is involved in the interaction with UNG. We also demonstrate by in vitro experiments that the enzymatic activity of UNG is retained upon interaction with Vpr.
A Nonsense Mutation in a Novel Gene Is Associated With Retinitis Pigmentosa in a Family Linked to the RP1 Locus (1999)

Retinitis pigmentosa (RP) represents a group of inherited human retinal diseases which involve degeneration of photoreceptor cells resulting in visual loss and often leading to blindness. In order to identify candidate genes for the causes of these diseases, we have been studying a pool of photoreceptor-specific cDNAs isolated by subtractive hybridization of mRNAs from normal and photoreceptorless rd mouse retinas. One of these cDNAs was of interest because it mapped to proximal mouse chromosome 1 in a region homo-logous to human 8q11-q13, the locus of autosomal dominant RP1. Therefore, using the mouse cDNA as probe, we cloned the human cDNA (hG28) and its corresponding gene and mapped it near to D8S509, which lies in the RP1 locus. This gene consists of four exons with an open reading frame of 6468 nt encoding a protein of 2156 amino acids with a predicted mass of 240 kDa. Given its chromosomal localization, we screened this gene for mutations in a large family affected with autosomal dominant RP previously linked to the RP1 locus. We found an R677X mutation that co-segregated with disease in the family and is absent from unaffected members and 100 unrelated controls. This mutation is predicted to lead to rapid degradation of hG28 mRNA or to the synthesis of a truncated protein lacking approximately 70% of its original length. Our results suggest that R677X is responsible for disease in this family and that the gene corresponding to hG28 is the RP1 gene.