gebhart/patrepeval huggingface dataset:
Differential nucleotide binding to catalytic and noncatalytic sites and related conformational changes involving .alpha./.beta.-subunit interactions as monitored by sensitive intrinsic-fluorescence in Schizosaccharomyces pombe mitochondrial F1 (1992)

Mitochondrial F1 from the yeast Schizosaccharomyces pombe exhibits an intrinsic tryptophan fluorescence sensitive to adenine nucleotides and inorganic phosphate [Divita, G., Di Pietro, A., Deléage, G., Roux, B., & Gautheron, D.C. (1991) Biochemistry 30, 3256-3262]. The present results indicate that the intrinsic fluorescence is differentially modified by nucleotide binding to either catalytic or noncatalytic sites. Guanine or hypoxanthine nucleotides, which selectively bind to the catalytic site, produce a hyperbolic saturation monitored by fluorescence quenching at 332 nm, the maximal emission wavelength. On the contrary, adenine nucleotides, which bind to both catalytic and noncatalytic sites, exhibit a biphasic saturation. High-affinity ATP binding produces a marked quenching as opposed to the lower-affinity one. In contrast, ADP exhibits a sigmoidal saturation, with high-affinity binding producing no quenching but responsible for positive cooperativity of binding to the lower-affinity site. The catalytic-site affinity for GDP is almost 20-fold higher at pH 5.0 as compared to pH 9.0, and the high sensitivity of the method allows detection of the 10-fold lower-affinity GMP binding. In contrast, high-affinity binding of ADP, or AMP, is not pH-dependent. The selective catalytic-site saturation induces a F1 conformational change decreasing the Stern-Volmer constant for acrylamide and the tryptophan fraction accessible to iodide. ATP saturation of both catalytic and noncatalytic sites produces an additional reduction of the accessible fraction to acrylamide.
TGF-b2 Induction Regulates Invasiveness of Theileria-Transformed Leukocytes and Disease Susceptibility (2010)

Theileria parasites invade and transform bovine leukocytes causing either East Coast fever (T. parva), or tropical theileriosis (T. annulata). Susceptible animals usually die within weeks of infection, but indigenous infected cattle show markedly reduced pathology, suggesting that host genetic factors may cause disease susceptibility. Attenuated live vaccines are widely used to control tropical theileriosis and attenuation is associated with reduced invasiveness of infected macrophages in vitro. Disease pathogenesis is therefore linked to aggressive invasiveness, rather than uncontrolled proliferation of Theileria-infected leukocytes. We show that the invasive potential of Theileria-transformed leukocytes involves TGF-b signalling. Attenuated live vaccine lines express reduced TGF-b2 and their invasiveness can be rescued with exogenous TGF-b. Importantly, infected macrophages from disease susceptible Holstein-Friesian (HF) cows express more TGF-b2 and traverse Matrigel with great efficiency compared to those from disease-resistant Sahiwal cattle. Thus, TGF-b2 levels correlate with disease susceptibility. Using fluorescence and time-lapse video microscopy we show that Theileria-infected, disease-susceptible HF macrophages exhibit increased actin dynamics in their lamellipodia and podosomal adhesion structures and develop more membrane blebs. TGF-b2-associated invasiveness in HF macrophages has a transcription-independent element that relies on cytoskeleton remodelling via activation of Rho kinase (ROCK). We propose that a TGF-b autocrine loop confers an amoeboid-like motility on Theileria-infected leukocytes, which combines with MMP-dependent motility to drive invasiveness and virulence.
Issues in the Design of the Fluconazole Prophylaxis Trials in Patients Undergoing Hematopoietic Stem Cell Transplantation (2004)

Today, invasive candidal infections are much less of a problem in patients undergoing hematopoietic stem cell transplantation (HSCT) than they were in the 1980s, principally because of widespread application of effective antifungal prophylaxis strategies. Two randomized, placebo-controlled studies performed in the early 1990s were instrumental in demonstrating the protective effects of fluconazole. Although both studies showed that candidiasis is prevented by fluconazole prophylaxis, controversies regarding optimal administration guidelines and the impact on survival after HSCT have persisted over the last decade. Details of how these trials were done, including the patients enrolled and end points evaluated, explain many of the different findings and controversies. An understanding of design issues can help explain current controversies and can assist in development of future prophylaxis studies.
Surface Stability in Liquid-Crystalline Block Copolymers with Semifluorinated Monodendron Side Groups (2000)

Block copolymers with semifluorinated monodendron side groups were synthesized by attachment of a first generation 2- or 3-armed monodendron acid chloride to a hydroxylated poly(styrene-b-1,2/3,4-isoprene). A convergent growth strategy was developed to synthesize the monodendron groups in good yield using an approach that could be extended to higher generation monodendrons. High extents of attachment were achieved despite the steric effects of the bulky monodendron side groups. The resulting polymers formed a smectic B mesophase at room temperature as determined by WAXS data. The transition temperatures, mesophase range, and enthalpy of the smectic B−isotropic transition were all affected by side-group structural factors such as flexible spacer length, mesogen length, and monodendron core. The critical surface tensions of the resulting semifluorinated polymers were as low as ∼8 mN/m as determined by Zisman analysis. Surface stability of polymer films in a polar liquid environment was strongly dependent on the extent of attachment exhibited by the semifluorinated groups. The monodendron −CF2− helix within 1 nm of the surfaces has a net orientation normal to the surface as measured by near-edge X-ray absorption fine structure (NEXAFS) methods, but the orientational order parameter Shelix is much higher for the 2-armed monodendrons than for the 3-armed monodendrons. In both cases Shelix seems insensitive to monodendron attachment density along the isoprene block. We suggest that packing frustration of the monodendron subunits produces surfaces with spontaneous curvature that differs depending on whether the monodendrons are 2- or 3-armed. The more highly curved surface topology of the 3-armed monodendrons may provide a partial explanation for its decreased orientational order.
Single-Molecule Speckle Analysis of Actin Filament Turnover in Lamellipodia (2002)

Lamellipodia are thin, veil-like extensions at the edge of cells that contain a dynamic array of actin filaments. We describe an approach for analyzing spatial regulation of actin polymerization and depolymerization in vivo in which we tracked single molecules of actin fused to the green fluorescent protein. Polymerization and the lifetime of actin filaments in lamellipodia were measured with high spatial precision. Basal polymerization and depolymerization occurred throughout lamellipodia with largely constant kinetics, and polymerization was promoted within one micron of the lamellipodium tip. Most of the actin filaments in the lamellipodium were generated by polymerization away from the tip.
Photonic Millimeter-Wave Generation and Distribution Techniques for Millimeter/Sub-Millimeter Wave Radio Interferometer Telescope (2010)

Advances in Lasers and Electro Optics 480 converted into millimeter-wave signal by the photo mixer at the remote antenna. The region from 27 GHz to 122 GHz (Table The two-tone generator requires polarization maintaining capability as well as mechanical vibration and acoustic noise robustness to avert the impact of the polarization effect on the photo-mixer and that of the polarization mode dispersion on the transmission fiber.
Pharmacology and Pharmacokinetics of A Novel Nonpeptide Angiotensin II Receptor Antagonist–DMP 811 (1995)

DMP 811 exhibited high binding affinity for the angiotensin II subtype receptor AT1 in rat adrenal tissues with an IC50 of 6 nM, but not for the subtype receptor AT2. In the isolated rabbit aorta, DMP 811 inhibited the contractile response to angiotensin II selectively and noncompetitively with a KB value of 0.1 nM. In conscious renal hypertensive rats, DMP 811 decreased blood pressure with i.v. and p.o. ED30s of 0.005 and 0.03 mg/kg, respectively (p.o. ED30 for losartan = 0.59 mg/kg). In conscious furosemide-treated dogs, DMP 811 given either at 0.3 or 1 mg/kg p.o. decreased blood pressure. DMP 811 has oral bioavailabilities of 7 and 29% in rats and dogs, respectively, after a solution dose and 8 and 13%, respectively, after a suspension or capsule dosing. Our study indicates that DMP 811 is a selective and insurmountable AT1 receptor antagonist and is a 20-fold more potent orally-active antihypertensive agent than losartan.
Shock wave induced enhancement of optical properties of benzil crystal (2018)

In this article, we present the results of the experimental work on the impact of shock waves on optical properties of benzyl crystalline material. Test material of benzil crystal is grown along [100] plane by Sankaranarayana — Ramasamy method. In the present work, the functional shock waves of Mach number 1.7 are generated from pressure driven shock tube. The optical properties of test material are investigated by UV-Visible spectrometer over the range between 200 and 800 nm. The observed results show that the intensity of the absorption spectrum is inversely proportional to the number of exposed shock waves. The direct and indirect optical band gap energy (Eg) and Urbach tail energy (Ug) are determined from the optical absorption spectrum for pre and post shock wave loaded condition and found that shock wave loaded test crystal has high band gap energy. The optical constants namely extinction coefficient, real and imaginary parts of the dielectric constant, skin depth, optical density, optical conductivity and electrical conductivity are investigated and the obtained results are compared with post shock wave loaded benzil crystal with the incident light possessing wavelength at 700 nm. The results are found to be very impressive for the shock wave recovery experiments that are to be clearly discussed.
[Sleep-wake regulation by prostaglandin D2 and adenosine]. (2012)

Prostaglandin (PG) D2 and adenosine are potent endogenous somnogens that accumulate in the brain during prolonged wakefulness. Lipocalin-type PGD synthase (L-PGDS) catalyzes the isomerization of PGH2, a common precursor of various prostanoids, to produce PGD2. L-PGDS is localized in the leptomeninges, choroid plexus, and oligodendrocytes of the central nervous system. PGD2 stimulates DP1 receptors localized in the basal forebrain and increases the local extracellular concentration of adenosine, a paracrine signaling molecule, to promote sleep. Adenosine activates adenosine A2A receptor-expressing neurons in the basal forebrain and ventrolateral preoptic area (VLPO) and inhibits adenosine A1 receptor-possessing arousal neurons. Sleep-promoting neurons in the VLPO send inhibitory signals to suppress the histaminergic neurons in the tuberomammillary nucleus (TMN); the histaminergic neurons contribute to arousal through histamine H1 receptors. GABAergic inhibition of TMN is involved in the induction of non-rapid eye movement (non-REM) sleep by PGD2 and adenosine A2A agonists. The neural network between the VLPO and TMN is considered to play a key role in regulation of vigilance states. Administering an L-PGD inhibitor (SeCl4), DP1 antagonist (ONO-4127Na), or adenosine A2A receptor antagonist (caffeine) suppresses both non-REM and REM sleep, indicating that the PGD2-adenosine system is crucial for maintaining physiological sleep. Selective gene-deletion strategies based on Cre/loxP technology and focal RNA interference have been used for silencing the expression of the A2A receptor by local infection with adeno-associated virus carrying Cre-recombinase or short hairpin RNA. The results of these studies have shown that the A2Asubreceptors in the shell region of the nucleus accumbens are responsible for the effect of caffeine on wakefulness.
Predicting indirect branches via data compression (2002)

Branch prediction is a key mechanism used to achieve high performance on multiple issue, deeply pipelined processors. By predicting the branch outcome at the instruction fetch stage of the pipeline, superscalar processors become able to exploit Instruction Level Parallelism (ILP) by providing a larger window of instructions. However, when a branch is mispredicted, instructions from the mispredicted path must be discarded. Therefore, branch prediction accuracy is critical to achieve high performance. Existing branch prediction schemes can accurately predict the direction of conditional branches, but have difficulties predicting the correct targets of indirect branches. Indirect branches occur frequently in Object-Oriented Languages (OOL), as well as in Dynamically-Linked Libraries (DLLs), two programming environments rapidly increasing in popularity. In addition, certain language constructs such as multi-way control transfers (e.g., switches), and architectural features such as 64-bit address spaces, utilize indirect branching. In this paper, we describe a new algorithm for predicting unconditional indirect branches called Prediction by Partial Matching (PPM). We base our approach on techniques proven to work optimally in the field of data compression. We combine a viable implementation of the PPM algorithm with dynamic per-branch selection of path-based correlation and compare its prediction accuracy against a variety of predictors. Our results show that, for approximately the same hardware budget, the combined predictor can achieve a misprediction ratio of 9.47%, as compared to 11.48% for the previously published most accurate indirect branch predictor.
ChemInform Abstract: Regio‐ and Enantioselective Hydroamination of Dienes by Gold(I)/Menthol Cooperative Catalysis. (2012)

Abstract Pyrrolidine and piperidine adducts are formed with high regio‐and enantioselectivities only in the presence of menthol.
Tolerance of RZ-DPSK signal to pattern effects in Raman amplifier with forward pumping (2003)

Waveform distortion in forward-pumped Raman amplifiers with dynamic pump depletion is numerically studied. The RZ-DPSK format, which shows 17 dB higher tolerance than the NRZ format to the forward Raman gain, provides significant flexibility in system design.
Synthesis of Pyridopyrazine-1,6-dione γ-Secretase Modulators via Selective 4-Methylimidazole N1-Buchwald Arylation (2019)

An efficient synthesis of pyridopyrazine-1,6-dione γ-secretase modulators (GSMs) is described. Our route features the construction of a crystalline lactone intermediate via a selective palladium-catalyzed 4-methylimidazole N<sup>1</sup>-arylation using the Buchwald Xantphos Pd G4 precatalyst, which does not require a preactivation step. The weak inorganic base KHCO<sub>3</sub> was employed to minimize saponification of a particularly sensitive lactone substrate. Additional key transformations include DABAL-Me<sub>3</sub>-mediated lactone aminolysis and a mild TBD/ethyl trifluoroacetate mediated lactam ring closure to afford a representative GSM in high yield.
New measurements of the D→μν form factor ratios (2002)

Using a large sample of D+→K−π+μ+ν decays collected by the FOCUS photoproduction experiment at Fermilab, we present new measurements of two semileptonic form factor ratios: rv and r2. We find rv=1.504±0.057±0.039 and r2=0.875±0.049±0.064. Our form factor results include the effects of the s-wave interference discussed in Phys. Lett. B 535 (2002) 43.
Coordinating Investment, Production, and Subcontracting (1999)

We value the option of subcontracting to improve financial performance and system coordination by analyzing a competitive stochastic investment game with recourse. The manufacturer and subcontractor decide separately on their capacity investment levels. Then demand uncertainty is resolved and both parties have the option to subcontract when deciding on their production and sales. We analyze and present outsourcing conditions for three contract types: (1) price-only contractswhere an ex-ante transfer price is set for each unit supplied by the subcontractor; (2) incomplete contracts, where both parties negotiate over the subcontracting transfer; and (3) state-dependentprice-only and incomplete contracts for which we show an equivalence result. While subcontracting with these three contract types can coordinate productiondecisions in the supply system, only state-dependent contracts can eliminate all decentralization costs and coordinate capacity investmentdecisions. The minimally sufficient price-only contract that coordinates our supply chain specifies transfer prices for a small number (6 in our model) of contingent scenarios. Our game-theoretic model allows the analysis of the role of transfer prices and of the bargaining power of buyer and supplier. We find that sometimes firms may be better off leaving some contract parameters unspecified ex-ante and agreeing to negotiate ex-post. Also, a price-focused strategy for managing subcontractors can backfire because a lower transfer price may decrease the manufacturer's profit. Finally, as with financial options, the option value of subcontracting increases as markets are more volatile or more negatively correlated.
ChemInform Abstract: BN 80927: A Novel Homocamptothecin with Inhibitory Activities on Both Topoisomerase I and Topoisomerase II. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Selective Repopulation of Normal Mouse Liver by Hepatocytes Transduced in Vivo with Recombinant Adeno-Associated Virus (2001)

The use of recombinant adeno-associated virus (rAAV) as gene therapy vector for treating liver metabolic diseases is limited by its low transduction efficiency. We describe a strategy for achieving stable and efficient genetic reconstitution in liver after direct administration of rAAV and selective expansion of transduced cells. We have exploited the biology of apoptosis to develop a generic approach for selectively repopulating liver with vector-transduced hepatocytes. Low-level, stable transduction of hepatocytes was achieved by direct injection of rAAV into mouse liver. Expansion of these vector-transduced cells was achieved by incorporating into the construct a minigene expressing Bcl-2 followed by induction of apoptosis in non-vector-containing hepatocytes by systemic administration of a Fas antibody (Ab). Western and Southern blot analysis demonstrated amplification of bcl-2 gene product and viral copy number, respectively, in vector-treated mouse liver when placed under selection. In addition, the percentage of vector transduced cells increased from 2 to 20% after three administrations of Fas Ab, based on immunohistochemical studies.
F-Band Bidirectional Amplifier Using 75-nm InP HEMTs (2012)

We have developed an F-band (90 to 140 GHz) bidirectional amplifier MMIC using a 75-nm InP HEMT technology for short-range millimeter-wave multi-gigabit communication systems. Inherent symmetric common-gate transistors and parallel circuits consisting of an inductor and a switch realizes a bidirectional operation with a wide bandwidth of over 50 GHz. Small signal gains of 12-15 dB and 9-12 dB were achieved in forward and reverse directions, respectively. Fractional bandwidths of the developed bidirectional amplifier were 39% for the forward direction and 32% for the reverse direction, which were almost double as large as those of conventional bidirectional amplifiers. The power consumption of the bidirectional amplifier was 15 mW under a 2.4-V supply. The chip measures 0.70 × 0.65 mm. The simulated NF is lower than 5 dB, and P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</sub> is larger than 5 dBm. The use of this bidirectional amplifier provides miniaturization of the multi-gigabit communication systems and eliminates signal switching loss.
Author response: Safety and efficacy of venoplasty in MS: A randomized, double-blind, sham-controlled phase II trial (2019)

On behalf of all coauthors, we thank Juurlink et al. for the comment on our article.1 Regarding flow: The preplanned experimental procedure was dilation of extracranial venous narrowing as proposed by Zamboni et al.2 Up to 3 dilation attempts were permitted to ensure optimal expansion of the narrowing.
Dopamine Receptor Subtype-Selective Drugs: D2-Like Receptors (2009)

Drugs that are known to activate or block dopamine receptors are widely used for the treatment of a number of severe diseases. In most cases, dopaminergic drugs preferentially interact with the subtypes of the D2 family (D2, D3, D4). However, only minor selectivity has been observed between D2, D3, and D4. Nevertheless, in recent years D3 and D4 subtype-selective agonists, partial agonists, and antagonist have been developed. The most interesting structural features required for high selectivity and affinity are presented as well as structure–activity relationship (SAR) studies. Moreover, the use of subtype-selective radioligands is discussed.
3-D Enzymatic Nanomaterial Architectures for Energy Harvesting (2016)

Abstract : In this innovative and highly collaborative 4 year proposal, we had two overriding objectives: 1) to design, develop, and demonstrate new techniques for engineering biological components that are optimized for integration with nanoscale materials and 2) to create and characterize multifunctional heterogeneous biomacromolecular assemblies that will facilitate energy harvesting applications. To accomplish these goals, a holistic approach was taken both experimentally and computationally that helped build a foundation for a new paradigm in biotechnology. Specifically, we designed, developed and created these systems at the molecular level while using a systems level process view to guide the designs.
The uptake of ampicillin-loaded nanoparticles by murine macrophages infected with Salmonella typhimurium (1994)

The purpose of this study was to investigate the in-vitro interaction between [3H]ampicillin-loaded polyisohexylcyanoacrylate nanoparticles and murine macrophages (peritoneal and J774) infected with Salmonella typhimurium. The multiplicity of infection was ten bacteria to each macrophage and the mean (+/- S.D.) diameter of the nanoparticles was 220 (+/- 20 nm), corresponding to an ampicillin concentration of 2 g/L. The uptake of nanoparticle-bound [3H]ampicillin by non-infected J774 and peritoneal macrophages was six- and 24-fold greater respectively than that of free [3H]ampicillin. For infected cells, uptake by J774 and peritoneal macrophages was nine- and 20-fold greater respectively. However, there was no difference between nanoparticle-bound ampicillin and free ampicillin in terms of bactericidal activity against intracellular S. typhimurium. This unexpected observation might be accounted for by bacterium-induced inhibition of phagosome-lyosome fusion within the macrophages, thereby preventing contact between the bacteria in the phagosomes and the nanoparticles in the secondary lysosomes.