gebhart/patrepeval huggingface dataset:
A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening (2022)

Virtual screening methods focus on searching molecules with similar properties to a given compound. Molecule databases are made up of large numbers of compounds and are constantly increasing. Therefore, fast and efficient methodologies and tools have to be designed to explore them quickly. In this context, ligand-based virtual screening methods are a well-known and helpful tool. These methods focus on searching for the most similar molecules in a database to a reference one. In this work, we propose a new tool called 2L-GO-Pharm, which requires less computational effort than OptiPharm, an efficient and robust piece of software recently proposed in the literature. The new-implemented tool maintains or improves the quality of the solutions found by OptiPharm, and achieves it by considerably reducing the number of evaluations needed. Some of the strengths that help 2L-GO-Pharm enhance searchability are the reduction of the search space dimension and the introduction of some circular limits for the angular variables. Furthermore, to ensure a trade-off between exploration and exploitation of the search space, it implements a two-layer strategy and a guided search procedure combined with a convergence test on the rotation axis. The performance of 2L-GO-Pharm has been tested by considering two different descriptors, i.e. shape similarity and electrostatic potential. The results show that it saves up to 87.5 million evaluations per query molecule.
[The problem of the radiosensitivity of bone marrow cellular elements and assessments of the postradiation kinetics of myelopoiesis (an analysis based on data on the sequelae of the accident at the Chernobyl Atomic Electric Power Station]. (1992)

On the basis of the data obtained from 61 cases of accidental exposure (0.1-12.5 Gy) at the Chernobyl A.P.S. the kinetics of acute radiation bone-marrow syndrome was analyzed and radiosensitivity of the entire spectrum of human granulocytic compartment cells was estimated. The radiosensitivity estimates were made by a "functional" criterion, developed by the authors, which was based on the comparative ability of irradiated and nonirradiated bone marrow cells of different maturity to produce peripheral blood neutrophils. Changes were found in physiology of myeloid cells during their maturation: the maturation mechanism, for cells of the committed pool, was "attached" to the division process, whereas these processes were independent for cells of the dividing and maturing pool. It is once again confirmed that the transit time of a maturing myeloid cell, to begin with the primarily committed one and to end with a peripheral blood neutrophil, is not constant and lasts normally for 32 days.
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation (2004)

The Web server is available at http://www.imtech.res.in/raghava/srf and http://www2.imtech.res.in/raghava/srf
An automated rotor time-constant measurement system for indirect field-oriented drives (1988)

An automated scheme to measure the open-circuit rotor time constant and set the slip gain of a field-oriented controller is presented. The test utilizes the pulse-width-modulated inverter of the drive itself and is conducted at zero speed so that the result can be used for automated calibration of the slip gain in the controller of an indirect field-oriented drive system. The accuracy of the test is verified by a simple measurement that checks for the existence of a linear relation between the input torque command and output torque at steady state.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Toward Stable Solar Hydrogen Generation Using Organic Photoelectrochemical Cells (2015)

Organic photoactive materials are promising candidates for the generation of solar fuels in terms of efficiency and cost. However, their low stability in aqueous media constitutes a serious problem for technological deployment. Here we present organic photocathodes for the generation of hydrogen in aqueous media with outstanding stability. The device design relies on the use of water-resistant selective contacts, which protect a P3HT:PCBM photoactive layer. An insoluble cross-linked PEDOT:PSS hole-selective layer avoids delamination of the film, and an electron-selective TiOx layer in contact with the aqueous solution electrically communicates the organic layer with the hydrogen-evolving catalyst (Pt). We developed a novel method for the synthesis of the TiOx layer compatible with low-temperature conditions. Tuning the thickness of the TiOx/Pt layer leads to a trade-off between the achievable photocurrent (∼1 mAcm–2) and the stability of the photocathode (stable hydrogen generation of 1.5 μmol h–1 cm–2 for >3 h).
A Comparison of Molten Sn and Bi for Solid Oxide Fuel Cell Anodes (2010)

Molten Sn and Bi were examined at 973 and 1073 K for use as anodes in solid oxide fuel cells with yttria-stabilized zirconia (YSZ) electrolytes. Cells were operated under “battery” conditions, with dry He flow in the anode compartment, to characterize the electrochemical oxidation of the metals at the YSZ interface. For both metals, the open-circuit voltages (OCVs) were close to that expected based on their oxidation thermodynamics, ~0.93 V for Sn and ~0.48 V for Bi. With Sn, the cell performance degraded rapidly after the transfer of approximately 0.5-1.5 Ccm{sup 2} of charge due to the formation of a SnO{sub 2} layer at the YSZ interface. At 973 K, the anode impedance at OCV for freshly reduced Sn was approximately 3 {ohm}cm{sup 2} but this increased to well over 250 {ohm}cm{sup 2} after the transfer of of charge. Following the transfer of 8.2 Ccm{sup 2} at 1073 K, the formation of a 10{micro}m thick SnO{sub 2} layer was confirmed by scanning electron microscopy. With Bi, the OCV anode impedance at 973 K was less than 0.25 {ohm}cm{sup 2} and remained constant until essentially all of the Bi had been oxidized to BiO{sub 2}. Some implications of these results formore » direct carbon fuel cells are discussed.« less
Minimizing Data Transfers in Distributed Query Processing: A Comparative Study and Evaluation (1996)

Journal Article Minimizing Data Transfers in Distributed Query Processing: A Comparative Study and Evaluation Get access J. M. Morrissey, J. M. Morrissey School of Computer Science, University of Windsor, 401 Sunset, Windsor, Ontario, Canada N9B 3P4. Email: joan@cs.uwindsor.ca Search for other works by this author on: Oxford Academic Google Scholar W. T. Bealor W. T. Bealor School of Computer Science, University of Windsor, 401 Sunset, Windsor, Ontario, Canada N9B 3P4. Email: joan@cs.uwindsor.ca Search for other works by this author on: Oxford Academic Google Scholar The Computer Journal, Volume 39, Issue 8, 1996, Pages 675–687, https://doi.org/10.1093/comjnl/39.8.675 Published: 01 January 1996
Antiferromagnetism in disordered B.C.C. Cr-Mn Alloys (1964)

The neutron diffraction, electrical resistivity and magnetic susceptibility measurements on b.c.c. Cr-Mn alloys containing manganese from 7.0 to 25.3 atomic percent have shown that the alloys are antiferromagnetic but disordered atomically. The obtained results are shown to be compatible with the theoretical conclusions from the spin density wave model.
The eardrums move when the eyes move: A multisensory effect on the mechanics of hearing (2017)

ABSTRACT Interactions between sensory pathways such as the visual and auditory systems are known to occur in the brain, but where they first occur is uncertain. Here we show a novel multimodal interaction evident at the eardrum. Ear canal microphone measurements in humans ( n =19 ears in 16 subjects) and monkeys ( n =5 ears in 3 subjects) performing a saccadic eye movement task to visual targets indicated that the eardrum moves in conjunction with the eye movement. The eardrum motion was oscillatory and began as early as 10 ms before saccade onset in humans or with saccade onset in monkeys. These eardrum movements, which we dub Eye Movement Related Eardrum Oscillations (EMREOs), occurred in the absence of a sound stimulus. The EMREOs’ amplitude and phase depended on the direction and horizontal amplitude of the saccade. They lasted throughout the saccade and well into subsequent periods of steady fixation. We discuss the possibility that the mechanisms underlying EMREOs create eye movement-related binaural cues that may aid the brain in evaluating the relationship between visual and auditory stimulus locations as the eyes move. SIGNIFICANCE STATEMENT The peripheral hearing system contains several motor mechanisms that allow the brain to modify the auditory transduction process. Movements or tensioning of either the middle-ear muscles or the outer hair cells modify eardrum motion, producing sounds that can be detected by a microphone placed in the ear canal (e.g. as otoacoustic emissions). Here, we report a novel form of eardrum motion produced by the brain via these systems -- oscillations synchronized with and covarying with the direction and amplitude of saccades. These observations suggest that a vision-related process modulates the first stage of hearing. In particular, these eye-movement related eardrum oscillations may help the brain connect sights and sounds despite changes in the spatial relationship between the eyes and the ears.
Diffusion of a pulse in densely distributed scatterers (1978)

This paper presents a theoretical study on propagation and scattering characteristics of a short optical pulse in a dense distribution of scatterers. Examples include pulse diffusion in whole blood and in a dense distribution of particulate matter in the atmosphere and the ocean. The parabolic equation technique is applicable to the forward-scatter region where the angular spread is confined within narrow forward angles. When the angular spread becomes comparable to the order of unit steradian, there is as much backscattering as forward scattering and diffusion phenomena take place. We start with the integral and differential equations for the two-frequency mutual coherence function under the first-order smoothing approximation, and a general diffusion equation and boundary conditions are obtained. As examples, we present solutions for diffusion of a pulse from a point source and a plane wave incident on a slab of scatterers.
Transforming IC layout description from the unrestricted to a restricted format (2002)

A technology independent processor for transforming integrated circuit layout description from the unrestricted to a restricted format is developed. We use doubly-linked lists and a vector of pointers to store and process geometrical objects (rectangles) of a circuit layout. The restricted format contains a set of non-overlapping rectangles that abut only along horizontal edges. The performance of this transformer is illustrated on the example of integrated circuit CHIP by the analysis of total number of rectangles and extracted critical areas for shorts before and after processing.
Localization of Urotensin-II Immunoreactivity in Normal Human Kidneys and Renal Carcinoma (2002)

Human urotensin-II (U-II) is a cyclic 11-amino-acid residue peptide with a wide range of vasoactive properties dependent on the anatomic site and the species studied. The purpose of this study was to determine the localization of human U-II in normal human kidneys and in renal carcinoma. Normal human kidneys (n=11) and eight cases of clear-cell carcinoma were immunostained with a polyclonal antibody to human U-II. In normal human kidneys, U-II was mostly present in the epithelial cells of tubules and ducts, with greater intensity in the distal convoluted tubules. Moderate U-II immunoreactivity was seen in the endothelial cells of renal capillaries, but only focal immunoreactivity was found in the endothelial cells of the glomeruli. No staining was found in the veins. All tumors expressed moderate U-II immunoreactivity in the cancer cells and vasculature. Here we demonstrate abundant expression of U-II in normal human kidneys and renal carcinoma. These findings suggest that the vasoactive and growth-mediator peptide U-II may contribute to the pathophysiology of the human renal system.
Transcriptional Landscape of Cardiomyocyte Maturation (2015)

Decades of progress in developmental cardiology has advanced our understanding of the early aspects of heart development, including cardiomyocyte (CM) differentiation. However, control of the CM maturation that is subsequently required to generate adult myocytes remains elusive. Here, we analyzed over 200 microarray datasets from early embryonic to adult hearts and identified a large number of genes whose expression shifts gradually and continuously during maturation. We generated an atlas of integrated gene expression, biological pathways, transcriptional regulators, and gene regulatory networks (GRNs), which show discrete sets of key transcriptional regulators and pathways activated or suppressed during CM maturation. We developed a GRN-based program named MatStat(CM) that indexes CM maturation status. MatStat(CM) reveals that pluripotent-stem-cell-derived CMs mature early in culture but are arrested at the late embryonic stage with aberrant regulation of key transcription factors. Our study provides a foundation for understanding CM maturation.
Total Synthesis of 6-Hydroxy-<i>epi</i>-PS 5 and 6-Methoxy-<i>epi</i>-PS 5 (1987)

Abstract The stabilizing effect of the 6-methoxyl or 6-hydroxyl substituent on dehydropeptidase I sensitivity of PS 5 was examined by a new total synthesis of 6-methoxy-epi-PS 5 and 6-hydroxy-epi-PS 5 from dimethyl benzyloxycarbonylaminomalonate. The Wittig reaction of α-(t-butoxycarbonyl)propylidenetriphenylphosphorane with a pyrrolidine derivative predominantly afforded a trans-α,β unsaturated ester, which was epoxidated, N-deprotected and cyclized to give a bicyclic carbapenam with a C-6 hydroxyl group. After the 6-hydroxyl group was methylated, the 2-(acetamido)ethylthio side chain was introduced at C-3 of the carbapenam by benzeneselenenylation of the geminal diester, followed by elimination of the seleninyl group. The resulting carbapenam was converted to 6-methoxy-epi-PS 5. Furthermore, 6-hydroxy-epi-PS 5 was synthesized by the use of tetrahydropyranyl and trimethylsilyl ethers for protection of the 6-hydroxyl group in a process similar to that for synthesis of 6-methoxy-epi-PS 5.
A <sup>7</sup>Li NMR study of visibility, spin relaxation, and transport in normal human erythrocytes (1991)

The behavior of the lithium (Li) ion in normal human erythrocytes has been studied by 7Li NMR. The uptake of Li into the cells was followed as a function of solution conditions, temperature, hematocrit, and blood age using dysprosium tripolyphosphate shift reagent. Under our conditions the uptake of Li increases with increasing hematocrit and blood age. For packed cells the extracellular 7Li spin-lattice relaxation time was only slightly longer than the intracellular relaxation time. Thus, T1 may not be useful for separate observation of intra- and extracellular Li in vivo. The intra- and extracellular T2s were substantially shorter than the corresponding T1s. Also, the intracellular T2 was considerably shorter than that for the extracellular compartment, suggesting that T2 may provide a noninvasive handle for observation of intracellular Li. Nuclear Overhauser enhancements could be observed for both extra- and intracellular 7Li, confirming that dipolar coupling to 1H is a contributing relaxation mechanism. The 7Li NMR visibility was essentially 100% at high Li concentrations, decreasing to about 84% at 1 mM Li. Based on time course studies of the invisibility, and a comparison of NMR and inductively coupled plasma results, it appears that the invisibility of the intra- and extracellular compartments for packed cells is the same. Although a 23Na double-quantum signal could be observed for red blood cells, no double-quantum signal was observed for 7Li.
Scalable Method for the Fabrication and Testing of Glass-Filled, Three-Dimensionally Sculpted Extraordinary Transmission Apertures (2013)

This Letter features a new, scalable fabrication method and experimental characterization of glass-filled apertures exhibiting extraordinary transmission. These apertures are fabricated with sizes, aspect ratios, shapes, and side-wall profiles previously impossible to create. The fabrication method presented utilizes top-down lithography to etch silicon nanostructures. These nanostructures are oxidized to provide a transparent template for the deposition of a plasmonic metal. Gold is deposited around these structures, reflowed, and the surface is planarized. Finally, a window is etched through the substrate to provide optical access. Among the structures created and tested are apertures with height to diameter aspect ratios of 8:1, constructed with rectangular, square, cruciform, and coupled cross sections, with tunable polarization sensitivity and displaying unique properties based on their sculpted side-wall shape. Transmission data from these aperture arrays is collected and compared to examine the role of spacing, size, and shape on their overall spectral response. The structures this Letter describes can have a variety of novel applications from the creation of new types of light sources to massively multiplexed biosensors to subdiffraction limit imaging techniques.
Digital radiography of the chest: clinical experience with a prototype unit. (1983)

A prototype digital unit dedicated to chest radiography was used to examine 50 selected patients for a comparison study of the capability of digital images and conventional chest radiographs to reveal normal anatomic structures and a variety of pathologic states. The images in both modes were submitted for interpretation to seven experienced radiologists and a standardized questionnaire completed for each. Visibility of seven anatomic structures in the mediastinum was consistently better on the digital images than on the conventional radiographs. With minor exceptions, pathologic states were equally well seen in the two systems. Despite the less familiar viewing format of the digital images, the mean confidence levels achieved were higher than for those on the conventional radiographs; this difference was statistically significant both for normal anatomic structures (p = 0.001) and pathologic states (p = 0.01). The advantages and disadvantages of the digital technique are discussed.
Desorption electrospray ionization mass spectrometry reveals surface-mediated antifungal chemical defense of a tropical seaweed (2009)

Organism surfaces represent signaling sites for attraction of allies and defense against enemies. However, our understanding of these signals has been impeded by methodological limitations that have precluded direct fine-scale evaluation of compounds on native surfaces. Here, we asked whether natural products from the red macroalga Callophycus serratus act in surface-mediated defense against pathogenic microbes. Bromophycolides and callophycoic acids from algal extracts inhibited growth of Lindra thalassiae, a marine fungal pathogen, and represent the largest group of algal antifungal chemical defenses reported to date. Desorption electrospray ionization mass spectrometry (DESI-MS) imaging revealed that surface-associated bromophycolides were found exclusively in association with distinct surface patches at concentrations sufficient for fungal inhibition; DESI-MS also indicated the presence of bromophycolides within internal algal tissue. This is among the first examples of natural product imaging on biological surfaces, suggesting the importance of secondary metabolites in localized ecological interactions, and illustrating the potential of DESI-MS in understanding chemically-mediated biological processes.
Microwave phototubes with transmission photocathodes (1963)

Summary form only. An abstract of the above-titled article, taken from the 1963 IEEE International Convention (held March 25-28, New York, NY, USA), is presented.
Development and applications of cholesteric liquid crystals (2015)

The development and realisation of applications utilising the cholesteric or chiral nematic phase have benefited from the materials research work carried out by George Gray and his colleagues. His work on cholesteric materials started in the 1950s with the synthesis of cholesteryl esters and the observation in them of an unusual blue fog phase which he later studied in more detail. He went on to identify the molecular features that give rise to the characteristic cholesteric helical structure and the role of molecular structure and chirality on the properties of the cholesteric phase. This pioneering work paved the way for a wide range of applications of which a few are exemplified.
An Intergradient Population Connecting Anniella pulchra pulchra and Anniella pulchra nigra (1943)

THE Monterey Peninsula, on the coast of Monterey County, California, is the source of most typical specimens of Anniella pulchra nigra. These limbless lizards range over the entire peninsula, but are more common in the coastal sand dunes. Coastal sand dunes extend north from the city of Monterey along the shore of Monterey Bay to within one mile of Capitola on the northern arm of the bay (see Fig. 1), the limbless lizards range north in these dunes to Watsonville. An intergradient population occurs in the dunes near the mouth of the Salinas River north of the Monterey Peninsula. The relationship between this population and those of true A. p. pulchra and A. p. nigra is herein analyzed on the basis of the composite dorsal coloration of living lizards, the ratio of tail length to total length, and the degree of anomalous fusion of head plates. I wish to express my appreciation to Dr. Alden H. Miller of the Museum of Vertebrate Zoology for suggestions and criticisms and for the use of specimens in the Museum, and to Mr. Joseph R. Slevin for the use of the collections of the California Academy of Sciences. The live lizards used in color determinations were collected by the author and are now in the collection of the Museum of Vertebrate Zoology. The color determinations were made by a window with a north light on a clear day; colors in Ridgway's nomenclature are distinguished by capitalization. J. G. Fischer (1885: 9) described Anniella nigra from a black individual that was sent to him by J. Behrens. Accompanying the black lizard was a specimen of Anniella pulchra. Both lizards were said to have been collected in Diego, California. Anniella pulchra pulchra is common at San Diego, but this locality is approximately 300 miles south of the present known range of A. p. nigra. The black lizard was probably mislabeled, as the only locality known where black individuals have been taken is the Monterey Peninsula. Specimens of the limbless lizard taken at Morro and at Pismo Beach, San Luis Obispo County, are regarded as intergrades between A. p. pulchra and A. p. nigra (Grinnell and Camp, 1917: 170; Klauber, 1940: 16); they show longitudinal lines like the younger individuals from Monterey. Fischer does not mention longitudinal lines in his description, which contains an excellent account of the coloration. The dorsal color of Anniella p. nigra varies from silvery drab in the young lizards through silver brown (Hair Brown), light brown (Chaetura Drab), and dark brown (Chaetura Black) to black in the large adults. The ventral surface varies from Wood Brown in the young individuals, through Pinkish Olive and Olive Lake, to Pyrite Yellow and Sulphine Yellow of young adults, to yellower than Lemon Chrome in old adults. The young have two or three lateral stripes on each side of the body and one fairly well defined dorsal stripe along the middorsal line. As the lizards become older, the dorsal stripe becomes less distinct. It is completely lost