gebhart/patrepeval huggingface dataset:
DNA-Binding Specificity of NGFI-A and Related Zinc Finger Transcription Factors (1995)

NGFI-A is the prototypic member of a family of immediate-early gene-encoded transcription factors which includes NGFI-C, Egr3, and Krox20. These proteins possess highly homologous DNA-binding domains, composed of three Cys2-His2 zinc fingers, and all bind to and activate transcription from the sequence GCGGGGGCG. We used a PCR-mediated random site selection protocol to determine whether other sites could be bound by these proteins and the extent to which their binding site preferences are similar or different. The high-affinity consensus sites generated from the selection data are similar, and the combined consensus sequence is T-G-C-G-T/g-G/A-G-G-C/a/t-G-G/T (lowercase letters indicate bases selected less frequently). Using gel shift assays, we found that sequences that diverge from the consensus were bound by NGFI-A, confirming that there is greater variability in binding sites than has generally been acknowledged. We also provide evidence that protein-DNA interactions not noted, or whose importance was not apparent from the X-ray cocrystal structure of the NGFI-A zinc fingers complexed with DNA, contribute significantly to the binding energy of these proteins and confirm that an optimal site is at least 10 instead of 9 nucleotides in length. In contrast to the similarities in binding specificity among these proteins we found that while NGFI-A, Egr3, and Krox20 have comparable DNA binding affinities and kinetics of dissociation, the affinity of NGFI-C is more than threefold lower. This could result in differential regulation of target genes in cells where NGFI-C and the other proteins are coexpressed. Furthermore, we show that this affinity difference is a property not of the zinc fingers themselves but rather of the protein context of the DNA-binding domain.
Synthesis and characterization of binuclear zirconocenophane hydrides. The molecular structure of [SiMe2(C5H4)2][(.eta.5-C5H5)ZrCl(.mu.-H)]2 (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of binuclear zirconocenophane hydrides. The molecular structure of [SiMe2(C5H4)2][(.eta.5-C5H5)ZrCl(.mu.-H)]2Karuna P. Reddy and Jeffrey L. PetersenCite this: Organometallics 1989, 8, 2, 547–549Publication Date (Print):February 1, 1989Publication History Published online1 May 2002Published inissue 1 February 1989https://pubs.acs.org/doi/10.1021/om00104a040https://doi.org/10.1021/om00104a040research-articleACS PublicationsRequest reuse permissionsArticle Views85Altmetric-Citations22LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Tetra-n-butylammonium Fluoride as an Efficient Transesterification Catalyst for Functionalizing Cyclic Carbonates and Aliphatic Polycarbonates (2013)

We have developed a general method for the functionalization of cyclic carbonate monomers having a pentafluorophenyl ester substituent at the 5-position (MTC-OC<sub>6</sub>F<sub>5</sub>), as well as the postpolymerization modification of the subsequent polymer, poly(MTC-OC<sub>6</sub>F<sub>5</sub>), with alcohols. The transesterifications are achieved under mild conditions using catalytic tetra-<i>n</i>-butylammonium fluoride (TBAF) as the nucleophilic acyl transfer agent. As an organic-soluble form of fluoride, TBAF loadings as low as 5 mol % were sufficient in bringing about high conversions at room temperature. The mild reaction conditions preserved the integrity of the sensitive carbonate moieties even without the use of Schlenk techniques. In addition to commercial TBAF solutions, we also found solid-supported forms of TBAF to be effective for transesterification, thus enabling facile postreaction workup and purification. More importantly, with only minor adjustments to the reaction conditions, we show that TBAF also promotes the postpolymerization modification of poly(MTC-OC<sub>6</sub>F<sub>5</sub>), whereby fluoride-mediated transesterification with various alcohols proceeded quantitatively across the pendant pentafluorophenyl esters. Synthesizing a series of pendant ester-functionalized polycarbonates from a common precursor polymer was previously unattainable with existing methods, an issue that is now resolved by the current work.
Osteoblast response to alumina and titania nanometer wear debris (2003)

Osteoblast (bone-forming cells) response to different sizes of alumina and titania wear debris particles were investigated in the present in vitro study. Such wear debris may result from friction between articulating components of orthopedic implants composed of nanophase ceramics. Results provided the first evidence of increased osteoblast proliferation in the presence of nanometer compared to conventional-dimension (i.e., micrometer) ceramic particles. The present study also indicated a different early response (through altered mRNA expression and protein synthesis) of osteoblasts exposed to nanometer as apposed to micrometer particle size ceramics. Evidence of a less detrimental effect of nanometer compared to conventional-dimension wear debris on osteoblast function offers additional evidence that nanophase ceramics may become the next generation of bone prosthetic materials with improved osseointegrative (that is, ability to bond to juxtaposed bone in situ) properties.
Optimization of Substituted N-3-Benzylimidazoquinazolinone Sulfonamides as Potent and Selective PDE5 Inhibitors (2000)

A previous report from these laboratories identified the N-3-benzylimidazoquinazolinone nucleus as a more selective PDE5 inhibitor template compared to the pyrazolopyrimidine of sildenafil. This paper describes in detail the structure-activity relationships of a set of sulfonamide analogues, several of which are both more potent and more selective PDE5 inhibitors in vitro than sildenafil. The synthesis, in vitro enzyme activity and selectivity, and in vitro functional and preclinical pharmacokinetic assessment of molecules in this series are described.
Real-time correction of atmospherically degraded telescope images through image sharpening (1974)

We present a new technique for the correction of atmospheric distortion in telescope images. Most of this distortion arises from a random phase variation of the incoming light across the telescope aperture. This variation limits the resolving power of even large telescopes to about one arc second. If the sharpness of the images is defined in a suitable way, this sharpness is maximized only when the phase distortion of the incoming light is zero. We present computer simulations of a simple feedback system in which active optical elements, set to maximize the sharpness, correct most of the atmospheric distortion. Photon statistics set the limiting magnitude of the object for which a practical feedback system can work. Details in a sixth magnitude object smaller than 0.1 sec of arc should be resolvable. The system can be conveniently employed within existing telescopes.
Differential effects of anti‐rat CD11b monoclonal antibodies on granulocyte adhesiveness (1999)

Four different monoclonal antibodies (mAbs) reactive with rat CD11b (ED7, ED8, OX-42 and 1B6c) have been characterized for their ability to induce homotypic aggregation of granulocytes or to modify granulocyte adhesiveness triggered by phorbol myristate acetate (PMA) or N-formyl-methionyl-leucyl-phenylalanine (fMLP). Cross-blocking experiments showed that these mAbs recognize at least three different epitopes on CD11b. OX-42 mAb recognizes an inhibitory epitope since the mAb inhibited homotypic aggregation of granulocytes and their adherence to plastic in the presence of PMA or fMLP. ED7 and ED8 induced homotypic aggregation of granulocytes which was blocked by OX-42 and anti-CD18 mAb (WT3) suggesting that CR3 itself is involved in the adhesion process. The aggregation was dependent on active cell metabolism, intact cytoskeleton, divalent cations and activation of tyrosine kinases sensitive to genistein. Staurosporine, okadaic acid and orthovanadate potentiated the aggregation. ED7 and ED8 potentiated homotypic aggregation and adhesion of granulocytes to plastic caused by fMLP, but inhibited granulocyte adhesion to plastic induced by PMA. 1B6c recognizes an epitope that transmits a proaggregatory signal upon binding of the mAb but only if the granulocytes are in contact with plastic or are activated by fMLP. In contrast, 1B6c inhibited granulocyte adhesion to plastic triggered by PMA or fMLP. These data suggest the existence of functionally different epitopes on rat CD11b and indicate that some anti-CD11b mAbs are able to functionally activate CR3.
SYNTHESIS OF 3-VINYLINDOLES FROM 3-ALKYLIDENEINDOL-2(3H)-ONES (1995)

(1995). SYNTHESIS OF 3-VINYLINDOLES FROM 3-ALKYLIDENEINDOL-2(3H)-ONES. Organic Preparations and Procedures International: Vol. 27, No. 1, pp. 113-117.
Why do plaques rupture? (1992)

Rupture of the plaque surface, often with thrombosis superimposed, occurs frequently during the evolution of coronary atherosclerotic lesions. It is probably the most important mechanism underlying the sudden, rapid plaque progression responsible for acute coronary syndromes. The risk of plaque rupture depends on plaque type (composition) rather than plaque size (volume), because only plaques rich in soft extracellular lipids are vulnerable (rupture-prone). Most ruptures are tiny, occurring at the periphery of the fibrous cap that covers the lipid-rich core--points where the cap is usually thinnest and most heavily infiltrated by macrophage foam cells. Compared with intact caps, ruptured ones usually have less tensile strength and are more extensible, containing less collagen and glycosaminoglycans, more extracellular lipid, fewer smooth muscle cells, and more macrophages. Progressive extracellular lipid accumulation (lipid core formation) and cap weakening (macrophage related?) predispose the plaque to rupture and determine the actual vulnerability, which may change with time. Luckily, the plaque components responsible for vulnerability (soft lipid and probably macrophages) are apparently most likely to regress with treatment. The dynamic interplay between the actual plaque vulnerability and external stresses ("triggers") probably determines the particular moment and point of rupture, if this occurs. Vulnerability probably plays a more important role in rupture than triggers, because exercise stress testing of patients with advanced coronary artery disease rarely triggers a rupture/thrombus-related acute heart attack. A prerequisite is the presence of a vulnerable plaque.
Mucosal model of immunization against human immunodeficiency virus type 1 with a chimeric influenza virus (1995)

Previously, we constructed a chimeric influenza virus that expresses the highly conserved amino acid sequence ELDKWA of gp41 of human immunodeficiency virus type 1 (HIV-1). Antisera elicited in mice by infection with this chimeric virus showed neutralizing activity against distantly related HIV-1 isolates (T. Muster, R. Guinea, A. Trkola, M. Purtscher, A. Klima, F. Steindl, P. Palese, and H. Katinger, J. Virol. 68:4031-4034, 1994). In the present study, we demonstrated that intranasal immunizations with this chimeric virus are also able to induce a humoral immune response at the mucosal level. The immunized mice had ELDKWA-specific immunoglobulins A in respiratory, intestinal, and vaginal secretions. Sustained levels of these secretory immunoglobulins A were detectable for more than 1 year after immunization. The results show that influenza virus can be used to efficiently induce secretory antibodies against antigens from foreign pathogens. Since long-lasting mucosal immunity in the genital and intestinal tracts might be essential for protective immunity against HIV-1, influenza virus appears to be a promising vector for HIV-1-derived immunogens.
Strategies to Adapt Adenoviral Vectors for Targeted Delivery (1999)

The utility of current generation adenoviral vectors for targeted, cell-specific gene delivery is limited by the promiscuous tropism of the parent virus. To address this issue, we have developed both genetic and immunologic methods to alter viral tropism. Immunologic retargeting has been achieved via conjugates comprised of an antifiber knob Fab and a targeting moiety consisting of a ligand or antireceptor antibody. Gene delivery by this approach has been accomplished via a variety of cellular pathways including receptors for folate, FGF, and EGF. In addition to cell-specific gene delivery, this strategy has allowed enhanced gene delivery to target cells lacking the native adenoviral receptor, CAR. Of note, this specific and extended gene delivery allowed enhanced survival in murine models of human carcinoma via cancer gene therapy. Genetic strategies to alter adenoviral tropism have included both fiber modification and fiber replacement. In the former, we have identified the HI loop of fiber as a propitious locale for introduction of heterologous peptides. Incorporation of an RGDC peptide at this locale allowed gene delivery via cellular integrins with dramatic efficiency augmentations. As a strategy to achieve both new tropism as well as to ablate native tropism, methods have been developed to replace the fiber protein with heterologous motif which preserves the key trimeric quaternary structure of fiber and allows for propagation. Such a fiber-replacement virus has been rescued and has demonstrated capacities consistent with its utility as a novel vector agent. These strategies have allowed the achievement of cell-specific gene delivery via adenoviral vectors and thus have the potential to enhance the utility of this vector agent.
2‐Substituted‐4‐aryl‐6,7,8,9‐tetrahydro‐5H‐pyrimido[4,5‐b] [1,5]oxazocin‐5‐one as a Structurally New NK1 Antagonist. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
An experimental study of throughput for UDP and VoIP traffic in IEEE 802.11b networks (2004)

We present experimental studies on the throughput of IEEE 802.11b wireless networks for UDP and VoIP traffic. Our experiments show that the maximum data throughput of a single station sending out UDP traffic is 6.1 Mbps. The maximum number of VoIP calls in a single cell of an IEEE 802.11b network is six if the ITU G711a-Law codec is used with 10 milliseconds of audio per RTP packet. The experiments also show that the effective available bandwidth in the wireless network is reduced by ongoing VoIP connections. Specifically, for the above codec settings, each VoIP connection reduces the bandwidth available for data traffic by 900 kbps.
The modification of human immunoglobulin binding to staphylococcal protein A using diethylpyrocarbonate. (1982)

Human IgG subclasses 1, 2, and 4, as well as proteins of the IgG3 subclass that are allotype G3m (s+t+), bind avidly to staphylococcal protein A by means of their Fc portion. Proteins of the IgG3 subclass that are allotype G3m (s-t-) do not bind. The importance of a histidine residue at position 435 has been implicated from comparison of amino acid sequences of immunoglobulins that bind with those that do not bind to staphylococcal protein A, as well as from crystallographic data. Modification of histidines at a low concentration of diethylpyrocarbonate successfully and reversibly alters the binding of immunoglobulins to staphylococcal protein A with only minimal change in the antigenic properties. This method provides strong evidence for the critical importance of histidine in the binding of immunoglobulins to staphylococcal protein A.
Morphology Control of Cadmium Selenide Nanocrystals: Insights into the Roles of Di-n-octylphosphine Oxide (DOPO) and Di-n-octylphosphinic Acid (DOPA) (2012)

Di-n-octylphosphine oxide (DOPO) and di-n-octylphosphinic acid (DOPA), as two of impurities found in commercial tri-n-octylphosphine oxide (TOPO), generate significant differences in the outcomes of CdSe-nanocrystal (NC) syntheses. Using n-tetradecylphosphonic acid (TDPA) as the primary acid additive, quantum dots (QDs) are grown with DOPO added, whereas quantum rods (QRs) are grown in the presence of DOPA. While using oleic acid (OA) as the primary acid additive, QDs are generated and the QDs produced with DOPA exhibit larger sizes and size distributions than those produced with DOPO. (31)P NMR analyses of the reaction mixtures reveal that the majority of the DOPO has been converted into DOPA and di-n-octylphosphine (DOP) with DOP being removed via evacuation over the course of Cd-precursor preparation. The origin of the puzzling differences in the shape control of CdSe NCs in the presence of DOPO and DOPA is elucidated to be the small quantity of DOPO present, which liberates DOP during NC synthesis. In the presence of DOP, regardless of DOPA, the precursor-conversion kinetics and thus the nucleation kinetics are dramatically accelerated, generating a large number of nuclei by consuming a significant amount of CdSe nutrients, favoring QD growth. Similarly, QD growth is favored by the fast nucleation kinetics in the presence of OA, and the broader size distributions of QDs with DOPA are due to a second nucleation event initiated by the more stable Cd-di-n-octylphosphinate component. In contrast, a slow nucleation event results in the growth of QRs in the case of using DOPA and TDPA, where no DOPO or DOP is present. The results, thus, demonstrate the important role of precursor-conversion kinetics in the control of NC morphologies.
NOTES ON THE BREEDING BIOLOGY, HUNTING BEHAVIOR, AND ECOLOGY OF THE TAITA FALCON IN ZIMBABWE (1993)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
A full genome scan for late onset Alzheimer's disease (1999)

We have genotyped 292 affected sibling pairs (ASPs) with Alzheimer's disease (AD) according to NINCDS-ADRDA diagnostic criteria and with onset ages of >/=65 years using 237 microsatellite markers separated by an average distance of 16.3 cM. Data were analysed by SPLINK and MAPMAKER/SIBS on the whole sample of 292 ASPs and subsets of 162 ASPs where both members possessed an apolipoprotein E (APOE)straightepsilon4 allele and 63 pairs where neither possessed anstraightepsilon4 allele. Sixteen peaks with a multipoint lod score (MLS) >1 either in the whole sample, the straightepsilon4-positive or -negative subgroups were observed on chromosomes 1 (two peaks), 2, 5, 6, 9 (two peaks), 10 (two peaks), 12, 13, 14, 19, 21 and X (two peaks). Simulation studies revealed that these findings exceeded those expected by chance, although many are likely to be false positives. The highest lod scores on chromosomes 1 (MLS 2.67), 9 (MLS 2.38), 10 (MLS 2.27) and 19 (MLS 1.79) fulfilLander and Kruglyak's definition of 'suggestive' in that they would be expected to occur by chance once or less per genome scan. Several other peaks were only marginally less significant than this, in particular those on chromosomes 14 (MLS 2.16), 5 (MLS 2.00), 12, close to alpha2-macroglobulin (MLS 1.91), and 21, close to amyloid precursor protein (MLS 1.77). This is the largest genome scan to date in AD and shows for the first time that this is a genetically complex disorder involving several, perhaps many, genes in addition to APOE. Moreover, our data will be of interest to those hoping to identify positional candidate genes using information emerging from neurobiological studies of AD.
Evolutionary optimization of speed and accuracy of decoding on the ribosome (2011)

Speed and accuracy of protein synthesis are fundamental parameters for the fitness of living cells, the quality control of translation, and the evolution of ribosomes. The ribosome developed complex mechanisms that allow for a uniform recognition and selection of any cognate aminoacyl-tRNA (aa-tRNA) and discrimination against any near-cognate aa-tRNA, regardless of the nature or position of the mismatch. This review describes the principles of the selection-kinetic partitioning and induced fit-and discusses the relationship between speed and accuracy of decoding, with a focus on bacterial translation. The translational machinery apparently has evolved towards high speed of translation at the cost of fidelity.
Childhood Acute Lymphoblastic Leukemia: Is There a Tumor Suppressor Gene in Chromosome 12p 12.3 ? (1999)

Cytogenetic deletions on the short arm of chromosome 12 are common, recurring alterations found in a wide range of hematological neoplasias, including childhood acute lymphoblastic leukemia (ALL), the most frequent pediatric malignancy. This loss of genetic material suggests the presence of a tumor suppressor gene playing an important role in growth regulation or in the differentiation of hematopoietic stem cells. In order to substantiate this hypothesis and determine the chromosomal location of this putative gene, we and others have applied a deletion mapping strategy based on the detection of loss of heterozygosity (LOH) at specific genomic loci in leukemic cells. Hemizygous deletions at chromosome 12p12.3 were observed in childhood B cell precursor ALL, and proved to be one of the most frequent genetic alterations seen in this disease. The shortest region of overlapping deletions (SRO) was delimited by the markers D12S89 (distal) and D12S358 (proximal), separated by a genetic interval of approximately 3 cM. LOH in the same region in other hematological diseases, as well as in a variety of solid tumors, suggests either the presence of several tumor suppressor genes or the existence of a single gene with a wide range of activity. This genetic interval contains two known genes: TEL/ETV6, an ets-like transcription factor, and the cyclin-dependant kinase inhibitor, p27/kip1. Accumulating evidence suggests that an as yet unidentified tumor suppressor gene is closely linked to these two genes. Long-range restriction mapping of the SRO region allowed the construction of a approximately 750 kb physical map containing 4 known genes, 7 STSs, 3 chromosome 12 ESTs and 8 CpG islands. The construction of a 12p12.3 framework map is a crucial step towards the identification of candidate genes and should provide a valuable tool for the characterization of transcriptional units.
Demand Dispatch (2010)

In this article we touch on some background requirements for demand dispatch and how the Internet can be used for communication and control. In addition, we review some of the basics of the operation of the electric power grid. We show how loads that meet the communication and control requirements can be aggregated and dispatched-turned on or off-to help manage the grid. Aggregated loads will be able to perform many of the same ancillary services for the grid that are provided by power plants today. We describe some benefits of load-based ancillary services, such as the potential for very fast response, and explain how some characteristics of load-based services differ from power plants. Finally, we give a concrete example of demand dispatch as it can be applied to plug-in electric vehicles: smart charging.