gebhart/patrepeval huggingface dataset:
Assessing the Protonation State of Drug Molecules:  The Case of Aztreonam (2006)

Herein we examine the viability of physicochemical approaches based on standard computational chemistry tools to characterize the structure and energetics of flexible drug molecules with various titratable sites. We focus on the case of the monobactam antibiotic aztreonam, whose structure and physicochemical properties have been ascribed to several tautomeric forms, although it is still unclear which protonation states are responsible for its biological activity. First, we experimentally determined the pKa values for aztreonam over the pH range 0.8-7.0 using both 1H NMR and 13C NMR spectroscopy. Second, we carried out quantum chemical calculations on snapshots extracted from classical molecular dynamics simulations. Various levels of approximation were used in the energy calculations: ONIOM(HF/3-21G*:AMBER) for geometry relaxation, B3LYP/6-31+G** for electronic and electrostatic solvation energies, and molecular mechanics for attractive dispersion energy. The value of the free energy of solvation of a proton was treated as a parameter and chosen to give the best match between calculated and experimental pKa values for small molecules. Overall, this computational scheme can give satisfactory results in the pKa calculations for drug molecules.
Automatic vehicle identification systems—Methods of approach (1970)

Many agencies, both governmental and private, in the highway transportation field need a system which would automatically identify motor vehicles. The basic concept of such a system requires a vehicle-mounted coded device, a transponder, that uniquely identifies that vehicle. As this vehicle comes within the range of a system interrogator installed along or on the highway, the code is read by this interrogator and the identification of the vehicle is obtained. The ideal transponder is passive and requires no power; has no effect on, and is not affected by the vehicle; does not require physical contact with the interrogator, and requires no action by the vehicle operator. Sensing at a distance (noncontact) involves the detection of some type of energy; either radiated or reflected from the object being monitored. Many different sensing techniques, including magnetic, infrared, optical, sonic, radioactive, radio frequency (RF) transmission, microwaves, have been surveyed, investigated, and analyzed to determine their applicability for an automatic vehicle identification (AVI) system. This analysis has concluded that a low-frequency induction system is presently the most appropriate method for use on the highway environment, Several diverse systems differing in design details have been constructed and tested, utilizing this basic technique. This paper describes the design of these systems as well as the methods that have been proposed and/or developed using the other sensing technologies.
A convenient procedure for the efficient preparation of alkyl (<i>Z</i>)-3-iodo-2-alkenoates (1994)

Reaction of alkyl 2-alkynoates with sodium iodide (1.6–5.5 equiv.) in acetic acid (6.2–13 equiv.) at 115 °C provides good to excellent yields of the corresponding alkyl (Z)-3-iodo-2-alkenoates.
Influence of Season and Moonlight on Temporal-Activity Patterns of Indian Crested Porcupines (Hystrix indica) (1988)

During a 1-year period, onset and termination of nocturnal surface activity were monitored in as many as eight free-ranging Indian crested porcupines (Hystrix indica) in the Negev desert highlands of southern Israel by radio-location telemetry. Porcupines optimized winter (October–March) activity for minimal exposure to moonlight, but moonlight avoidance waned thereafter and disappeared by late summer (August–September). Rain curtailed activity, but there was no correlation between duration of activity and minimum near-ground temperatures. Individual variation in activity was large in all seasons. Duration of activity and the proportions of dark and nights hours used increased from winter to late summer. Adult-sized animals (14.1 ± 3.0 kg body mass) averaged 7.0 ± 0.4 h surface activity year-round, but this peaked at 9.2 ± 1.3 h in late summer when nearly all night hours were used. In winter, activity averaged 6.7 ± 0.8 h and porcupines were active for longer periods on dark nights than on moonlit nights. Seasonal changes in duration of activity (and moonlight exposure) may have been caused by variations in available dark hours relative to surface-activity requirements or to food-density fluctuations, but they did not clearly correspond to key stages of porcupine reproduction.
The Cordycepin Analogue of 2,5A and Its Threo Isomer. Chemical Synthesis, Conformation and Biological Activity. (1986)

A new synthesis of the cordycepin analogue of 2,5A and its threo isomer is reported along with an assessment of their conformations by circular dichroism spectroscopy. Evidence is also presented showing that these compounds are stable against 2,5A-specific phosphodiesterase and are not able to activate the 2,5A-dependent endoribonuclease, possibly due to a reduced binding to the latter enzyme as compared to that of 2,5A.
Synthesis and Antibacterial Activity of Urea and hiourea Derivatives at C-8 Alkyl Chain of Anacardic Acid Mixture Isolated from a Natural Product Cashew Nut Shell Liquid (CNSL) (2011)

Synthesis and antibacterial activity of some novel urea and thiourea derivatives (7a-7k, 8a-8f) of anacardic acid prepared from commercially available anacardic acid which is obtained from natural product Cashew Nut Shell Liquid (CNSL). Compounds (7a-7k, 8a-8f) were tested for Gram positive and Gram negative bac- terial cultures. Most of the compounds were showed active compared with standard drug ampicilline.
The Active Camera as a Projective Pointing Device. (1995)

This paper demonstrates an approach which exploits an active camera as a projective pointing mechanism. The optical centre of a static camera is notionally substituted by the centre of rotation of the active camera, as is the image plane by a frontal plane, a plane perpendicular to the optical axis of the active camera in its resting direction. Algorithms devised for 3D motion and 3D structure recovery using a single passive camera become immediately applicable to the active camera without need for reformulation. Furthermore, because the active camera can access a panoramic field of view, instabilities which may arise when the field of view is small, or because the shared field of view between successive after movement is small, are lessened. Two quite different applications of the idea are presented. In the first, the homography between a planar surface in the scene and the frontal plane is recovered and used to recover scene trajectories. In the second, the essential matrix between points in two frontal-plane views is recovered and used to determine the motion of a mobile vehicle.
New approach to grow pseudomorphic structures over the critical thickness (1991)

We propose to grow pseudomorphic and heteroepitaxial structures on thin, free-standing substrates. From the theoretical analysis, pseudomorphic layers of arbitrary thickness can be grown on a substrate thinner than the critical thickness. Even if the substrate is twice as thick as the critical thickness, very high-quality heteroepitaxy can still be achieved with all the threading dislocations gettered by the thin substrate. The conclusions derived from the theoretical models can be applied to most of the pseudomorphic and heteroepitaxial material systems of current interest.
Proline dehydrogenase (oxidase), a mitochondrial tumor suppressor, and autophagy under the hypoxia microenvironment (2012)

Proline dehydrogenase (oxidase, PRODH/POX), the first enzyme in the pathway of proline catabolism, has been identified as a mitochondrial, metabolic tumor suppressor, which is downregulated in a variety of human tumors. However, our recent findings show that PRODH/POX is upregulated by hypoxia in vitro and in vivo. The combination of low glucose and hypoxia produces additive effects on PRODH/POX expression. Both hypoxia and glucose depletion enhance PRODH/POX expression through AMP-activated protein kinase (AMPK) activation to promote tumor cell survival. Nevertheless, the mechanisms underlying PRODH/POX prosurvival functions are different for hypoxia and low-glucose conditions. Glucose depletion with or without hypoxia elevates PRODH/POX and proline utilization to supply ATP for cellular energy needs. Interestingly, under hypoxia PRODH/POX induces protective autophagy by generating reactive oxygen species (ROS). AMPK is the main initiator of stress-triggered autophagy. Thus, PRODH/POX acts as a downstream effector of AMPK in the activation of autophagy under hypoxia. This regulation was confirmed to be independent of the mechanistic target of rapamycin (MTOR) pathway, a major downstream target of AMPK signaling.
The Mitochondrial Isovaleryl-Coenzyme A Dehydrogenase of Arabidopsis Oxidizes Intermediates of Leucine and Valine Catabolism (2001)

We recently identified a cDNA encoding a putative isovaleryl-coenzyme A (CoA) dehydrogenase in Arabidopsis (AtIVD). In animals, this homotetrameric enzyme is located in mitochondria and catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA as an intermediate step in the leucine (Leu) catabolic pathway. Expression of AtIVD:smGFP4 fusion proteins in tobacco (Nicotiana tabacum) protoplasts and biochemical studies now demonstrate the in vivo import of the plant isovaleryl-CoA dehydrogenase (IVD) into mitochondria and the enzyme in the matrix of these organelles. Two-dimensional separation of mitochondrial proteins by blue native and SDS-PAGE and size determination of the native and overexpressed proteins suggest homodimers to be the dominant form of the plant IVD. Northern-blot hybridization and studies in transgenic Arabidopsis plants expressing Ativd promoter:gus constructs reveal strong expression of this gene in seedlings and young plants grown in the absence of sucrose, whereas promoter activity in almost all tissues is strongly inhibited by exogeneously added sucrose. Substrate specificity tests with AtIVD expressed in Escherichia coli indicate a strong preference toward isovaleryl-CoA but surprisingly also show considerable activity with isobutyryl-CoA. This strongly indicates a commitment of the enzyme in Leu catabolism, but the activity observed with isobutyryl-CoA also suggests a parallel involvement of the enzyme in the dehydrogenation of intermediates of the valine degradation pathway. Such a dual activity has not been observed with the animal IVD and may suggest a novel connection of the Leu and valine catabolism in plants.
Design challenges for sense amplifier and wireless link in high-density neural recording implants (2010)

In this paper we discuss the challenges in designing high-density biomedical neural implants. We discuss in more detail the constraints of the sense amplifier and the wireless link. Different techniques to design the front-end low-noise sense amplifier are discussed. We compare between different wireless designs and we show that trading off the transmitter power consumption and complexity with that of the external receiver will be mandatory to minimize the power dissipation and area of the implant.
Stability of two-dimensional strip casting processes (2000)

The solidification of molten materials is of great significance in modern metallurgical engineering. We study disturbances of a process that is characterized by three disparate lengths: the solidification length L, the wavelength Λ, and the depth of the slab δ∝. The present analysis is motivated by the relation δ∞&lt;Λ≪L, which is always true in practical strip casting processes. This justifies the use of an asymptotic expansion based on shallow water equations for long waves to describe the linear stability of disturbances. The leading-order equations govern a quasiparallel flow. In this limit we found two different types of disturbances: a weakly damped stable mode that runs downstream and a strongly damped perturbation traveling upstream. We focus on the downstream moving mode and show that this disturbance is strongly frequency dependent. Although the velocity disturbances are damped, there is a regime of parameters where the perturbations of the displacement grow in the horizontal direction. In our analyses we found a region of preferred frequencies. The displacement grows at these frequencies faster than for neighboring frequencies. The wavelengths of disturbances oscillating at these preferred frequencies are in qualitative agreement with the experimental observation of the wavelengths of harmonically varying grooves in the completely solidified material.
SPARC expression is associated with impaired tumor growth, inhibited angiogenesis and changes in the extracellular matrix (2005)

Secreted protein, acidic and rich in cysteine (SPARC), is a multifunctional matricellular glycoprotein. In vitro, SPARC has antiangiogenic properties, including the ability to inhibit the proliferation and migration of endothelial cells stimulated by bFGF and VEGF. Previously, we demonstrated that platelet-derived SPARC also inhibits angiogenesis and impairs the growth of neuroblastoma tumors in vivo. In the present study, we produced rhSPARC in the transformed human embryonic kidney cell line 293 and show that the recombinant molecule retains its ability to inhibit angiogenesis. Although 293 cell proliferation was not affected by exogenous expression of SPARC in vitro, growth of tumors formed by SPARC-transfected 293 cells was significantly impaired compared to tumors comprised of wild-type cells or 293 cells transfected with a control vector. Consistent with its function as an angiogenesis inhibitor, significantly fewer blood vessels were seen in SPARC-transfected 293 tumors compared to controls, and these tumors contained increased numbers of apoptotic cells. Light microscopy revealed small nests of tumor cells surrounded by abundant stromal tissue in xenografts with SPARC expression, whereas control tumors were comprised largely of neoplastic cells with scant stroma. Mature, covalently cross-linked collagen was detected in SPARC-transfected 293 xenografts but not in control tumors. Our studies suggest that SPARC may regulate tumor growth by inhibiting angiogenesis, inducing tumor cell apoptosis and mediating changes in the deposition and organization of the tumor microenvironment.
Hydroxylamines as Oxygen Atom Nucleophiles in Transition-Metal-Catalyzed Allylic Substitution (2005)

[reaction: see text] The viability of hydroxylamines as nucleophiles in transition-metal-catalyzed allylic substitutions was examined. We have found that the oxygen atom of hydroxylamines having an N-electron-withdrawing substituent (also known as hydroxamic acids) acts as a reactive nucleophile. The palladium-catalyzed O-allylic substitution of hydroxylamines with allylic carbonate afforded the linear hydroxylamines. The selective formation of the branched hydroxylamines was observed in iridium-catalyzed reaction. Regio- and enantioselective allylic substitution of the unsymmetrical phosphates with hydroxylamines was studied by using the iridium complex of chiral pybox ligand. The aqueous-medium reaction with hydroxylamines proceeded smoothly in the presence of Ba(OH)(2).H(2)O to give the branched products with good enantioselectivities.
A Computer Assisted Ringdector Positron Camera System for Reconstruction Tomography of the Brain (1978)

A ring detector positron camera system for brain metabolism studies is being constructed at the Institute of Physics, University of Stockholm, in collaboration with the Departments of Neuroradiology and clinical Neurophysiology, Karolinska Sjukhuset, Stockholm, Sweden. The instrument utilizes 95 NaI(Tl) detectors and will simultaneously record coincidences from 1900 detector combinations. Each detector is coupled in coincidence with forty detectors on the opposite side of the ring. In the conventional stationary mode of operation the experimental system resolution is 10.5 mm. A new sampling technique has been developed to reduce the system resolution. Based on this technique, an experimental system resolution of 7 mm has been obtained.
<i>Clostridium perfringens</i>in poultry: an emerging threat for animal and public health (2004)

The incidence of Clostridium perfringens-associated necrotic enteritis in poultry has increased in countries that stopped using antibiotic growth promoters. Necrotic enteritis and the subclinical form of C. perfringens infection in poultry are caused by C. perfringens type A, producing the alpha toxin, and to a lesser extent type C, producing both alpha toxin and beta toxin. Some strains of C. perfringens type A produce an enterotoxin at the moment of sporulation and are responsible for foodborne disease in humans. The mechanisms of colonization of the avian small intestinal tract and the factors involved in toxin production are largely unknown. It is generally accepted, however, that predisposing factors are required for these bacteria to colonize and cause disease in poultry. The best known predisposing factor is mucosal damage, caused by coccidiosis. Diets with high levels of indigestible, water-soluble non-starch polysaccharides, known to increase the viscosity of the intestinal contents, also predispose to necrotic enteritis. Standardized models are being developed for the reproduction of colonization of poultry by C. perfringens and the C. perfringens-associated necrotic enteritis. One such model is a combined infection with Eimeria species and C. perfringens. Few tools and strategies are available for prevention and control of C. perfringens in poultry. Vaccination against the pathogen and the use of probiotic and prebiotic products has been suggested, but are not available for practical use in the field at the present time. The most cost-effective control will probably be achieved by balancing the composition of the feed.
Differential effects of BMP‐2 and TGF‐β1 on chondrogenic differentiation of adipose derived stem cells (2007)

Prevention of BMP-2-induced osteogenic transdifferentiation by TGF-beta1 seemed not to be mediated by transcriptional regulation of Dlx-5. Due to these findings, simultaneous stimulation of ASC with BMP-2 and TGF-beta1 seemed to be beneficial for complete differentiation of ASC into chondrocytes.
Influence of exercise on oxidant stress products in elite Indian cyclists (2007)

The influence of exercise on free-radical chemistry is not well understood. It is yet to be confirmed whether an adequate biochemical defence system exists in the human body to provide protection from oxy-centred radicals generated by exercise. Fifty trained elite cyclists undertaking exhaustive endurance training were compared with a control group of 50 sedentary workers. Serum malondialdehyde (MDA), uric acid, superoxide dismutase (SOD), catalase, vitamin E, vitamin C and susceptibility to oxidative stress were assessed. Exhaustive exercise resulted in significantly (p<0.05) higher concentrations of serum MDA, vitamin E and vitamin C, significantly (p<0.001) higher SOD activity, but less significantly (p<0.01) higher concentrations of uric acid and significantly (p<0.05) lower catalase activity in elite cyclists than in the controls. Alterations in the activities of erythrocyte scavenger enzymes (SOD) and higher level of non-enzymatic defences in trained subjects may not be sufficient to counteract the increase in reactive oxygen species produced by endurance training.
<i>Ex Vivo</i> Gene Transfer of Brain‐derived Neurotrophic Factor to the Intact Rat Forebrain: Neurotrophic Effects on Cholinergic Neurons (1996)

Neurotrophic effects of human brain-derived neurotrophic factor (hBDNF) on forebrain cholinergic neurons were addressed after ex vivo gene transfer to the intact adult rat brain, using a conditionally immortalized neural progenitor cell line (CINP) engineered to secrete the neurotrophin (2.8 ng/h/10(6) cells). This cell line was derived by repeated retroviral infection of the parental neural precursor line HiB5 followed by subcloning. The cells survived well in the host brain for long periods of time (up to 4 weeks), and induced a hypertrophic response of cholinergic neurons (positive for acetylcholinesterase, choline acetyltransferase or low-affinity nerve growth factor receptor) in the nucleus basalis magnocellularis and striatum. We conclude that these cholinergic cell groups are responsive to a low-level supply (nanograms per day) of BDNF in vivo when the neurotrophin is administered locally in the vicinity of the cell bodies.
High-speed cyclic voltammetry (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh-speed cyclic voltammetryR. Mark Wightman and David O. WipfCite this: Acc. Chem. Res. 1990, 23, 3, 64–70Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/ar00171a002https://doi.org/10.1021/ar00171a002research-articleACS PublicationsRequest reuse permissionsArticle Views1450Altmetric-Citations86LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts