gebhart/patrepeval huggingface dataset:
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs (2011)

Detailed and systematic understanding of the biological effects of millions of available compounds on living cells is a significant challenge. As most compounds impact multiple targets and pathways, traditional methods for analyzing structure-function relationships are not comprehensive enough. Therefore more advanced integrative models are needed for predicting biological effects elicited by specific chemical features. As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical space) of 1159 drugs with the gene expression responses (biological space) they elicited in three cancer cell lines. The analysis covering 11350 genes was based on data from the Connectivity Map. We decomposed these biological response profiles into components, each linked to a characteristic chemical descriptor profile. The integrated quantitative analysis of the chemical and biological spaces was more informative about protein-target based drug similarity than either dataset separately. We identified ten major components that link distinct VolSurf features across multiple compounds to specific biological activity types. For example, component 2 (hydrophobic properties) strongly links to DNA damage response, while component 3 (hydrogen bonding) connects to metabolic stress. Individual structural and biological features were often linked to one cell line only, such as leukemia cells (HL-60) specifically responding to cardiac glycosides. In summary, our approach identified specific chemical structures shared across multiple drugs causing distinct biological responses. The decoding of such systematic chemical-biological relationships is necessary to build better models of drug effects, including unidentified types of molecular properties with strong biological effects.
Fluconazole-Resistant Candida albicans (1993)

Mucocutaneous candidiasis caused by Candida albicans is a common complication of human immunodeficiency virus (HIV) infection. Recent reports of isolation of resistant strains of C. albicans raise the specter of more widespread resistance, but limited series are available to analyze situations in which the likelihood of resistance is greatest. We present our experience with fluconazole-resistant candidiasis in patients with HIV infection obtained from retrospective chart review and by testing strains of C. albicans isolated during relapse for susceptibility to antifungal agents. The possible reasons for failure of antifungal therapy are discussed, as well the correlation between in vivo and in vitro data. Resistant candidiasis in patients with HIV disease is an emerging problem of considerable concern that merits further study.
Rapid, effective deprotection of tert-butoxycarbonyl (Boc) amino acids and peptides at high temperatures using a thermally stable ionic liquid (2015)

A method for high temperature Boc deprotection of amino acids and peptides in a phosphonium ionic liquid is described.
Ultra‐short wavelength filters using mode‐related dispersion in dual‐mode waveguides (2005)

Abstract An ultra‐short‐wavelength filter using photonic band gap (PBG) mode‐related dispersion in a two‐moded waveguide is proposed. It is verified using the finite‐difference time‐domain (FDTD) method, such that two channels on the PBG edges are affected by opposite dispersive effects and can be separated by an ultra‐short coupler length much shorter than the required length without the assistance of PBG dispersion. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 46: 225–227, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20951
Chirality (1999)

Abstract The sections in this article are Natural Optical Activity Chiral Media: Natural and Artificial Constitutive Relations of an Isotropic Chiral Medium Artificial Isotropic Chiral Media Beltrami Fields in an Isotropic Chiral Medium Representation of Beltrami Fields Sources in an Isotropic Chiral Medium Theorems for Scattering in an Isotropic Chiral Media Structurally Chiral Media
A Thick Origami Four-Patch Array (2019)

This paper presents a thick-origami based on a four patch antenna array with a packing efficiency of 50%. The antenna array is differentially fed using the origami structure and creating a symmetric radiation pattern. The array is designed on low-cost FR4 substrate having a thickness of 1.5 mm and an overall dimension of 290 mm × 100 mm. The peak gain is approximately 8.2 dB, at broadside. The ability of the array to compress its size and its fabrication simplicity makes it a very good candidate for applications where space savings are critical.
KERNEL-BASEDDETECTION OF DEFECTS ON SEMICONDUCTORWAFERS (2009)

Recent computational methods of wafer defect detection often rely on the difference image between an inspected image and its refer­ ence image, and highly depend on registration accuracy. In this paper, we present a novel method for defect detection in patterned wafers, based on reconstruction of the inspected image from the ref­ erence image using anisotropic kernels. This method avoids regis­ tration between the inspected and reference image and compensates for pattern variations, thus reducing the false detection rate. Ex­ perimental results demonstrate the advantages and robustness of the proposed method. Efficient implementation of the algorithm makes it be suitable for industrial use. We also demonstrate extension of the kernel-based similarity concept to the multichannel Scanning Elec­ tron Microscope (SEM) images.
A BiCMOS synchronous pulse discriminator for the LHCb calorimeter system (2002)

A monolithic prototype for the analogue readout of the Scintillator Pad Detector (SPD) of the LHCb calorimeter is presented. A low power version that works at 3.3 V has been designed using the 0.8 mu m Bi CMOS technology of AMS. It consists of a charge discriminator with a dual path structure formed by an integrator, a pile-up correction, a subtractor and a comparator. The chip also includes a DAC and serial digital control interface to program the threshold of the discriminator. Design, simulation and test results for different prototypes of the circuit will be presented and described. (8 refs).
Degradation of extracellular matrix by mouse trophoblast outgrowths: a model for implantation (1983)

During implantation the embryo attaches to the endometrial surface and trophoblast traverses the uterine epithelium, anchoring in the uterine connective tissue. To determine whether trophoblast can facilitate invasion of the uterus by degrading components of normal uterine extracellular matrix, mouse blastocysts were cultured on a radio-labeled extracellular matrix that contained glycoproteins, elastin, and collagen. The embryos attached to the matrix, and trophoblast spread over the surface. Starting on day 5 of culture there was a release of labeled peptides into the medium. The radioactive peptides released from the matrix by the embryos had molecular weights ranging from more than 25,000 to more than 200. By day 7 there were areas where individual trophoblast cells had separated from one another, revealing the underlying substratum that was cleared of matrix. When trophoblast cells were lysed with NH(4)OH on day 8, it was apparent that the area underneath the trophoblast outgrowth had been cleared of matrix. Scanning electron microscopy and time-lapse cinemicrography confirmed that the digestion of matrix was highly localized, taking place only underneath the trophoblast, with no evidence of digestion of the matrix beyond the periphery of the trophoblast outgrowth. The sharp boundaries of degredation observed may be due to localized proteinase secretion by trophoblast, to membrane proteinases on the surface of trophoblast, or to endocytosis. Digestion of the matrix was not dependent on plasminogen, thus ruling out a role for plasminogen activator. Digestion was not inhibited by a variety of hormones and inhibitors, including progesterone, 17beta-estradiol, leupeptin, EDTA, colchicine, NH(4)Cl, or epsilon-aminocaproic acid. This system of culturing embryos on extracellular matrix may be useful in determining the processes that regulate trophoblast migration and invasion into the maternal tissues during implantation.0
Numerical Investigation on Unstable Oscillations of Two Circular Cylinders in Tandem Arrangement (2003)

Three-dimensional simulations of incompressible and viscous flow around tandem circular cylinders at Re = 20000 in unstable oscillations can be carried out by means of finite difference method without any turbulence model. The numerical response behaviors are in good agreement with the previous experimental ones. The mechanism of negative damping force in vortex-induced oscillations and wake-galloping is investigated.
Alterations in Skin Temperature and Sleep in the Fear of Harm Phenotype of Pediatric Bipolar Disorder (2014)

In children diagnosed with pediatric bipolar disorder (PBD), disturbances in the quality of sleep and wakefulness are prominent. A novel phenotype of PBD called Fear of Harm (FOH) associated with separation anxiety and aggressive obsessions is associated with sleep onset insomnia, parasomnias (nightmares, night-terrors, enuresis), REM sleep-related problems, and morning sleep inertia. Children with FOH often experience thermal discomfort (e.g. feeling hot, excessive sweating) in neutral ambient temperature conditions, as well as no discomfort during exposure to the extreme cold, and alternate noticeably between being excessively hot in the evening and cold in the morning. We hypothesized that these sleep- and temperature-related symptoms were overt symptoms of an impaired ability to dissipate heat, particularly in the evening hours near the time of sleep onset. We measured sleep/wake variables using actigraphy, and nocturnal skin temperature variables using thermal patches and a wireless device, and compared these data between children with PBD/FOH and a control sample of healthy children. The results are suggestive of a thermoregulatory dysfunction that is associated with sleep onset difficulties. Further, they are consistent with our hypothesis that alterations in neural circuitry common to thermoregulation and emotion regulation underlie affective and behavioral symptoms of the FOH phenotype.
Sequencing Analysis of Mutation Points in the Biotin Operon of Biotin-overproducing<i>Escherichia coli</i>Mutants (1993)

We analyzed mutation points of the biotin operon from biotin-overproducing mutants of Escherichia coli resistant to two biotin analogs, actithiazic acid and 5-(2-thienyl)-valeric acid, by DNA sequencing. The biotin operons cloned from these mutants were classified into three groups. One point mutation, which was a GC-->AT change within the operator overlapping the -10 region of the rightward (bioB) promoter, was considered to result in disruption of operator structure and enhancement of promoter activity. Two other point mutations, which were both GC-->AT changes just before and after the initiation codon of the bioB gene, were considered to activate the translation efficiency. These mutations significantly accelerated the biotin-forming activity from dethiobiotin in cell-free extracts.
ChemInform Abstract: Carbyne ‐ the Third Allotropic Form of Carbon (1994)

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.
Multiphoton ionization of vinylchloride, trifluoroethylene, and benzene at 193 nm (1987)

The multiphoton ionization–fragmentation pattern of vinylchloride, trifluoroethylene and benzene has been measured at 193 nm using time-of-flight mass spectrometry and gas chromatographic analysis. Relative cross sections for multiphoton ionization and the laser power dependence have been determined for the three species at 193 nm at low laser fluence (&lt;10 mJ/cm2) and relative cross sections for multiphoton ionization of benzene have been obtained at 193 and 248 nm. The dominant fragmentation and ionization channels in the two substituted ethylenes are discussed.
ChemInform Abstract: Development of a Pharmacophore Model for Histamine H<sub>3</sub> Receptor Antagonists, Using the Newly Developed Molecular Modeling Program SLATE. (2001)

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.
Occlusal Contact of Subjects with Temporomandibular Disfunction and Symptoms of TMD. (1995)

This study was conducted to clarify the relationship between extraordinary occlusal contact and temporomandibular disfunction (TMD) symptoms. The subjects were 25 persons with normal occlusion and 100 patients with TMD. These occlusal contacts were recorded at intercuspal, protrusive and lateral positions.Then the differences of the extraordinary occlusal contact were examined, and comparison was made between the patients with and without orofacial pain as well as the patients with and without the articular disk displacement in TMJ.The results were as follows:1. The majority of patients showed occlusal contacts distinctly different from those of the normal subjects.2. The ratio of the extraordinary occlusal contact was higher for the patients with orofacial pain than those without pain. This tendency was clear especially at intercuspal and protrusive positions.3. At the ratio of the extraordinary occlusal contact, there was no fixed tendency between the patients with disk displacement and those without disk displacement. But if the patients were divided into three groups (one group without disk displacement, one with disk displacement on one side and one with disk displacement on both sides), at the intercuspal and lateral positions the patients with disk displacement on both sides indicated the highest ratio, and at the protrusive position the patients without disk displacement indicated the highest ratio.
Adiabatic Normal Zone Development in&lt;tex&gt;$rm MgB_2$&lt;/tex&gt;Superconductors (2005)

A-priori knowledge of the normal zone development in MgB/sub 2/ conductors is essential for quench protection of applications. Therefore the normal zone propagation in a monofilament MgB/sub 2//Fe conductor under near-adiabatic conditions at 4.2 K has been measured and simulated. The results show normal zone propagation velocities up to several meters per second. In addition, by including the voltage-current relation into the computational model, the influence of the n-value on the normal zone propagation is determined. The simulations show that lower n-values suppress the normal zone propagation velocity due to lower heat generation in the MgB/sub 2/ filaments.
Plate section (2008)

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Mechanism of inactivation of glutamine amidotransferases by the antitumor drug L-(alpha S, 5S)-alpha-amino-3-chloro-4,5-dihydro-5-isoxazoleacetic acid (AT-125). (1980)

L-(alphaS, 5S)-alpha-Amino-3-chloro-4,5-dihydro-5-isoxazoleacetic acid (AT-125), an antitumor drug isolated from Streptomyces sviceus, is an active site-directed affinity analog of glutamine. It selectively inactivates the glutamine-dependent activities of two bacterial glutamine amidotransferases, anthranilate synthase and glutamate synthase. A reversible noncovalent complex is formed prior to irreversible enzyme modification. Inactivation of anthranilate synthase results from incorporation of approximately 1 eq of AT-125/enzyme protomer. Active site cysteine-83 in Serratia marcescens anthranilate synthase Component II is the residue alkylated by AT-125. Anthranilate synthase is rapidly inactivated by AT-125 IN S. marcescens cells. In vivo inactivation is by the same mechanism as in vitro.
Effect of Zn doping on differential gain and damping of 1.55 μm InGaAs/InGaAsP MQW lasers (1992)

The differential gain and nonlinear damping in 16 well MQW lasers has been studied using relative intensity noise (RIN) measurements. Zinc doping the active region increases the differential gain by 50% to 10−19 m2 and reduces the nonlinear damping factor by 20% to 0.20 nS. This represents a maximum intrinsic 3 dB bandwidth of 45 GHz.
<i>JAK2 V617F</i> Gene Mutation in the Laboratory Work-Up of Myeloproliferative Disorders: Experience of a Major Referral Center in Lebanon (2011)

Our unique study in this sample of Lebanese patients shows extensive similarities of positivity of JAK2 V617F as compared with the international literature and for the same categories of clinical entities. This will constitute a baseline for future clinical studies that would also help determine prognosis of cases based on the absence or presence of this mutation.
Evidence for tribochemical wear on amorphous carbon thin films (1990)

The friction and wear properties between a smooth oxide-based ceramic sliding and an amorphous carbon surface are greatly influenced by the surface chemistry of the carbon layer. Like most carbon compounds, surface oxides can form if the surface is exposed to oxygen. These surface species can desorb as carbon monoxide and/or carbon dioxide under the rubbing action of the slider. Such a gradual tribochemical wear mechanism induces a greater area of true contact, and the friction coefficient increases dramatically from 0.2 to 1.2 or higher when repeated sliding contacts are made. In contrast, similar tribological experiments carried out in an inert environment show no friction increase.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases (2020)

Abstract The identification of rare variants that contribute to complex diseases is challenging due to low statistical power. Here we propose a novel and powerful rare variants association test based on the deviation of the observed mutational burden in a genomic region from a baseline mutation burden predicted by weighted recursive truncated negative-binomial regression (RUNNER) on genomic features available from public data. Simulation studies show that RUNNER is substantially more powerful than state-of-the-art rare variant association methods (including SKAT, CMC and KBAC), while maintaining correct type 1 error rates under population stratification and in small samples. Applied to real data, RUNNER “rediscovered” known genes of Hirschsprung disease missed by current methods, and detected promising new candidate genes, including NXPE4 for Hirschsprung disease and CXCL16 for Alzheimer’s disease. The proposed approach provides a powerful and robust method to identify rare risk variants for complex diseases.
Effect of ventilating holes on radial flux and losses in stator slots of turbogenerators (1975)

An accepted practice among some manufacturers of turbogenerators is to provide for the ventilation of stator laminations through axial holes in the teeth in addition to the core. This is especially the case for machines without radial ducts separating packs of laminations. These holes are located in areas of the teeth subject to high degrees of saturation. Under these conditions, flux is diverted into adjacent stator slots. The main component of the diverted flux is radial and is in the area of the strands. Furthermore, this radial flux component is time varying and hence establishes eddy currents in the strands. These eddy currents create additional losses. Therefore, the size and location of such ventilation holes is critical if the added component of radial flux losses is not to produce spots of excessive heating in the winding. This phenomenon is presented through results of a comprehensive magnetic field study on two 4 pole, 659 MVA asymmetrically slotted rotor and 2 pole, 733 MVA standard rotor turbogenerators. From flux density and loss distribution curves, recommendations as to the size and location of these holes, to significantly reduce these losses are made.
Reaction of 2,2-dibromotricyclo[7.1.01,9.01,3]decane with methyllithium: synthesis of bicyclo[7.1.0]decadiene-1,2 and dibromotriangulane rearrangement (1999)

Reaction of 2,2-dibromotricyclo[7.1.01,9.01,3]decane with methyllithium gives strained cyclic allene 1 containing an ethenylidenecyclopropane unit in a nine-membered ring and dimer 6 resulting from a dibromotriangulane rearrangement.
Regulation of Glyoxysomal Enzymes during Germination of Cucumber (1978)

The glyoxysomal enzymes isocitrate lyase and catalase have been isolated from etiolated cucumber (Cucumis sativus) cotyledons. The enzymes co-purified through polyethyleneimine precipitation and (NH(4))(2)SO(4) precipitation, and were resolved by gel filtration on Sepharose 6B followed by chromatography on diethylaminoethyl-cellulose (isocitrate lyase) or hydroxylapatite (catalase). Purity of the isolated enzymes was assessed by sodium dodecyl sulfate-polyacrylamide electrophoresis, isoelectric focusing, and immunoelectrophoresis. Antibodies raised to both enzymes in rabbits and in tumor-bearing mice were shown to be monospecific by immunoelectrophoresis against total homogenate protein. Isocitrate lyase and catalase represent about 0.56% and 0.1%, respectively, of total extractable cotyledonary protein. Both enzymes appear to be present in a single form. Molecular weights of the native enzymes and its subunits are 225,000 and 54,500 for catalase, and 325,000 and 63,500 for isocitrate lyase. The pH optimum for isocitrate lyase is about 6.75 in morpholinopropane sulfonic acid buffer, but varies significantly with buffer used. The K(m) for d-isocitrate is 39 micromolar. A double antibody technique (rabbit anti-isocitrate lyase followed by (125)I-labeled goat anti-rabbit immunoglobulin G) has been used to visualize isocitrate lyase subunit protein on sodium dodecyl sulfate-polyacrylamide with high specificity and sensitivity.
ACUTE RETINAL TOXICITY CAUSED BY THE BIMETALLIC ELECTROCHEMICAL ACTION OF A GALVANIZED STEEL INTRAOCULAR FOREIGN BODY (1998)

STEEL, DAVID H.W. FRCOphth; ROSSEINSKY, DAVID R. FRSC; JAMES, CHARLIE R. FRCOphth Author Information
Requirements for Recruitment of a G Protein-coupled Receptor to Clathrin-coated Pits in Budding Yeast (2009)

Endocytic internalization of G protein-coupled receptors (GPCRs) plays a critical role in down-regulation of GPCR signaling. The yeast mating pheromone receptor Ste2p has been used as a model to investigate mechanisms of signal transduction, modification, and endocytic internalization of GPCRs. We previously used a fluorescently labeled mating pheromone derivative to reveal unappreciated molecular and spatiotemporal features of GPCR endocytosis in budding yeast. Here, we identify recruitment of Ste2p to preexisting clathrin-coated pits (CCPs) as a key step regulated by receptor phosphorylation and subsequent ubiquitination upon ligand binding. The yeast casein kinase I homologue Yck2p directly phosphorylates six serine residues located in the C-terminal tail of Ste2p, and mutation of these serine residues to alanine significantly decreased recruitment of Ste2p to CCPs. We also found that the clathrin adaptors Ent1p, Ent2p, and Ede1p work cooperatively to recruit ubiquitinated Ste2p to CCPs. In addition, ubiquitination has a role in ligand-independent constitutive recruitment of Ste2p to CCPs, although this process is much slower than ligand-induced recruitment. These results suggest that ubiquitination of Ste2p is indispensable for recruiting Ste2p to CCPs in both ligand-dependent and ligand-independent endocytosis.