gebhart/patrepeval huggingface dataset:
Identification of Novel Small-Molecule Inhibitors of West Nile Virus Infection (2007)

West Nile virus (WNV) has spread throughout the United States and Canada and now annually causes a clinical spectrum of human disease ranging from a self-limiting acute febrile illness to acute flaccid paralysis and lethal encephalitis. No therapy or vaccine is currently approved for use in humans. Using high-throughput screening assays that included a luciferase expressing WNV subgenomic replicon and an NS1 capture enzyme-linked immunosorbent assay, we evaluated a chemical library of over 80,000 compounds for their capacity to inhibit WNV replication. We identified 10 compounds with strong inhibitory activity against genetically diverse WNV and Kunjin virus isolates. Many of the inhibitory compounds belonged to a chemical family of secondary sulfonamides and have not been described previously to inhibit WNV or other related or unrelated viruses. Several of these compounds inhibited WNV infection in the submicromolar range, had selectivity indices of greater than 10, and inhibited replication of other flaviviruses, including dengue and yellow fever viruses. One of the most promising compounds, AP30451, specifically blocked translation of a yellow fever virus replicon but not a Sindbis virus replicon or an internal ribosome entry site containing mRNA. Overall, these compounds comprise a novel class of promising inhibitors for therapy against WNV and other flavivirus infections in humans.
The gravity method (2012)

The gravity method of geophysical exploration is based on the measurement of variations in the gravity field caused by horizontal variations of density within the subsurface. It is an important technique for many problems that involve subsurface mapping, and it is the principal method in a number of specific types of geological studies. The method, which has its roots in geodetic studies from the seventeenth to the twentieth centuries, has developed rapidly over the past century as a result of significant technological advances: primarily high-accuracy gravity measuring instruments for use on land, sea, and air, and in space, as well as the increasing computational and graphics power of digital computers. These advances are backed up by continuing improvements in data processing, interpretational schemes, practical experience, and surveying methodologies.
Short Communication: PPARγ Mediates a Direct Antiangiogenic Effect of ω3-PUFAs in Proliferative Retinopathy (2010)

These results identify a direct, PPARgamma-mediated effect of omega3-PUFAs on retinal neovascularization formation and retinal angiogenic activation that is independent of vascular endothelial growth factor.
Efficacy of the botanical repellents geraniol, linalool, and citronella against mosquitoes (2009)

We determined the degree of personal protection provided by citronella, linalool, and geraniol in the form of commercially available candles or diffusers, both indoors and outdoors. Under the uniform conditions of the experiments, all substances repelled significantly more mosquitoes than the unprotected control. Furthermore, the repellents tested were more active when in the form of a continuous release diffuser than in candle form. All candles were 88 g containing 5% of the active ingredient and all diffusers contained 20 g of 100% active ingredient. Indoors, the repellency rate of citronella candles was only 14% while the repellency rate of citronella diffusers was 68%. The repellency of geraniol candles was 50% while the diffusers provided a repellency rate of 97%. No linalool candles were available for study but linalool diffusers repelled mosquitoes by 93%. Outdoors, citronella diffusers placed 6 m from mosquito traps repelled female mosquitoes by 22%, linalool repelled females by 58%, and geraniol repelled females by 75%. Trap catches were significantly reduced again when diffusers were placed 3 m from the traps. We concluded that geraniol had significantly more repellent activity than citronella or linalool in both indoor and outdoor settings.
Pseudopolymorph:  A Polemic (2004)

The author argues against the use of the term “pseudopolymorph”, since the scientific community gains no new understanding by its introduction, its use is pedagogically misleading, and a long-established and well-understood term “solvate” already exists.
Electron transfer to nitrogenase in Klebsiella pneumoniae. nifF gene cloned and the gene product, a flavodoxin, purified (1985)

The nifF gene of Klebsiella pneumoniae was cloned into a multicopy plasmid in order to construct a strain that synthesizes and retains an elevated concentration of the gene product relative to the wild-type strain. Characterization of the isolated flavodoxin, which serves as an electron donor to nitrogenase, shows unambiguously that it is the product of the nifF gene.
Post-translational Processing of β-Secretase (β-Amyloid-converting Enzyme) and Its Ectodomain Shedding (2001)

Processing of the beta-amyloid precursor protein (betaAPP) by beta- and gamma-secretases generates the amyloidogenic peptide Abeta, a major factor in the etiology of Alzheimer's disease. Following the recent identification of the beta-secretase beta-amyloid-converting enzyme (BACE), we herein investigate its zymogen processing, molecular properties, and cellular trafficking. Our data show that among the proprotein convertase family members, furin is the major converting enzyme of pro-BACE into BACE within the trans-Golgi network of HK293 cells. While we demonstrate that the 24-amino acid prosegment is required for the efficient exit of pro-BACE from the endoplasmic reticulum, it may not play a strong inhibitory role since we observe that pro-BACE can produce significant quantities of the Swedish mutant betaAPP(sw) beta-secretase product C99. BACE is palmitoylated at three Cys residues within its transmembrane/cytosolic tail and is sulfated at mature N-glycosylated moieties. Data with three different antibodies show that a small fraction of membrane-bound BACE is shed into the medium and that the extent of ectodomain shedding is palmitoylation-dependent. Overexpression of full-length BACE causes a significant increase in the production of C99 and a decrease in the alpha-secretase product APPsalpha. Although there is little increase in the generation of Abeta by full-length BACE, overexpression of either a soluble form of BACE (equivalent to the shed form) or one lacking the prosegment leads to enhanced Abeta levels. These findings suggest that the shedding of BACE may play a role in the amyloidogenic processing of betaAPP.
IL-15 Expression at Human Endometrium and Decidua (2000)

A large number of natural killer (NK) cells appear in human uterine mucosa during the secretory phase and first trimester pregnancy. We investigated the expression of interleukin (IL)-15, a possible stimulator for these NK cells, in human endometrium and first trimester decidua. Semiquantitative reverse transcriptase-polymerase chain reaction revealed that IL-15 mRNA expression was stronger during the secretory phase and first trimester pregnancy than during the proliferative phase. Immunohistochemistry revealed that immunoreactivity for anti-IL-15 was higher during the secretory phase than it was during the proliferative phase. This was prominent in the perivascular stromal cells around invading spiral arteries during the mid- to late-secretory phase. In first trimester decidua, endothelial cells were also stained as strongly as stromal cells. A membrane-bound IL-15 molecule was detected on the surface of first trimester decidual cells by flow cytometry. Progesterone stimulated the release of soluble IL-15 in the supernatant of cultured decidual cells. These results suggest that IL-15 expression in human uterine mucosa corresponds to the fluctuation of uterine NK cells and that its production is hormonally controlled, especially by progesterone.
Methanogens: Methane Producers of the Rumen and Mitigation Strategies (2010)

Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the methanogen population in the rumen of cattle and sheep, as well as the relationship that methanogens have with other microorganisms. The rumen methanogen species differ depending on diet and geographical location of the host, as does methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effective in vivo.
Intelligent power supply controller (2002)

A power supply controller has been developed which would combine 20-b precision, simple interfacing, and versatile software control. It performs many tasks internal to the power supply and communicates with an external host computer. Parameters can be entered and/or read over a serial link using one of the 82 command words. In addition, an optional remote control panel can be located up to thousands of feet away. This controller will reduce the software development time normally spent by the user, while increasing the reliability of the system. The cost is less than buying the equivalent separate CAMAC system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular Mechanisms of Magnetosome Formation (2007)

Magnetotactic bacteria are a diverse group of microorganisms with the ability to use geomagnetic fields for direction sensing. This unique feat is accomplished with the help of magnetosomes, nanometer-sized magnetic crystals surrounded by a lipid bilayer membrane and organized into chains via a dedicated cytoskeleton within the cell. Because of the special properties of these magnetic crystals, magnetotactic bacteria have been exploited for a variety of applications in diverse disciplines from geobiology to biotechnology. In addition, magnetosomes have served as a powerful model system for the study of biomineralization and cell biology in bacteria. This review focuses on recent advances in understanding the molecular mechanisms of magnetosome formation and magnetite biomineralization.
Nearly-automated metadata hierarchy creation (2004)

Currently, information architects create metadata category hierarchies manually. We present a nearly-automated approach for deriving such hierarchies, by converting the lexical hierarchy WordNet into a format that reflects the contents of a target information collection. We use the term "nearly-automated" because an information architect should have to make only small adjustments to produce an acceptable metadata structure. We contrast the results with an algorithm that uses lexical co-occurrence statistics.
Estrogen receptor expression in human breast cancer associated with an estrogen receptor gene restriction fragment length polymorphism. (1989)

Estrogen receptor (ER) content is a well-known predictor of clinical outcome in human breast cancer. The recent cloning of a human ER complementary DNA has made possible the characterization of the ER gene on a molecular level. We have examined in human breast cancers a single, two-allele restriction fragment length polymorphism using the restriction enzyme PvuII. Initial studies in human breast cancer cell lines suggested a possible association between the absence of one allele and the absence of ER expression; subsequent analysis of allele distribution and frequency in 188 primary human breast tumor biopsies did indeed show a significant but not complete correlation between the absence of one allele and the failure to express ER. Preliminary data suggest that this restriction fragment length polymorphism is located within gene sequences coding for the putative DNA or hormone-binding domains of the ER.
Inhibition of a C‐rich oligodeoxynucleotide on activation of immune cells in vitro and enhancement of antibody response in mice (2010)

To explore the possibility that human mitochondrial genomic DNA-mimicking oligodeoxynucleotides could regulate the immune response, a series of mitochondrial DNA-based oligodeoxynucleotides (MTODNs) were designed and studied to determine their immunoregulatory effects on immune cells activated by toll-like receptor (TLR) stimulation. The results showed that a C-rich MTODN, designated MT01, was able to inhibit the proliferation of human peripheral blood mononuclear cells (PBMCs) induced by cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides (ODNs) and the production of type I interferon (IFN) from human PBMCs stimulated by TLR agonists, including inactivated influenza virus, imiquimod, inactivated herpes simplex virus-1 (HSV-1) and CpG ODNs. In addition, MT01 inhibited the CpG ODN-enhanced antibody response and this inhibition could be related to the antagonism of TLR9-activation pathways in B cells. Notably, unlike the G-rich suppressive ODNs reported, MT01 is composed of ACCCCCTCT repeats. These data imply that MT01 represents a novel class of immunosuppressive ODNs that could be candidate biologicals with therapeutic use in TLR activation-associated diseases.
Anticancer Flavonoids Are Mouse-Selective STING Agonists (2013)

The flavonoids FAA and DMXAA showed impressive activity against solid tumors in mice but failed clinical trials. They act on a previously unknown molecular target(s) to trigger cytokine release from leukocytes, which causes tumor-specific vascular damage and other antitumor effects. We show that DMXAA is a competitive agonist ligand for mouse STING (stimulator of interferon genes), a receptor for the bacterial PAMP cyclic-di-GMP (c-di-GMP) and an endogenous second messenger cyclic-GMP-AMP. In our structure-activity relationship studies, STING binding affinity and pathway activation activity of four flavonoids correlated with activity in a mouse tumor model measured previously. We propose that STING agonist activity accounts for the antitumor effects of FAA and DMXAA in mice. Importantly, DMXAA does not bind to human STING, which may account for its lack of efficacy or mechanism-related toxicity in man. We propose that STING is a druggable target for a novel innate immune activation mechanism of chemotherapy.
Radioimmunoimaging of venous thrombi using iodine-131 monoclonal antibody. (1985)

Murine monoclonal antibody (Mab) specific for the NH2-terminal region of human fibrin, but not cross-reactive with fibrinogen, was used in radioimmuno-imaging of fresh, induced venous thrombi in three dogs. Iodine-131-labeled Mab was injected intravenously, with iodine 125-labeled polyclonal murine gamma-G globulin (IgG) simultaneously injected as a control. Images were strongly positive at 24 and 48 hours in all three animals, with thrombus-to-blood and thrombus-to-muscle ratios of 8.4 and 228.0, respectively, for I-131-labeled Mab; these ratios for control IgG were 1.2 and 13.0. Radioimmunodetection of thrombi in vivo is feasible in dogs and may have clinical application since Mab is specific to human fibrin.
The Comparison of Control Strategies for the Interior PMSM Drive used in the Electric Vehicle (2010)

The interior permanent magnet synchronous motor (PMSM) can offer many advantages, including high power-to-weight ratio, high efficiency, rugged construction, low cogging torque and the capability of reluctance torque, so it is widely used in electric vehicle (EV). Two control schemes, namely field oriented control (FOC) and direct torque control (DTC) are used in PMSM drive. In order to decrease current and torque ripple and fix switching frequency, an improved DTC scheme based on the control of stator flux, torque angle and torque was proposed, which used voltage vector selection strategy and the technology of space vector modulation (SVM) to generate the applied voltage vector instead of switching table. And this paper compared these three control schemes based on a 15-kW interior PMSM used in Honda Civic 06My hybrid electrical vehicle. Experimental results show for the FOC using the hysteresis current control, due to the lower sampling period, stator current is more sinusoidal. But it needs the continuous rotor position information and the switching frequency of the VSI is not constant. For the DTC using switching table, current ripple is higher and the switching frequency of the VSI is also not constant. But it does not need the rotor position information except for the initial rotor position. Compared with switching table, the proposed DTC can decrease current and torque ripple and fix switching frequency.
The Antioxidant Defense System Keap1-Nrf2 Comprises a Multiple Sensing Mechanism for Responding to a Wide Range of Chemical Compounds (2008)

Animals have evolved defense systems for surviving in a chemically diverse environment. Such systems should demonstrate plasticity, such as adaptive immunity, enabling a response to even unknown chemicals. The antioxidant transcription factor Nrf2 is activated in response to various electrophiles and induces cytoprotective enzymes that detoxify them. We report here the discovery of a multiple sensing mechanism for Nrf2 activation using zebrafish and 11 Nrf2-activating compounds. First, we showed that six of the compounds tested specifically target Cys-151 in Keap1, the ubiquitin ligase for Nrf2, while two compounds target Cys-273. Second, in addition to Nrf2 and Keap1, a third factor was deemed necessary for responding to three of the compounds. Finally, we isolated a zebrafish mutant defective in its response to seven compounds but not in response to the remaining four. These results led us to categorize Nrf2 activators into six classes and hypothesize that multiple sensing allows enhanced plasticity in the system.
Role of Factor H Binding Protein in Neisseria meningitidis Virulence and Its Potential as a Vaccine Candidate To Broadly Protect against Meningococcal Disease (2013)

Neisseria meningitidis is a Gram-negative microorganism that exists exclusively in humans and can cause devastating invasive disease. Although capsular polysaccharide-based vaccines against serogroups A, C, Y, and W135 are widely available, the pathway to a broadly protective vaccine against serogroup B has been more complex. The last 11 years has seen the discovery and development of the N. meningitidis serogroup B (MnB) outer membrane protein factor H binding protein (fHBP) as a vaccine component. Since the initial discovery of fHBP, a tremendous amount of work has accumulated on the diversity, structure, and regulation of this important protein. fHBP has proved to be a virulence factor for N. meningitidis and a target for functional bactericidal antibodies. fHBP is critical for survival of meningococci in the human host, as it is responsible for the primary interaction with human factor H (fH). Binding of hfH by the meningococcus serves to downregulate the host alternative complement pathway and helps the organism evade host innate immunity. Preclinical studies have shown that an fHBP-based vaccine can elicit serum bactericidal antibodies capable of killing MnB, and the vaccine has shown very encouraging results in human clinical trials. This report reviews our current knowledge of fHBP. In particular, we discuss the recent advances in our understanding of fHBP, its importance to N. meningitidis, and its potential role as a vaccine for preventing MnB disease.
An ambipolar host material provides highly efficient saturated red PhOLEDs possessing simple device structures (2008)

A highly efficient red electrophosphorescent device exhibited saturated red emission and an impressive external quantum efficiency [eta(ext) = 10.8% (ph/el)] with simple device configuration of doping an iridium complex (Mpq(2)Iracac) into a novel ambipolar spiro-configured donor-acceptor host material (D2ACN) has been developed.
Synthesis and biological evaluation of 9-[5'-(2-oxo-1,3,2-oxazaphosphorinan-2-yl)-.beta.-D-arabinosyl]adenine and 9-[5'-(2-oxo-1,3,2-dioxaphosphorinan-2-yl)-.beta.-D-arabinosyl]adenine: potential neutral precursors of 9-[.beta.-D-arabinofuranosyl]adenine 5'-monophosphate (1985)

9-[5'-(2-Oxo-1,3,2-oxazaphosphorinan-2-yl)-beta-D-arabinosyl]adeni ne (1c) and 9-[5'-(2-oxo-1,3,2-dioxaphosphorinan-2-yl)-beta-D-arabinosyl]adeni ne (1d) were synthesized by reaction of 9-[beta-D-arabinofuranosyl]adenine with phosphoryl chloride with 1-amino-3-propanol and 1,3-propanediol, respectively. 1c consisted of a mixture of diastereomers, while 1d was enantiomerically homogeneous. The structures of these compounds were established by spectral (1H NMR, MS, UV) and elemental analyses. Both 1c and 1d were resistant to degradation by 5'-nucleotidase, alkaline phosphatase, venom phosphodiesterase, crude snake venom, adenosine deaminase, and adenylate deaminase. Neither compound was significantly biotransformed by mouse hepatic microsomal preparations in the presence of an NADPH-generating system. Compound 1c was marginally effective at prolonging the life span of mice bearing P-388 leukemia; compound 1d, however, was inactive.
The antimicrobial effects in vivo of minocycline, doxycycline and tetracycline in humans (1996)

AbstractIn addition to the importance of bioavailability to reliable therapy, the three leading tetracyclines used in the treatment of acne have dissimilar tissue distributions and lipophilic characteristics which may impart different antimicrobial efficacy. The purpose of this study was to compare the in vivo antimicrobial effects of minocycline, doxycycline and tetracycline. The results of this study confirm that normal dosages of minocycline hydrochloride capsules in fast-release powder form produced significanctly superior in vivo reductions in Propionibacterium acnes compared to that produced by normal dosages of doxycycline monohydrate and tetracycline hydrochloride. In addition, minocycline produced much greater residual antimicrobial activity than the other two drugs after the end of the treatment period.Key Words: AcneAntimicrobial therapyPropionibacterium acne reductionMinocycline hydrochlorideDynacinDoxycycline hyclateMonodoxSumycinTetracycline hydrochloride
Effect of Biointerfacing Linker Chemistries on the Sensitivity of Silicon Nanowires for Protein Detection (2013)

Point-of-care diagnostics show promise in removing reliance on centralized lab testing facilities and may help increase both the survival rate for infectious diseases as well as monitoring of chronic illnesses. CMOS compatible diagnostic platforms are currently being considered as possible solutions as they can be easily miniaturized and can be cost-effective. Top-down fabricated silicon nanowires are a CMOS-compatible technology which have demonstrated high sensitivities in detecting biological analytes, such as proteins, DNA, and RNA. However, the reported response of nanowires to these analytes has varied widely since several different functionalization protocols have been attempted with little characterization and comparison. Here we report protocols for fabrication and functionalization of silicon nanowires which yield highly stable nanowires in aqueous solutions and limits of detection to ∼1 pg/mL of the model protein used in the study. A thorough characterization was done into optimizing the release of the silicon nanowires using combined dry and wet etch techniques, which yielded nanowires that could be directly compared to increase output statistics. Moreover, a range of different linker chemistries were tried for reacting the primary antibody, and its response to target and nonspecific antigens, with polyethylene glycol based linker BS(PEG)5 providing the best response. Consequently, this chemistry was used to characterize different oxide thicknesses and their responses to the mouse IgG antigen, which with the smallest oxide thickness yielded 0.1-1 pg/mL limits of detection and a dynamic range over 3 orders of magnitude.