gebhart/patrepeval huggingface dataset:
Engineering Novel Metalloproteins:  Design of Metal-Binding Sites into Native Protein Scaffolds (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEngineering Novel Metalloproteins: Design of Metal-Binding Sites into Native Protein ScaffoldsYi Lu, Steven M. Berry, and Thomas D. PfisterView Author Information Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 Cite this: Chem. Rev. 2001, 101, 10, 3047–3080Publication Date (Web):October 10, 2001Publication History Received27 March 2001Published online10 October 2001Published inissue 1 October 2001https://pubs.acs.org/doi/10.1021/cr0000574https://doi.org/10.1021/cr0000574research-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views4410Altmetric-Citations323LEARN 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:Bioinorganic chemistry,Copper,Genetics,Monomers,Peptides and proteins Get e-Alerts
Neuroprotective effects of eliprodil in retinal excitotoxicity and ischemia. (1999)

Eliprodil is neuroprotective of retinae subjected to either an excitotoxic or ischemic challenge and may be useful for treating a variety of retinal and optic nerve head disorders.
Electrochromism in the mixed-valence hexacyanides. 1. Voltammetric and spectral studies of the oxidation and reduction of thin films of Prussian blue (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochromism in the mixed-valence hexacyanides. 1. Voltammetric and spectral studies of the oxidation and reduction of thin films of Prussian blueD. Ellis, M. Eckhoff, and V. D. NeffCite this: J. Phys. Chem. 1981, 85, 9, 1225–1231Publication Date (Print):April 1, 1981Publication History Published online1 May 2002Published inissue 1 April 1981https://pubs.acs.org/doi/10.1021/j150609a026https://doi.org/10.1021/j150609a026research-articleACS PublicationsRequest reuse permissionsArticle Views2300Altmetric-Citations413LEARN 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 options Get e-Alerts
X-Ray CT and NMR Imaging of Rocks (1986)

Introduction In little more than a decade, X-ray computerized tomography (CT) and nuclear magnetic resonance (NMR) imaging have become the premier modalities of medical radiology. Both of these imaging techniques also promise to be useful tools in petrophysics and reservoir engineering, because CT and NMR can nondestructively image a host of physical and chemical properties of porous rocks and multiple fluid phases contained within their pores. The images are taken within seconds to minutes, at reservoir temperatures and pressures, with spatial resolution on the millimeter and submillimeter level. The physical properties imaged by the two techniques are complementary. CT images bulk density and effective atomic number. NMR images the nuclide concentration, Mo, of a variety of nuclei ( H, 19-F, 23-Na, 31-P, etc.), their longitudinal and transverse relaxation-time curves (t1 and t2 ), and their chemical shift spectra. In rocks, CT images both rock matrix and pore fluids, while NMR images only mobile fluids and the interactions of these mobile fluids with the confining surfaces of the pores. Principles CT uses an X-ray source that rotates around the sample to obtain one-dimensional projections of X-ray attenuation at different angles. From these projections, a crosssectional slice through the sample is reconstructed by computer. Finally. a three-dimensional image is reconstructed from sequential cross-sectional slices taken as the sample is moved through the scanner. To obtain both density and effective atomic number, CT images are taken at two X-ray energies. One energy is high enough for the X-rays to be predominantly Compton-scattered and one is low enough for them to be mostly photoelectrically absorbed. A combination of the two images in the computer. on a pixel-by-pixel basis, generates separate images of bulk density and effective atomic number. In NMR imaging, the sample is placed inside an intense, homogeneous, magnetic field, one preferably generated by a superconducting magnet. Radio frequency (RF) coils apply RF magnetic fields at the precise Larmor frequency to cause the particular nuclear species to precess. The RF coils then detect the signals generated by the precessing nuclei. Spatial localization within the sample is obtained by x. y, and z magnetic-field gradient coils that cause nuclei in different parts of the sample to precess at slightly different frequencies. The resulting frequency-modulated signal is Fourier-transformed to obtain the spatial distribution of nuclear-spin density. Unlike CT, an image is obtained of the entire sample volume within the RF coil. JPT P. 257^
Fabrication, modification, and application of poly(methyl methacrylate) microfluidic chips (2008)

Poly(methyl methacrylate) (PMMA) is particularly useful for microfluidic chips with the features of low price, excellent optic transparency, attractive mechanical and chemical properties, ease of fabrication and modification, biocompatibility, etc. During the past decade, significant progress in the PMMA microfluidic chips has occurred. This review, which contains 120 references, summarizes the recent advances and the key strategies in the fabrication, modification, and application of PMMA microfluidic chips. It is expected that PMMA microchips should find a wide range of applications and will lead to the creation of truly disposable microfluidic devices.
Experimental panic provocation in healthy man—a translational role in anti-panic drug development? (2011)

Experimental neurochemical provocation of panic attacks in susceptible human subjects has considerably expanded our knowledge of the pathophysiology and psychopharmacology of panic disorder. Some panicogens also elicit short-lived panic-like states in healthy man. This offers the opportunity to assess the anti-panic action of drugs in proof-of-concept studies. However, from current data it is still unclear whether experimental panic in healthy man is a valid translational model. Most such studies in healthy volunteers have been performed using a cholecystokinin tetrapeptide (CCK-4) challenge. While CCK-4 panic was blocked by alprazolam pretreatment, escitalopram showed negative results in healthy man. Preliminary findings on novel investigational drugs and a few problematic results will be reviewed. Small sample sizes in many panic provocation studies, lack of dose-response aspects, and still-insufficient knowledge about the biological underpinning of experimental and spontaneous panic limit the interpretation of existing findings and should inspire further research.
Substrate properties of cycloadenosines with adenosine aminohydrolase as evidence for the conformation of enzyme-bound adenosine (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstrate properties of cycloadenosines with adenosine aminohydrolase as evidence for the conformation of enzyme-bound adenosineAlexander Hampton, Peter J. Harper, and Takuma SasakiCite this: Biochemistry 1972, 11, 25, 4736–4739Publication Date (Print):December 1, 1972Publication History Published online1 May 2002Published inissue 1 December 1972https://pubs.acs.org/doi/10.1021/bi00775a016https://doi.org/10.1021/bi00775a016research-articleACS PublicationsRequest reuse permissionsArticle Views46Altmetric-Citations36LEARN 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
Synthesis of some novel pyrazoline and cyanopyridine derivatives as antimicrobial agents. (1996)

Substituted chalcones 2a-j prepared by the treatment of 4'(p-chlorophenylsulphonamido)acetophenone 1 with araldehydes, on condensation with hydrazine hydrate in ethanol and acetic acid provided the desired pyrazolines of the type 3a-j and 4a-j. The same chalcones 2a-j made to react with malononitrile in the presence of ammonium acetate yielded cyanopyridines 5a-j. The structure was confirmed by elemental analyses, IR, NMR and MS spectral studies. The pharmacological profile of the compounds synthesised is described. Most of the compounds displayed their maximum activity against E. coli. Compounds 2b, 2d, 5b, 5d, 5e, 5h and 5i have been selected for their agrochemical screening by DuPont Agricultural Products, U.S.A.
Ligand-regulated Chimeric Receptor Approach Reveals Distinctive Subcellular Localization and Signaling Properties of the Toll-like Receptors (2004)

Toll-like receptors (TLRs) are sensors for the detection of invading infectious agents and can initiate innate immune responses. Because the innate immune system induces an appropriate defense against different pathogens, different TLR signaling domains may have unique properties that are responsible for eliciting distinctive responses to different types of pathogens. To test this hypothesis, we created ligand-regulated TLR chimeric receptors composed of the extracellular region of TLR4 and the transmembrane and cytoplasmic regions of other TLRs and expressed these chimeras in macrophages lacking endogenous TLR4. Interestingly, the chimeras between TLR4 and either TLR3, TLR7, or TLR9 were localized completely intracellularly whereas other chimeras were expressed on the cell surface. Lipopolysaccharide (LPS), a ligand for these chimeras, induced the activation of nuclear factor kappa B and mitogen-activated protein kinases and the subsequent production of pro-inflammatory cytokines in macrophages expressing TLR4, TLR4/TLR5, or TLR4/TLR8 chimeras but not in macrophages expressing TLR4/TLR1, TLR4/TLR2, or TLR4/TLR6 chimeras. Co-expression of unresponsive chimeras in some combinations (chimeras with TLR1+TLR2 or TLR2+TLR6 but not TLR1+TLR6) resulted in LPS responsiveness, indicating functional complementarity. Furthermore, the pair of TLR2+TLR6 chimera required approximately 10-fold less LPS to induce the same responses compared with the TLR1+TLR2 pair. Finally, LPS induced effective interferon-beta production and subsequent Stat1 phosphorylation in macrophages expressing full-length TLR4 but not other cell surface TLR chimeras. These results suggest that the functions of TLRs are diversified not only in their extracellular regions for ligand recognition but also in their transmembrane and cytoplasmic regions for subcellular localization and signaling properties.
The MLL partial tandem duplication: evidence for recessive gain-of-function in acute myeloid leukemia identifies a novel patient subgroup for molecular-targeted therapy (2005)

MLL (ALL-1) chimeric fusions and MLL partial tandem duplications (PTD) may have mechanistically distinct contributions to leukemogenesis. Acute myeloid leukemia (AML) blasts with the t(9;11)(p22; q23) express MLL-AF9 and MLL wild-type (WT) transcripts, while normal karyotype AML blasts with the MLL(PTD/WT) genotype express MLL PTD but not the MLL WT. Silencing of MLL WT in MLL(PTD/WT) blasts was reversed by DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors, and MLL WT induction was associated with selective sensitivity to cell death. Reduction of MLL PTD expression induced MLL WT and reduced blast colony-forming units, supporting opposing functions for MLL PTD and MLL WT whereby the MLL PTD contributes to the leukemic phenotype via a recessive gain-of-function. The coincident suppression of the MLL WT allele with the expression of the MLL PTD allele, along with the functional data presented here, supports the hypothesis that loss of WT MLL function via monoallelic repression contributes to the leukemic phenotype by the remaining mutant allele. These data from primary AML and the pharmacologic reversal of MLL WT silencing associated with a favorable alteration in the threshold for apoptosis suggest that these patients with poor prognosis may benefit from demethylating or histone deacetylase inhibitor therapy, or both.
Design of Cathepsin K Inhibitors for Osteoporosis (2005)

Osteoporosis is a progressive, debilitating bone disease resulting in increased cost and morbidity to the elderly. This review summarizes the therapeutic approaches taken in the treatment of osteoporosis with particular emphasis on cathepsin K inhibitors. Cathepsin K, a cysteine protease predominantly expressed in osteoclasts, is a key player involved in bone matrix degradation. Both genetic ablation and small molecule inhibitor strategies versus cathepsin K have validated the importance of this enzyme in bone resorption. Starting from aldehyde-based leads, this review synopsizes the design of improved small molecule inhibitors by GlaxoWellcome researchers. These efforts involved the evaluation of various warheads, including cyanamides, ketoheterocycles, and ketoamides. Initial structure/activity relationships of aldehyde-based inhibitors proved useful in the design of ketoamide-based cathepsin K inhibitors. Further exploration of S(3), S(2), S(1), and S(1') subsites with P(3), P(2), P(1), and P(1') probes have resulted in the identification of potent, selective, orally bioavailable ketoamide-based inhibitors of cathepsin K with demonstrated in vivo efficacy.
Liposomes containing lipid A: an effective, safe, generic adjuvant system for synthetic vaccines (2012)

Liposomes containing monophosphoryl lipid A (MPLA) have previously exhibited considerable potency and safety in human trials with a variety of candidate vaccines, including vaccines to malaria, HIV-1 and several different types of cancer. The long history of research and development of MPLA and liposomal MPLA as vaccine adjuvants reveals that there are numerous opportunities for creation and development of generic (nonproprietary) adjuvant system formulations with these materials that are not only highly potent and safe, but also readily available as native materials or as synthetic compounds. They are easily manufactured as potentially inexpensive and easy to use adjuvant systems and might be effective even with synthetic peptides as antigens.
First-in-Human Evaluation of the Safety and Immunogenicity of a Recombinant Adenovirus Serotype 26 HIV-1 Env Vaccine (IPCAVD 001) (2012)

NCT00618605.
Efficient correction of mismatched bases in plasmid heteroduplexes injected into cultured mammalian cell nuclei. (1985)

Heteroduplexes were prepared from two plasmids, pRH4-14/TK and pRH5-8/TK, containing different amber mutations in the neomycin resistance gene (Neor). The Neor gene was engineered to be expressed in both bacterial and mammalian cells. A functional Neor gene conferred kanamycin resistance to bacteria and resistance to the drug G418 to mammalian cells. In addition, the plasmids contained restriction site polymorphisms which did not confer a selectable phenotype but were used to follow the pattern of correction of mismatched bases in the heteroduplexes. In a direct comparison of the efficiency of transforming mouse LMtk- cells to G418r, the injection of heteroduplexes of pRH4-14/TK-pRH5-8/TK was 10-fold more efficient than the coinjection of pRH4-14/TK and pRH5-8/TK linear plasmid DNA. In fact, injection of 5 to 10 molecules of heteroduplex DNA per cell was as efficient in transforming LMtk- cells to G418r as the injection of 5 to 10 molecules of linear plasmid DNA per cell containing a wild-type Neor gene. To determine the pattern of mismatch repair of the injected heteroduplexes, plasmids were "rescued" from the G418r cell lines. From this analysis we conclude that the generation of wild-type Neor genes from heteroduplex DNA proceeds directly by correction of the mismatched bases, rather than by alternative mechanisms such as recombination between the injected heteroduplexes. Our finding that a cell can efficiently correct mismatched bases when confronted with preformed heteroduplexes suggests that this experimental protocol could be used to study a wide range of DNA repair mechanisms in cultured mammalian cells.
Accelerated Rejection of FAS Ligand-Expressing Heart Grafts (1999)

The Fas/Fas ligand (FasL) system plays an important role in the induction of lymphoid apoptosis and has been implicated in the suppression of immune responses. Recently, there has been renewed interest in immune privilege, as it was shown that two privileged sites (the eye and testes) constitutively express FasL, which kills lymphoid cells that invade these areas. We have established murine FasL-transgenic mice (B6) under the control of the cardiac alpha-myosin heavy chain promotor, and transplanted FasL-expressing F1(B6 x C3H/HeJ) heart grafts into syngeneic (F1) and allogeneic (C3H/HeJ) recipients. FasL-expressing F1 heart allografts placed in C3H/HeJ recipients as well as FasL-expressing F1 isografts placed in nontransgenic and FasL-transgenic F1 were more rapidly rejected, and their survival was much shorter than that of nontransgenic control F1 allografts placed in C3H/HeJ. Native control and FasL-expressing hearts looked normal in mice up to 8 wk of age on hematoxylin-eosin staining. Control heart allografts undergoing ordinally acute rejection showed moderate focal lymphocyte infiltrates, while FasL-expressing F1 allografts and isografts showed massive hemorrhage, edema, and massive neutrophil infiltration as early as 1 day after transplantation. In conclusion, FasL expression and surgical procedure (ischemia/reperfusion) were synergistic in the induction of accelerated heart graft rejection, while allogenicity was not necessary. It may be necessary to find ways of controlling neutrophilic reaction/apoptosis in infiltrating lymphocytes to use FasL in clinical organ transplantation.
Elastographic imaging of strain distribution within the anterior cruciate ligament and at the acl-bone insertions (2006)

The anterior cruciate ligament (ACL) functions as a mechanical stabilizer in the tibiofemoral joint. Over 250,000 Americans each year suffer from ACL ruptures and tears, making the ACL the most commonly injured knee ligament. A long term goal of our research program is to promote graft-bone integration via the regeneration of the native ligament-bone interface. To this end, we have focused on the design of biomimetic scaffolds combined with tissue engineering to induce organized interface regeneration. An understanding of mechanical properties of the ligament-bone interface is critical for biomimetic scaffold design and clinical evaluation. To date, experimental determination has been difficult due to the small length scale (< 1 mm) involved at the ACL insertions. This study utilizes ultrasound elastography to characterize the functional properties of the ACL and the ACL-bone interface under applied loading. Specifically, the tibiofemoral joints were mounted on a biomechanics material testing system and loaded in tension while RF data was collected. Axial elastograms between successive RF frames were generated using cross-correlation and recorrelation techniques. Elastography analyses revealed that when the joint is in tension, complex strains with both compressive and tensile components were found at the tibial insertion. These results are in agreement with those of prior finite element analysis (FEA) model predictions. In addition, the magnitude of displacement was found to be the highest at the ACL proper and decreased in value from ligament to bone. Our results indicate that elastography is a novel and useful method in understanding the mechanical properties of the ligament itself and the ligament-bone interface.
Anyonic interferometry without anyons: how a flux qubit can read out a topological qubit (2010)

Proposals to measure non-Abelian anyons in a superconductor by quantum interference of vortices suffer from the predominantly classical dynamics of the normal core of an Abrikosov vortex. We show how to avoid this obstruction using coreless Josephson vortices, for which the quantum dynamics has been demonstrated experimentally. The interferometer is a flux qubit in a Josephson junction circuit, which can nondestructively read out a topological qubit stored in a pair of anyons --- even though the Josephson vortices themselves are not anyons. The flux qubit does not couple to intra-vortex excitations, thereby removing the dominant restriction on the operating temperature of anyonic interferometry in superconductors.