gebhart/patrepeval huggingface dataset:
Pharmacophore-based virtual screening and docking studies on Hsp90 inhibitors (2010)

Hsp90 (Heat shock protein 90) is an important therapeutic target for the treatment of cancer. To identify important chemical features for Hsp90 inhibitory activity, a 3D-QSAR pharmacophore model was developed using a set of 61 inhibitors (a training set of 31 and a test set of 30 compounds) belonging to a series of 2-amino-6-halopurine and 7'-substituted benzothiazolothio- and pyridinothiazolothio-purines. The best HypoGen model consisted of five pharmacophoric features: one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD) and three hydrophobic (HY) groups. It showed a high correlation coefficient (r = 0.943) and low root mean square deviation (RMSD = 0.751). This model was validated against 30 known Hsp90 inhibitors, where it showed a high predictive value for R(2)pred = 0.805], thus confirming that HY, HBA and HBD features are essential for Hsp90 inhibition. The validated pharmacophore model (Hypo-1) was used as a 3D query for virtual screening to retrieve potential inhibitors from the Maybridge and National Cancer Institute (NCI) databases. The hit compounds were subsequently subjected to molecular docking studies and, finally, five hits were prioritized as potential leads based on GoldScore function.
Multiscale effects and capillary interactions in functional biomimetic surfaces for energy conversion and green engineering (2009)

Biological surfaces (plant leaves, lizard and insect attachment pads, fish scales, etc.) have remarkable properties due to their hierarchical structure. This structure is a consequence of the hierarchical organization of biological tissues. The hierarchical organization of the surfaces allows plants and creatures to adapt to energy dissipation and transition mechanisms with various characteristic scale lengths. At the same time, an addition of a micro-/nanoscale hierarchical level, for example of surface roughness, can change qualitatively the properties of a system and introduce multiple equilibriums, instability and dissipation. Thus, small roughness has a large effect. In particular, a small change of surface roughness can lead to a large change in the capillary force. The capillary effects are crucial for small-scale applications. Multiscale organization of the biomimetic surfaces and their adaptation to capillary effects make them suitable for applications using new principles of energy transition (e.g. capillary engines) and environment-friendly technologies (e.g. self-cleaning oleophobic surfaces).
Fluorinated COX-2 Inhibitors as Agents in PET Imaging of Inflammation and Cancer (2011)

COX-2 is a major contributor to the inflammatory response and cancer progression so it is an important target for prevention and therapy. COX-2 is absent or expressed at low levels in most epithelial cells but is found at high levels in inflammatory lesions, and many premalignant and malignant tumors. Thus, it is an attractive target for molecular imaging. We report a series of novel fluorinated imaging agents, derived from indomethacin or celecoxib that selectively inhibit COX-2. The most promising lead, compound 7, was a fluorinated derivative of celecoxib. Kinetic analysis revealed that this fluorinated compound is a slow, tight-binding inhibitor of COX-2 and exhibits minimal inhibitory activity against COX-1. Efficient incorporation of (18)F into compound 7 by radiochemical synthesis and intravenous injection provided sufficient signal for in vivo positron emission tomography (PET) imaging. Selective uptake of (18)F-7 was observed in inflamed rat paws compared with the noninflamed contralateral paws and uptake was blocked by pretreatment with the COX-2 inhibitor, celecoxib. Uptake of (18)F-7 was not observed when inflammation was induced in COX-2-null mice. In nude mice bearing both a COX-2-expressing human tumor xenograft (1483) and a COX-2-negative xenograft (HCT116), (18)F-7 selectively accumulated in the COX-2-expressing tumor. Accumulation was blocked by pretreatment of the animals with celecoxib. The in vitro and in vivo properties of compound 7 suggest it will be a useful probe for early detection of cancer and for evaluation of the COX-2 status of premalignant and malignant tumors.
A Survey of Applications of Polyoxometalates (1998)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Survey of Applications of PolyoxometalatesDimitris E. KatsoulisView Author Information Dow Corning Corporation, Central Research and Development, Midland, Michigan 48686 Cite this: Chem. Rev. 1998, 98, 1, 359–388Publication Date (Web):January 17, 1998Publication History Received2 June 1997Revised8 November 1997Published online17 January 1998Published inissue 1 February 1998https://pubs.acs.org/doi/10.1021/cr960398ahttps://doi.org/10.1021/cr960398aresearch-articleACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views9001Altmetric-Citations1111LEARN 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 SUBJECTS:Anions,Electrodes,Organic polymers,Salts Get e-Alerts
On the Mechanism of Action of the Antitumor Drug cis‐Platin(cis‐DDP) and its Second Generation Derivatives (1995)

The present article attempts to summarise the elements of the mechanism of action of the antitumor drug cis -Platin presented the last few years. Highlights on the discovery, of the drug and the development of it's second generation derivatives are presented, as well as the ways that cis -DDP reacts with biomolecules as DNA and proteins and their models e.g. nucleosides, nucleotides. Also the hydrolysis data are presented for cis -DDP and its' inactive congener trans -DDP, as well as for the second generation drug carboplatin. Finally, usefull conclusions are given from this work, pointing out the unanswered questions about the action of cis -DDP as well as its differences in action, in comparison with trans -DDP.
Comparative in vitro assessment of the primary stability of cementless press-fit acetabular cups. (2004)

Long-term stable osseointegration of porous-coated acetabular cups depends on bony ingrowth within their porous surface. For ingrowth to take place, one must ensure rigid initial fixation of the implant, by means of screws or by impaction or using a threaded ring. Primary stability is a prerequisite for long term stability through bony ingrowth. We tested several cups commonly used in our department to assess their primary stability. The study was done using synthetic EP-Dur polyurethane resin blocks (Bayer, Leverkusen, Germany). The blocks were fixed at a 45 degrees angle to the horizontal. They were subsequently reamed using the appropriate reamers and the cups tested were impacted into the resin blocks. Eleven 52-mm cups were tested. The pull out force necessary to extract each cup was measured. The pull-out strength ranged from 7.63 to 55.46 Nm. We noted that the closer the cup was to a hemisphere, the better was the initial stability. The contact zone was at the periphery, and the greater the contact was with the resin, the better was the stability. Micromovements exceeding 150 microns prevent any bony ingrowth in vivo. Solid osseointegration can thus only be achieved if movements between implant and bone can be prevented. Our study indicated that initial fixation is essentially peripheral and that those cups that demonstrated the highest pull-out values also had the best peripheral contact. Our observations suggest that the geometry of the cup is more important than its surface macrostructure in terms of primary stability. To achieve stable fixation, we recommend using an oversized cup with a flattened dome to allow maximum peripheral contact.
Applications of dielectric elastomer actuators (2001)

Dielectric elastomer actuators, based on the field-induced deformation of elastomeric polymers with compliant electrodes, can produce a large strain response, combined with a fast response time and high electromechanical efficiency. This unique performance, combined with other factors such as low cost, suggests many potential applications, a wide range of which are under investigation. Applications that effectively exploit the properties of dielectric elastomers include artificial muscle actuators for robots; low-cost, lightweight linear actuators; solid- state optical devices; diaphragm actuators for pumps and smart skins; acoustic actuators; and rotary motors. Issues that may ultimately determine the success or failure of the actuation technology for specific applications include the durability of the actuator, the performance of the actuator under load, operating voltage and power requirements, and electronic driving circuitry, to name a few.
Isolation of Llama Antibody Fragments for Prevention of Dandruff by Phage Display in Shampoo (2005)

As part of research exploring the feasibility of using antibody fragments to inhibit the growth of organisms implicated in dandruff, we isolated antibody fragments that bind to a cell surface protein of Malassezia furfur in the presence of shampoo. We found that phage display of llama single-domain antibody fragments (VHHs) can be extended to very harsh conditions, such as the presence of shampoo containing nonionic and anionic surfactants. We selected several VHHs that bind to the cell wall protein Malf1 of M. furfur, a fungus implicated in causing dandruff. In addition to high stability in the presence of shampoo, these VHHs are also stable under other denaturing conditions, such as high urea concentrations. Many of the stable VHHs were found to contain arginine at position 44. Replacement of the native amino acid at position 44 with arginine in the most stable VHH that lacked this arginine resulted in a dramatic further increase in the stability. The combination of the unique properties of VHHs together with applied phage display and protein engineering is a powerful method for obtaining highly stable VHHs that can be used in a wide range of applications.
Cloning of Murine Gelsolin and Its Regulation during Differentiation of Embryonal Carcinoma Cells (1989)

The regulation of gelsolin levels during differentiation of the murine embryonal carcinoma cell line, PC-13, was investigated using nucleic acid and immunological probes. A cDNA clone, Mu-319, which contained the entire coding sequence for the cytoplasmic form of murine gelsolin was isolated using a polyclonal antibody. Gelsolin was detected in several cell lines but was not detectable in three undifferentiated embryonal carcinoma cell lines. Levels of gelsolin mRNA increased 10-fold during the differentiation of the murine embryonal carcinoma cell line, PC-13. Differentiation of PC-13 was accompanied by changes in cell shape, from small indistinct cells to large flat cells. The accumulation of gelsolin mRNA in PC-13 cells began 12-24 h after addition of the differentiation-inducing agents. In comparison, 2-5A-dependent RNase activity showed a 40-fold increase beginning after 24 to 36 h and c-fos mRNA were shown to increase about 9-fold beginning 36 to 60 h after induction of differentiation. The levels of gelsolin per se, as determined by immunoreactivity were also shown to increase with differentiation of PC-13 cells. These results suggest that gelsolin may play a role in the restructuring of actin filaments which accompanies the dramatic changes in cell shape during differentiation.
X-ray diffraction data for flux-grown calcium hydroxyapatite whiskers (2001)

Calcium hydroxyapatite (Ca 10 (PO 4 ) 6 (OH) 2 ) whiskers were prepared by using the technique of molten salt synthesis with the fluxing agent of potassium sulphate (K 2 SO 4 ). A tentative x-ray diffraction (XRD) pattern was suggested for the produced whiskers. Phase purity, composition, and morphology of the whiskers were investigated by powder XRD, inductively coupled plasma-atomic emission spectroscopy, Fourier transform infrared spectroscopy, and scanning electron microscopy, respectively.
Switching spin valves using rf currents (2006)

We show that magnetization reversal in spin-injection devices can be significantly faster when using a chirped rf current, rather than a dc, pulse. Although one can use a simple sinusoidal rf pulse, an optimized series of alternating, equal-amplitude, pulses of varying width (a digitized approximation to a chirped rf pulse) produces more efficient switching.
Compensation of friction and backlash effects in an electrical actuator (2004)

In this paper, non-linear observers, based on an estimation of the friction force and the disturbed torque transmitted due to the dead zone, are developed for systems presenting mechanical imperfections such as friction and backlash. Then an adaptive controller using these non-linear observers is presented, to compensate for mechanical disturbances on-line. Simulation and experimental results applied on an electrical actuator are given to support the theoretical demonstrations.
Microinterferometric optical phase tomography for measuring small, asymmetric refractive-index differences in the profiles of optical fibers and fiber devices (2005)

A new technique, microinterferometric optical phase tomography, is introduced for use in measuring small, asymmetric refractive-index differences in the profiles of optical fibers and fiber devices. The method combines microscopy-based fringe-field interferometry with parallel projection-based computed tomography to characterize fiber index profiles. The theory relating interference measurements to the projection set required for tomographic reconstruction is given, and discrete numerical simulations are presented for three test index profiles that establish the technique's ability to characterize fiber with small, asymmetric index differences. An experimental measurement configuration and specific interferometry and tomography practices employed in the technique are discussed.
Protein Import into the Nucleus: An Integrated View (1995)

The directed movement of macromolecules into and out of the nucleus is a fundamental process in eukaryotes and occurs through the nuclear pore complex (NPC). A diverse array of molecules are transported across the nuclear envelope including proteins, mRNAs, tRNAs, snRNP complexes, ribosomal subunits, and in specialized cases, DNA. The structural and functional differences between these molecules point to the mechanistic complexity of NPCs and other components of the nuclear transport apparatus. This machinery must not only recognize within transported molecules specific targeting signals that differ between proteins, RNA, and RNA/protein complexes, it must translocate these molecules across the nuclear envelope. Additional levels of complexity are necessary because molecules such as proteins may continually undergo bidirectional transport across the envelope. Beyond these basic functions, the nuclear transport apparatus is regulated at the level of individual substrates and at more global levels such as coupling to cell cycle regression.
LIQUID CRYSTAL MATERIALS AND LIQUID CRYSTAL DISPLAYS (1997)

▪ Abstract Since the early 1970s, three major prerequisites have brought the success of the liquid crystal display (LCD) technology to its key role of today. Namely, the discovery of electro-optical field-effects on which the displays are based, the successful search for liquid crystals (LCs) with material properties that meet the complex requirements of electro-optical effects and render the effects applicable in displays, and last but not least, the development of the technological tools required for manufacturing displays. Virtually all of today's commercial LCDs are based on the twisted nematic (TN) or on various supertwisted nematic (STN) effects whose extensive development and improvement over the past 25 years is still rapidly progressing. Those liquid crystal material properties and electro-optical effects that essentially determine the performance of nematic displays are reviewed. Correlations between molecular functional structural groups, LC material properties, and their electro-optical relevance for TN and STN displays are outlined. Included are dual-frequency addressing phenomena in liquid crystal materials, in situ dielectric heating of displays, and conductivity phenomena that are related and that may either hamper or improve the performance of high-information content LCDs. Moreover, we review some recent developments made in our laboratories on novel electro-optical devices and device-specific functional organic materials, e.g. optical alignment of monomeric and polymeric liquid crystals by linearly polarized light; the generation of photo-patterned multidomain twisted nematic displays with broad field of view; the operation of displays with circularly polarized light, as well as compact and bright cholesteric LCD projection optics whose polarizers, filters, and modulators are all based on liquid crystal elements.
Evolutionary relationships among cyanobacteria and green chloroplasts (1988)

The 16S rRNAs from 29 cyanobacteria and the cyanelle of the phytoflagellate Cyanophora paradoxa were partially sequenced by a dideoxynucleotide-terminated, primer extension method. A least-squares distance matrix analysis was used to infer phylogenetic trees that include green chloroplasts (those of euglenoids, green algae, and higher plants). The results indicate that many diverse forms of cyanobacteria diverged within a short span of evolutionary distance. Evolutionary depth within the surveyed cyanobacteria is substantially less than that separating the major eubacterial taxa, as though cyanobacterial diversification occurred significantly after the appearance of the major eubacterial groups. Three of the five taxonomic sections defined by Rippka et al. (R. Rippka, J. Deruelles, J. B. Waterbury, M. Herdman, and R. Y. Stanier, J. Gen. Microbiol. 111:1-61, 1979) (sections II [pleurocapsalean], IV [heterocystous, filamentous, nonbranching], and V [heterocystous, filamentous, branching]) are phylogenetically coherent. However, the other two sections (I [unicellular] and III [nonheterocystous, filamentous]) are intermixed and hence are not natural groupings. Our results not only support the conclusion of previous workers that the cyanobacteria and green chloroplasts form a coherent phylogenetic group but also suggest that the chloroplast lineage, which includes the cyanelle of C. paradoxa, is not just a sister group to the free-living forms but rather is contained within the cyanobacterial radiation.
Carboxy-terminally truncated dengue virus envelope glycoproteins expressed on the cell surface and secreted extracellularly exhibit increased immunogenicity in mice (1991)

Recombinant vaccinia viruses expressing C-terminally truncated E's that ranged in length from 9 to 99% of the N-terminal sequence were constructed. The overall antigenicity of the E products was analyzed by radioimmunoprecipitation, using dengue virus hyperimmune mouse ascitic fluid (HMAF) or an anti-E peptide serum. Truncated E that was 79% or less in length did not bind HMAF efficiently, whereas E constructs greater than 79% were able to bind HMAF with high efficiency. The first 392 amino acids of the dengue type 4 virus E sequence, including the Arg-392 following the 79% E C terminus, appeared to be critical for proper antigenic structure required for efficient binding by HMAF. Truncated E's ranging from 59 to 81% in length were secreted extracellularly, whereas smaller or larger E's were retained intracellularly. Secreted E's contained carbohydrate side chains that were resistant to endoglycosidase H digestion, suggesting that the transport of E occurs via a pathway from the rough endoplasmic reticulum through the Golgi complex. 79% E-RKG (which possessed the three additional amino acids immediately downstream of 79% E) was expressed at a high concentration on the surface of recombinant virus-infected cells presumably being inserted into the plasma membrane by a hydrophobic C-terminal membrane anchor. Evaluation in mice of the protective efficacy of the various vaccinia virus E recombinants indicated that only truncated E's that were recognized efficiently by HMAF induced a high level of resistance to dengue virus encephalitis. 79% E-RKG which is expressed at a high concentration on the surface of infected cells was highly immunogenic when tested for induction of an E antibody response. This suggests that cell surface expression of 79% E-RKG was responsible for its enhanced immunogenicity. Finally, passive immunization studies indicated that serum antibodies to E played a major role in the complete or nearly complete resistance to dengue virus challenge induced by certain vaccinia virus-truncated E recombinants.
Goodpasture syndrome. Localization of the epitope for the autoantibodies to the carboxyl-terminal region of the alpha 3(IV) chain of basement membrane collagen. (1991)

The autoantibodies of patients with Goodpasture syndrome are primarily targeted to the noncollagenous (NC1) domain of the alpha 3(IV) chain of basement membrane collagen (Saus, J., Wieslander, J., Langeveld, J. P. M., Quinones, S., and Hudson, B. G. (1988) J. Biol. Chem. 263, 13374-13380). In the present study, the location of the Goodpasture epitope in human alpha 3NC1 was determined, and its structure was partially characterized. This was achieved by identification of regions of alpha 3NC1 which are candidates for the epitope and which are structurally unique among the five known homologous NC1 domains (alpha 1-alpha 5); amino acids that are critical for Goodpasture antibody binding, by selective chemical modifications; and regions that are critical for Goodpasture antibody binding, by synthesis of 12 alpha 3NC1 peptides and measurement of their antibody binding capacity. The carboxyl-terminal region, residues 198-233, was identified as the most likely region for the epitope. By experiment, lysine and cysteine were identified as critical amino acids for antibody binding. Three synthetic peptides were found to inhibit Goodpasture antibody binding to alpha 3NC1 markedly: a 36-mer (residues 198-233), a 12-mer (residues 222-233), and a 5-mer (residues 229-233). Together, these results strongly indicate that the Goodpasture epitope is localized to the carboxyl-terminal region of alpha 3NC1, encompassing residues 198-233 as the primary antibody interaction site and that its structure is discontinuous. These findings provide a conceptual framework for future studies to elucidate a more complete epitope structure by sequential replacement of residues encompassing the epitope using cDNA expression products and peptides synthesized chemically.
Impact of external cooling with icepacks on 68Ga-PSMA uptake in salivary glands (2018)

Impact of icepacks on PSMA uptake seems to be limited to the parotid glands. As clinical relevance of these findings is debatable, structural application of icepacks in the setting of lutetium-177 PSMA therapy needs careful consideration.
Self-Attention with Relative Position Representations (2018)

Peter Shaw, Jakob Uszkoreit, Ashish Vaswani. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 2 (Short Papers). 2018.