gebhart/patrepeval huggingface dataset:
Efficient activation of a visible light-activatable CA4 prodrug through intermolecular photo-unclick chemistry in mitochondria (2017)

Photo-unclick chemistry mediates visible and near IR-controlled drug release via a singlet oxygen (SO)-cleavable linker. Due to the limited diffusion distance of SO in biological systems, a photosensitizer and the SO-cleavable linker have been conjugated in one molecule or mixed in nano-drug delivery systems. In this communication, we demonstrate a new strategy to activate prodrugs with photo-unclick chemistry in an intermolecular fashion using an SO-cleavable CA4 prodrug and a mitochondria-specific photosensitizer, protoporphyrin IX, formed from prodrug hexyl-5-aminolevulinate.
HLM1, an Essential Signaling Component in the Hypersensitive Response, Is a Member of the Cyclic Nucleotide–Gated Channel Ion Channel Family[W] (2003)

The hypersensitive response (HR) in plants is a programmed cell death that is commonly associated with disease resistance. A novel mutation in Arabidopsis, hlm1, which causes aberrant regulation of cell death, manifested by a lesion-mimic phenotype and an altered HR, segregated as a single recessive allele. Broad-spectrum defense mechanisms remained functional or were constitutive in the mutant plants, which also exhibited increased resistance to a virulent strain of Pseudomonas syringae pv tomato. In response to avirulent strains of the same pathogen, the hlm1 mutant showed differential abilities to restrict bacterial growth, depending on the avirulence gene expressed by the pathogen. The HLM1 gene encodes a cyclic nucleotide-gated channel, CNGC4. Preliminary study of the HLM1/CNGC4 gene pro-duct in Xenopus oocytes (inside-out patch-clamp technique) showed that CNGC4 is permeable to both K(+) and Na(+) and is activated by both cGMP and cAMP. HLM1 gene expression is induced in response to pathogen infection and some pathogen-related signals. Thus, HLM1 might constitute a common downstream component of the signaling pathways leading to HR/resistance.
Inactivated parapoxvirus ovis (Orf virus) has antiviral activity against hepatitis B virus and herpes simplex virus (2003)

It is known that some viruses are able to induce vigorous immune reactions. This study shows that inactivated parapoxvirus ovis (Orf virus), strain D1701 (PPVO), induces an autoregulatory cytokine response that involves the upregulation of IL-12, IL-18, IFN-gamma and other T helper 1-type cytokines and their subsequent downregulation, which is accompanied by induction of IL-4. An increase in IL-10 expression was also found in the livers of PPVO-treated mice. PPVO protects mice from lethal herpes simplex virus type 1 infection and guinea pigs from recurrent genital herpes disease. With dosages as low as 500 000 virus particles, PPVO is more potent than the current standard 3TC therapy in hepatitis B virus transgenic mice. No signs of inflammation or any other side effects were observed. PPVO induces IL-12, TNF-alpha and, together with a suboptimal concentration of Concanavalin A, IFN-gamma in human peripheral blood leukocytes as well. The principle of an autoregulatory cytokine induction by an inactivated virus might have advantages over existing immune therapies and it is concluded that inactivated PPVO should be investigated further for its potential use in antiviral therapy.
Dynamics of the baseball–bat collision (2000)

A model is developed for the collision between the baseball and bat, taking into account the transverse bending vibrations of the bat. By coupling the flexible bat to the ball via a parametrized force that each mutually exerts on the other, a complete description of the collision process is obtained, including the exit speed of the ball vf. It is shown that vibrations play an important role in determining vf. The model is in excellent agreement with experimental data at low impact velocities. At the higher velocities more appropriate to the game of baseball, vf is shown to coincide with the rigid-body value only over a very small region in the barrel of the bat and to drop off sharply for impacts removed from that region. Some interesting insights into the collision process are obtained, including the observation that for impacts in the barrel of the bat, the momentum transferred to the ball is essentially complete by the time the elastic wave first arrives at the handle and that any clamping action of the hands will affect the bat at the impact point only after the ball and bat have separated. This suggests that vf is independent of the size, shape, and method of support of the bat at distances far from the impact location.
Altered growth-rate-dependent regulation of 6-phosphogluconate dehydrogenase level in hisT mutants of Salmonella typhimurium and Escherichia coli (1990)

In Escherichia coli, the level of 6-phosphogluconate dehydrogenase is directly proportional to the cellular growth rate during growth in minimal media. This contrasts with the report by Winkler et al. (M. E. Winkler, J. R. Roth, and P. E. Hartman, J. Bacteriol. 133:830-843, 1978) that the level of the enzyme in Salmonella typhimurium LT-2 strain SB3436 is invariant. The basis for the difference in the growth-rate-dependent regulation between the two genera was investigated. Expression of gnd, which encodes 6-phosphogluconate dehydrogenase, was growth rate uninducible in strain SB3436, as reported previously, but it was 1.4-fold growth rate inducible in other S. typhimurium LT-2 strains, e.g., SA535. Both the SB3436 and SA535 gnd genes were growth rate inducible in E. coli K-12. Moreover, the nucleotide sequences of the regulatory regions of the two S. typhimurium genes were identical. We concluded that a mutation unlinked to gnd is responsible for the altered growth rate inducibility of 6-phosphogluconate dehydrogenase in strain SB3436. Transductional analysis showed that the altered regulation is due to the presence of a mutation in hisT, the gene for the tRNA modification enzyme pseudouridine synthetase I. A complementation test showed that the regulatory defect conferred by the hisT mutation was recessive. In E. coli, hisT mutations reduced the extent of growth rate induction by the same factor as in S. typhimurium. The altered regulation conferred by hisT mutations was not simply due to their general effect of reducing the polypeptide chain elongation rate, because miaA mutants, which lack another tRNA modification and have a similarity reduced chain growth rate, had higher rather than lower 6-phosphogluconate dehydrogenase levels. Studies with genetic fusions suggested that hisT mutations lower the gnd mRNA level. The data also indicated that hisT is involved in translational control of gnd expression, but not the aspect mediated by the internal complementary sequence.
Extensions of Generalized Binary Search to Group Identification and Exponential Costs (2010)

Generalized Binary Search (GBS) is a well known greedy algorithm for identifying an unknown object while minimizing the number of yes or no questions posed about that object, and arises in problems such as active learning and active diagnosis. Here, we provide a coding-theoretic interpretation for GBS and show that GBS can be viewed as a top-down algorithm that greedily minimizes the expected number of queries required to identify an object. This interpretation is then used to extend GBS in two ways. First, we consider the case where the objects are partitioned into groups, and the objective is to identify only the group to which the object belongs. Then, we consider the case where the cost of identifying an object grows exponentially in the number of queries. In each case, we present an exact formula for the objective function involving Shannon or Renyi entropy, and develop a greedy algorithm for minimizing it.
FoxO3a (Forkhead Box O3a) Deficiency Protects Idiopathic Pulmonary Fibrosis (IPF) Fibroblasts from Type I Polymerized Collagen Matrix-Induced Apoptosis via Caveolin-1 (cav-1) and Fas (2013)

Idiopathic Pulmonary Fibrosis is a lethal fibrotic disease characterized by the unrelenting proliferation and persistence of fibroblasts in a type I collagen-rich matrix that result in an expanding reticular network of fibrotic tissue. However, the underlying mechanism responsible for the persistence of myofibroblasts in IPF remains unclear. During normal tissue repair, unwanted fibroblasts are eliminated during collagen-matrix contraction by a mechanism whereby high PTEN activity suppresses Akt. We have previously found that FoxO3a, a transcriptional activator of apoptosis-inducing proteins, is inactivated in IPF fibroblasts resulting from aberrantly high PI3K/Akt activity due to inappropriately low PTEN activity. Here we demonstrate that this low FoxO3a activity confers IPF fibroblasts with resistance to collagen-mediated apoptosis. We show that the mechanism by which low FoxO3a activity confers IPF fibroblasts with an apoptotic resistant phenotype involves suppression of Fas expression as a result of down regulation of cav-1 expression via a PTEN/Akt-dependent pathway. We demonstrate that PTEN over-expression or Akt inhibition increases FoxO3a expression in IPF fibroblasts, resulting in up-regulation of caveolin-1. We show that FoxO3a binds to the cav-1 promoter region and ectopic expression of FoxO3a transcriptionally increases cav-1 mRNA and protein expression. In turn, we show that overexpression of caveolin-1 increases Fas levels and caspase-3/7 activity and promotes IPF fibroblast apoptosis on polymerized type I collagen. We have found that the expression of caveolin-1, Fas and cleaved caspase-3 proteins in fibroblasts within the fibroblastic foci of IPF patient specimens is low. Our data indicate that the pathologically altered PTEN/Akt axis inactivates FoxO3a down-regulating cav-1 and Fas expression. This confers IPF fibroblasts with an apoptosis-resistant phenotype and may be responsible for IPF progression.
The effect of Lactobacillus buchneri, with or without homofermentative lactic acid bacteria, on the fermentation, aerobic stability and ruminal degradability of wheat, sorghum and maize silages (2003)

The use of L. buchneri, with or without homofermentative LAB, as a silage inoculant can improve the aerobic stability of silages by inhibition of yeast activity.
Generation of Secondary, Tertiary, and Quaternary Centers by Geminal Disubstitution of Carbonyl Oxygens (2010)

Methods for replacing the carbonyl oxygen by two new substituents (C=O→CR(1)R(2)) are discussed in this Minireview, whereby R may be H, NR(2), alkyl, allyl, benzyl, vinyl, alkynyl, aryl, heteroaryl, or acyl groups. The most frequently used starting materials for geminal disubstitution with the formation of two C-C bonds (R(1),R(2)≠H, NR(2)) are amides and thioamides, which react with organometallic nucleophiles R-M (M=Li, MgX, CeX(2), TiX(3), ZrX(3)) to give tertiary sec- and tert-alkylamines. Quaternary centers can be built directly from ketones by treatment with Me(3)Al, MeTiCl(3), or Me(2)TiCl(2) (R(1)R(2)C=O→R(1)R(2)CMe(2)). The scope and limitations of the various methods and mechanistic models are briefly discussed. The remarkable variety and diversity of structures thus accessible are demonstrated by numerous examples.
The CircleSegmentView: a visualization for query preview and visual filtering (2005)

Users of Information Retrieval systems have often been the target group of Human-Computer Interaction researchers. A lot of effort has been spent inventing new forms of visualizations to support the information seeking process. Information Retrieval and Information Visualization are tight coupled fields of research. Together with psychology (which answers questions like 'how' do users search) and usability engineering (answering questions like 'what' do user expect from user interfaces and their behavior) the research on improving information seeking systems goes on. This paper will concentrate on a meta-data driven, user-centered approach for the query formulation stage. In contrast to the intense research on result-set visualizations we will focus on the development of a visualization which supports human search behavior at the query stage. Additionally this visualization proved that it can compete with other visualizations like the scatter-plot as a visual filter in the result-set presentation.
Bright, Color-Tunable Fluorescent Dyes Based on π-Expanded Diketopyrrolopyrroles (2012)

A synthetic approach to the structurally diverse family of π-expanded diketopyrrolopyrroles is described. A three-step strategy appears to be very general and starts with the preparation of diketopyrrolopyrroles followed by N-alkylation with bromoacetaldehyde diethyl acetal and electrophilic aromatic substitution. The final reaction regioselectively furnishes S-shaped, violet and blue functional dyes of previously unknown structure. New dyes possess sharp absorption and emission peaks, with very high molar absorption coefficients and reasonable fluorescence quantum yields. As a proof of principle, cell uptake of selected dye was demonstrated.
Edar and Troy signalling pathways act redundantly to regulate initiation of hair follicle development (2008)

The development of ectodermal organs requires signalling by ectodysplasin (Eda), a tumor necrosis factor (TNF) family member, its receptor Edar and downstream activation of the nuclear factor kappaB (NF-kappaB) transcription factor. In humans, mutations in the Eda pathway components cause hypohidrotic ectodermal dysplasia, a syndrome characterized by missing teeth, sparse hair and defects in sweat glands. It has been postulated that Eda acts redundantly with another TNF pathway to regulate ectodermal organogenesis. A potential candidate is Troy (or TNFRSF19 or Taj), a TNF receptor which is homologous with Edar in its ligand-binding domain, and is expressed in an overlapping pattern. We have characterized Troy null mice and crossed them with Eda-deficient mice. Single Troy mutants had no defects in ectodermal organs. Analysis of the double mutants revealed an essential role for Troy in hair follicle development. In mice, hair follicles develop in three different waves. Only primary hair follicles are missing in Eda single mutants, whereas the compound mutants lacked also the follicles of the second wave, as well as all hair follicles in the middle of crown leading to focal alopecia. Assessment of NF-kappaB activity with a transgenic reporter construct indicated that Eda is the main activator of NF-kappaB signalling in developing skin appendages and surprisingly that the functional overlap of Troy and Eda signalling pathways is mediated by NF-kappaB independent pathways.
Broadleaf Herbicide Effects on Clethodim and Quizalofop-P Efficacy on Volunteer Wheat (<i>Triticum aestivum</i>) (2006)

Field experiments were conducted at three locations in 2003 and 2004 to examine clethodim and quizalofop-P efficacy on spring wheat seedlings when applied alone or in tank mixtures with herbicides used to control broadleaf weeds. Clethodim at the recommended rate of 30 g/ha reduced spring wheat biomass by 63 to 98% and was only >90% in three of six site years. In contrast, quizalofop-P at the recommended rate of 36 g/ha reduced wheat biomass >90% in all cases. Clethodim or quizalofop-P could be tank mixed with 2,4-D ester, bromoxynil, or bromoxynil plus MCPA ester with little risk of reduced efficacy on wheat. However, 2,4-D amine was highly antagonistic to both herbicides. The commercial mixture of thifensulfuron plus tribenuron reduced clethodim, but not quizalofop-P, efficacy on wheat. Herbicide options exist for simultaneous control of volunteer glyphosate-resistant canola and glyphosate-resistant wheat if the latter technology were to be commercialized in the future.
Influence of vehicle resistance on transdermal iontophoretic delivery of acetylcholine and sodium nitroprusside in humans (2004)

Iontophoresis is a valuable method of noninvasive drug delivery for assessment of skin microvascular function, but it is important to consider and minimize its potential nonspecific electrical effects on blood flow. The use of sodium chloride (NaCl) instead of water as the iontophoresis vehicle has been reported to reduce these effects because it has a lower electrical resistance. However, this argument may not be valid when an agonist is added to the vehicle because its resistance will be changed. The aim of our study was to determine whether there is a difference in resistance between water and NaCl when used as vehicles for iontophoresis of acetylcholine (ACh) and sodium nitroprusside (SNP). Four cumulative doses of each drug, dissolved in either water or NaCl, were delivered via iontophoresis to the forearm skin of 14 healthy volunteers. We measured the resulting blood flow responses by using laser-Doppler imaging and the voltage across the electrodes for each delivery as an index of resistance. For ACh and SNP, there were no significant differences between the voltages measured when either water or NaCl was used as the vehicle. However, the blood flow responses to both agonists were significantly lower with NaCl (ACh: 25% lower, P < 0.001; SNP: 15% lower, P = 0.019). The use of NaCl is therefore unlikely to decrease any nonspecific electrical effects, and it may in fact reduce the effective dose of drug delivered. Deionized water is a better iontophoresis vehicle for the assessment of microvascular function in skin when using ACh and SNP.
Characterization of the cDNA and Genomic Sequence of a G Protein γ Subunit (γ <sub>5</sub> ) (1992)

A cDNA from human placenta and liver tissues that contained both sequence for the lysosomal glycosidase di-N-acetylchitobiase and sequence homologous to the gamma subunit of GTP-binding proteins was previously isolated. Here we have shown that the gamma-subunit-homologous portion of this unusual cDNA is derived from a member of the gamma-subunit multigene family. The partial human gamma-subunit sequence was used to isolate the corresponding full-length cDNA clones from bovine and rat livers. The two cDNAs encode identical 68-amino-acid proteins (7.3 kDa) homologous to previously cloned G protein gamma subunits. The bovine gene sequence encoding this new gamma-subunit isoform (gamma 5) was determined and found to have an intron-exon structure consistent with the original human chitobiase-gamma 5-subunit hybrid mRNA being a product of alternative splicing. Genomic cloning also resulted in the isolation of a human gamma 5 pseudogene.
Design of an Inline Power Generating System for Remote Oil and Gas Production Installation (2012)

Abstract A major challenge faced by oil and gas production companies is the supply of a reliable, cost effective, low maintenance and renewable source of power supply to the remote wellheads especially in areas prone to vandalization. Strategies deployed to provide power supply at these remote locations range from the installation of diesel generator sets, solar panels, inverters and battery banks among others. These solutions have been found to require constant monitoring and fueling in the case of the diesel generators, been prone to vandalization as in the case of solar panels and batteries. The inline power supply system comprises of a turbine system installed in a branch pipe. The system is inserted on a flow line from the wellhead so that it utilizes the fluid flow to provide the required kinetic energy to turn the turbine which is direct coupled to a gear and a DC generator. The output of the generator is fed to an electronic board which comprises of a regulator and a DC/DC converter. The DC/DC converter is responsible for providing the required DC level for wellhead instruments and communication devices. The system comprises of two identical installations in branched pipes providing 100% redundancy. The main application for this technology is in the provision of safe and vandalization proof power supply to remote oil and gas production installations especially at the wellheads. No oil or gas preprocessing is required as the turbine requires only the kinetic energy in the fluid. The use of an active flow line also guarantees the system protection against vandalization. The 100% redundancy guarantees that the system has negligible impact on the production process once deployed. The system provides a safe and cost effective safe power supply system for wellhead locations and reduces the OPEX required to keep the production facility powered
A low voltage actuated micromirror with an extra vertical electrode for 90  rotation (2003)

We have proposed a new type of electrostatic actuator for optical switching which has trench structure to make low voltage driving possible. Its lower or fixed electrode consists of a horizontal electrode and an extra vertical one which acts as a stopper for the exact 90° rotation. To fabricate the proposed actuator, a new planarization approach, laminating an organic film on a wafer, has been introduced to make a planar sacrificial layer over the trench. Comparison of theoretical analysis with experimental result has been made for the actuator. We have found that the actuation voltage (47 V) could be reduced up to 50% of that of the conventional one. The rising and falling times were measured to be 5 and 15 ms, respectively. The planarization process can be very effective and powerful for structures with deep trenches or pits.
The Transcription Factor IRF3 Triggers “Defensive Suicide” Necrosis in Response to Viral and Bacterial Pathogens (2013)

Although molecular components that execute noninflammatory apoptotic cell death are well defined, molecular pathways that trigger necrotic cell death remain poorly characterized. Here, we show that in response to infection with adenovirus or Listeria monocytogenes, macrophages in vivo undergo rapid proinflammatory necrotic death that is controlled by interferon-regulatory factor 3 (IRF3). The transcriptional activity of IRF3 is, surprisingly, not required for the induction of necrosis, and it proceeds normally in mice deficient in all known regulators of necrotic death or IRF3 activation, including RIPK3, caspases 1, 8, or 11, STING, and IPS1/MAVS. Although L. monocytogenes triggers necrosis to promote the infection, IRF3-dependent necrosis is required for reducing pathogen burden in the models of disseminated infection with adenovirus. Therefore, our studies implicate IRF3 as a principal and nonredundant component of a physiologically regulated necrotic cell-death pathway that operates as an effective innate immune mechanism of host protection against disseminated virus infection.
Water treatment membrane processes (1996)

Part 1 An overview of membrane processes and their application in water treatment: the emergence of membranes in water and wastewater treatment membrane applications - a contaminant-based perspective categories of membrane technologies. Part 2 Principles of membrane performance: models of rejection in dP processes models for sensitivity in electrodialysis models for selectivity in multiphase processes mass transport and permeate flux in dP processes biofouling of membranes. Part 3 Process applications: field evaluation and piloting reverse osmosis nanofiltration ultrafiltration microfiltration electrodialysis. Part 4 Membrane reactors: PAC/membrane reactors coagulation and membrane separation membrane bioreactors ion exchange membrane reactors. Part 5 Future developments.