gebhart/patrepeval huggingface dataset:
Evidence for a repressive function of the long polyglutamine tract in the human androgen receptor: possible pathogenetic relevance for the (CAG)n-expanded neuronopathies (1995)

We have reported that polyglutamine (polyGln)-expanded human androgen receptors (hAR) have reduced transactivational competence in transfected cells. We presumed that maximal hAR transactivation requires a normal-size polyGln tract. Here we report, however, that hAR transactivity and polyGln-tract length are related inversely: n = 0 > 12 > 20 > 40 > 50. Thus, a normal-size polyGln tract represses the transactivational competence of a polyGln-free hAR, and polyGln expansion increases that negative effect. This observation has pathogenetic implications for X-linked spinobular muscular atrophy (Kennedy syndrome), and possibly for the autosomal dominant central neuronopathies associated with (CAG)n expansion in the translated portion of four different genes.
Bio-inspired 'surprise' for real-time change detection in visual imagery (2011)

This paper describes a fast and robust bio-inspired method for change detection in high-resolution visual imagery. It is based on the computation of surprise, a dynamic analogue to visual saliency or attention, that uses very little processing beyond that of the initial computation of saliency. This is different from prior surprise algorithms, which employ complex statistical models to describe the scene and detect anomalies. This algorithm can detect changes in a busy scene (e.g., a person crawling in bushes or a vehicle moving in a desert) in real-time on typical video frame rates and can be used as a front-end to a larger system that includes object recognition and scene understanding modules that operate on the detected surprising regions.
High performance Hybrid and Monolithic Backside Thinned CMOS Imagers realized using a new integration process (2006)

Hybrid and monolithic thinned backside illuminated CMOS imagers operating at full depletion at low substrate voltages were developed. The combination of a 50 μm EPI layer with varying doping concentration and trenches to reduce crosstalk is unique. All thin wafer processing is performed on 200 mm wafers using a specially developed temporary carrier process. As a result, working imagers exhibiting high pixel yield, high quantum efficiency and low dark current are demonstrated.
Bacterial Cell Surface Display of an Enzyme Library for Selective Screening of Improved Cellulase Variants (2000)

The bacterial surface display method was used to selectively screen for improved variants of carboxymethyl cellulase (CMCase). A library of mutated CMCase genes generated by DNA shuffling was fused to the ice nucleation protein (Inp) gene so that the resulting fusion proteins would be displayed on the bacterial cell surface. Some cells displaying mutant proteins grew more rapidly on carboxymethyl cellulose plates than controls, forming heterogeneous colonies. In contrast, cells displaying the nonmutated parent CMCase formed uniform tiny colonies. These variations in growth rate were assumed to result from altered availability of glucose caused by differences in the activity of variant CMCases at the cell surface. Staining assays indicate that large, rapidly growing colonies have increased CMCase activity. Increased CMCase activity was confirmed by assaying the specific activities of cell extracts after the expression of unfused forms of the variant genes in the cytoplasm. The best-evolved CMCases showed about a 5- and 2.2-fold increase in activity in the fused and free forms, respectively. Sequencing of nine evolved CMCase variant genes showed that most amino acid substitutions occurred within the catalytic domain of the enzyme. These results demonstrate that the bacterial surface display of enzyme libraries provides a direct way to correlate evolved enzyme activity with cell growth rates. This technique will provide a useful technology platform for directed evolution and high-throughput screening of industrial enzymes, including hydrolases.
Tetronic®904-Containing Polymeric Micelles Overcome the Overexpression of ABCG2 in the Blood–Brain Barrier of Rats and Boost the Penetration of the Antiretroviral Efavirenz into the CNS (2015)

Tetronic 904-containing polymeric micelles overcame the overexpression of ABCG2 in the BBB caused by chronic administration of EFV then boosting its penetration into the CNS.
Changes in the Epidemiology of Methicillin-Resistant Staphylococcus aureus in Intensive Care Units in US Hospitals, 1992-2003 (2006)

The proportion of Staphylococcus aureus isolates that were methicillin resistant (MRSA) increased from 35.9% in 1992 to 64.4% in 2003 for hospitals in the National Nosocomial Infections Surveillance system. During the same period, there was a decrease in resistance rates for several non- beta -lactam drugs among the MRSA isolates.
Surface Plasmon Resonance and Surface Plasmon Field-Enhanced Fluorescence Spectroscopy for Sensitive Detection of Tumor Markers (2009)

Surface plasmon resonance (SPR), which provides real-time, in situ analysis of dynamic surface events, is a valuable tool for studying interactions between biomolecules. In the clinical diagnosis of tumor markers in human blood, SPR is applied to detect the formation of a sandwich-type immune complex composed of a primary antibody immobilized on a sensor surface, the tumor marker, and a secondary antibody. However, the SPR signal is quite low due to the minute amounts (ng-pg/mL) of most tumor markers in blood. We have shown that the SPR signal can be amplified by applying an antibody against the secondary antibody or streptavidin-conjugated nanobeads that specifically accumulate on the secondary antibody. Another method employed for highly sensitive detection is the surface plasmon field-enhanced fluorescence spectroscopy-based immunoassay, which utilizes the enhanced electric field intensity at a metal/water interface to excite a fluorophore. Fluorescence intensity attributed to binding of a fluorophore-labeled secondary antibody is increased due to the enhanced field in the SPR condition and can be monitored in real time.
Mechanisms of Ischemic Preconditioning in Rat Hearts (1995)

Ischemic preconditioning in isolated, perfused rat hearts is caused by stimulation of alpha 1B-adrenoceptors by endogenous catecholamines through the activation of protein kinase C via a PTX-sensitive G protein. The PTX-sensitive inhibitory protein Gi, which can be activated by adenosine, muscarinic agonists, and alpha 1-adrenoceptor agonists, may play a central role in ischemic preconditioning mediated by protein kinase C across a broad range of species.
Enzymatic Formation of Isochamigrene, a Novel Sesquiterpene, by Alteration of the Aspartate-Rich Region of Trichodiene Synthase J. Am. Chem. Soc. 1996, 118, 8499−8500 (1997)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTEnzymatic Formation of Isochamigrene, a Novel Sesquiterpene, by Alteration of the Aspartate-Rich Region of Trichodiene Synthase J. Am. Chem. Soc.1996, 118, 8499−8500David E. Cane, Qun Xue, James E. Van Epp, and Youla S. TsantrizosCite this: J. Am. Chem. Soc. 1997, 119, 33, 7905Publication Date (Web):August 20, 1997Publication History Published online20 August 1997Published inissue 1 August 1997https://pubs.acs.org/doi/10.1021/ja975410ahttps://doi.org/10.1021/ja975410acorrectionACS PublicationsCopyright © 1997 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views325Altmetric-Citations1LEARN 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 PDF (66 KB) Get e-Alertsclose Get e-Alerts
Spreading Chromatin into Chemical Biology (2011)

Epigenetics, broadly defined as the inheritance of non-Mendelian phenotypic traits, can be more narrowly defined as heritable alterations in states of gene expression ("on" versus "off") that are not linked to changes in DNA sequence. Moreover, these alterations can persist in the absence of the signals that initiate them, thus suggesting some kind of "memory" to epigenetic forms of regulation. How, for example, during early female mammalian development, is one X chromosome selected to be kept in an active state, while the genetically identical sister X chromosome is "marked" to be inactive, even though they reside in the same nucleus, exposed to the same collection of shared trans-factors? Once X inactivation occurs, how are these contrasting chromatin states maintained and inherited faithfully through subsequent cell divisions? Chromatin states, whether active (euchromatic) or silent (heterochromatic) are established, maintained, and propagated with remarkable precision during normal development and differentiation. However, mistakes made in establishing and maintaining these chromatin states, often executed by a variety of chromatin-remodeling activities, can lead to mis-expression or mis-silencing of critical downstream gene targets with far-reaching implications for human biology and disease, notably cancer. Though chromatin biologists have identified many of the "inputs" that are important for controlling chromatin states, the detailed mechanisms by which these processes work remain largely opaque, in part due to the staggering complexity of the chromatin polymer, the physiologically relevant form of our genome. The primary objective of this article is to serve as a "call to arms" for chemists to contribute to the development of the precision tools needed to answer pressing molecular problems in this rapidly moving field.
Dynamics of Inter-heavy Chain Interactions in Human Immunoglobulin G (IgG) Subclasses Studied by Kinetic Fab Arm Exchange (2014)

Interdomain interactions between the CH3 domains of antibody heavy chains are the first step in antibody assembly and are of prime importance for maintaining the native structure of IgG. For human IgG4 it was shown that CH3-CH3 interactions are weak, resulting in the potential for half-molecule exchange ("Fab arm exchange"). Here we systematically investigated non-covalent interchain interactions for CH3 domains in the other human subclasses, including polymorphisms (allotypes), using real-time monitoring of Fab arm exchange with a FRET-based kinetic assay. We identified structural variation between human IgG subclasses and allotypes at three amino acid positions (Lys/Asn-392, Val/Met-397, Lys/Arg-409) to alter the strength of inter-domain interactions by >6 orders of magnitude. Each substitution affected the interactions independent from the other substitutions in terms of affinity, but the enthalpic and entropic contributions were non-additive, suggesting a complex interplay. Allotypic variation in IgG3 resulted in widely different CH3 interaction strengths that were even weaker for IgG3 than for IgG4 in the case of allotype G3m(c3c5*/6,24*), whereas G3m(s*/15*) was equally stable to IgG1. These interactions are sufficiently strong to maintain the structural integrity of IgG1 during its normal life span; for IgG2 and IgG3 the inter-heavy chain disulfide bonds are essential to prevent half-molecule dissociation, whereas the labile hinge disulfide bonds favor half-molecule exchange in vivo for IgG4.
Probing the Mechanical Stability of DNA in the Presence of Monovalent Cations (2008)

We examine the interaction between monovalent cations and DNA using several different assays that measure the stability of double-stranded DNA (dsDNA). The thermal melting of dsDNA and the mechanical separation of dsDNA into two single strands both depend on the stability of dsDNA with respect to ssDNA and are sensitive to the interstrand phosphate repulsion. We find that the experimentally measured melting temperatures and unzipping forces are approximately the same for all of the ions considered in this study. Likewise, the force required to transform B-DNA into the overstretched form is also similar for all of the ions. In contrast, for a given ion concentration, the force at which the overstretched state fully relaxes back to the canonical B-DNA form depends on the cation; however, for all cations, the overstretching force decreases with decreasing ion concentration, suggesting that this force is sensitive to screening. We observe a general trend for smaller ions to produce more efficient relaxation. Finally, for a given cation, the relaxation can also depend on the anion.
New attachment – reattachment following reconstructive periodontal surgery (1985)

The present study was designed to evaluate if the conditions for reformation of a connective tissue attachment are less favorable on root surfaces which have lost their fibrous attachment because of periodontal disease than on root surfaces surgically deprived of their attachment apparatus. In each of 4 Green monkeys, 2 maxillary and 2 mandibular teeth were selected for experimentation. Periodontal breakdown was produced and allowed to progress to the mid-root level around one of the experimental teeth in both the maxilla and mandible by placing elastic ligatures around the neck of these teeth. 3 months after removal of the ligatures, the crown of the teeth was resected and the epithelium and the subjacent granulation tissue were removed. Using a diamond bur, circumferential defects similar to those obtained by the ligature induced destruction were then produced around the remaining 2 experimental teeth following resection of the crown. The root cementum on both groups of teeth was removed to the level of the reduced bone height. Finally, all roots were submerged to complete coverage by a mucosal flap. After 3 months of healing, the animals were sacrificed and the jaws removed and placed in fixative. After decalcification, histological sections of the experimental roots and their surrounding periodontal tissues were produced. No histological differences in the result of healing were discernible between the specimens of previously periodontitis-affected roots and roots with surgically created defects. New cementum with inserting collagen fibers had formed in the apical part of the instrumented surface in both groups of teeth.(ABSTRACT TRUNCATED AT 250 WORDS)
Hidden Markov model multiarm bandits: a methodology for beam scheduling in multitarget tracking (2001)

We derive optimal and suboptimal beam scheduling algorithms for electronically scanned array tracking systems. We formulate the scheduling problem as a multiarm bandit problem involving hidden Markov models (HMMs). A finite-dimensional optimal solution to this multiarm bandit problem is presented. The key to solving any multiarm bandit problem is to compute the Gittins (1989) index. We present a finite-dimensional algorithm that computes the Gittins index. Suboptimal algorithms for computing the Gittins index are also presented. Numerical examples are presented to illustrate the algorithms.
Measurement of Resistant Starch by Enzymatic Digestion in Starch and Selected Plant Materials: Collaborative Study (2002)

Interlaboratory performance statistics was determined for a method developed to measure the resistant starch (RS) content of selected plant food products and a range of commercial starch samples. Food materials examined contained RS (cooked kidney beans, green banana, and corn flakes) and commercial starches, most of which naturally contain, or were processed to yield, elevated RS levels. The method evaluated was optimized to yield RS values in agreement with those reported for in vivo studies. Thirty-seven laboratories tested 8 pairs of blind duplicate starch or plant material samples with RS values between 0.6 (regular maize starch) and 64% (fresh weight basis). For matrixes excluding regular maize starch, repeatability relative standard deviation (RSDr) values ranged from 1.97 to 4.2%, and reproducibility relative standard deviation (RSDR) values ranged from 4.58 to 10.9%. The range of applicability of the test is 2-64% RS. The method is not suitable for products with <1% RS (e.g., regular maize starch; 0.6% RS). For such products, RSDr and RSDR values are unacceptably high.
Enhancement of Ischemia-Induced Angiogenesis by eNOS Overexpression (2003)

It remains undetermined whether continuous endothelial nitric oxide (NO) overexpression exerts angiogenic action. We surgically induced hindlimb ischemia in transgenic mice overexpressing endothelial NO synthase in the endothelium (eNOS-Tg) and studied neocapillary formation, ischemia-induced vascular endothelial growth factor (VEGF) expression, cGMP accumulation, and Akt/PKB signaling. Laser Doppler imaging revealed a markedly increased recovery of blood perfusion in ischemic limbs of eNOS-Tg mice (44% increase) compared with that in wild-type mice. Angiography showed a marked increase in basal and ischemia-induced collateral vessel formation in eNOS-Tg mice. Basal capillary densities and tissue cGMP levels were increased in eNOS-Tg mice (1.8-fold and 1.6-fold versus wild-type mice, respectively). Ischemia-induced neocapillary formation and cGMP accumulation were markedly increased in eNOS-Tg mice (3.6-fold and 4.1-fold versus preischemia levels, respectively), whereas those in wild-type mice were much less (1.8-fold and 1.5-fold, respectively). Basal and time-dependent VEGF expression in ischemic muscles did not differ between eNOS-Tg and wild-type mice. Basal and VEGF-mediated Akt phosphorylation in aortas was similar between eNOS-Tg and wild-type mice. Aortic basal eNOS expression was increased 3.3-fold, and VEGF-mediated eNOS phosphorylation was markedly induced in aortas of eNOS-Tg compared with preischemia levels (4.2-fold), whereas much smaller changes were observed in wild-type mice (1.8-fold increase). Our study demonstrates that overexpression of eNOS protein causes a marked increase in neocapillary formation in response to tissue ischemia without affecting ischemia-induced VEGF expression or VEGF-mediated Akt phosphorylation.
Chemical modifications of heparin that diminish its anticoagulant but preserve its heparanase-inhibitory, angiostatic, anti-tumor and anti-metastatic properties (1996)

Structural features of heparin potentially important for heparanase-inhibitory activity were examined by measuring the ability of heparin derivatives to affect the degradation of [3H]acetylated heparan sulphate by tumor cell heparanases. IC50 values were determined using an assay which distinguished degraded from undegraded substrate by precipitation of the latter with cetylpyridinium chloride (CPC). Removal of heparin's 2-O-sulphate and 3-O-sulphate groups enhanced heparanase-inhibitory activity (50%). Removal of its carboxyl groups slightly lowered the activity (18%), while combining the treatments abolished the activity. At least one negative charge on the iduronic acid/idose moiety, therefore, is necessary for heparanase-inhibitory activity. Replacing heparin's N-sulphate groups with N-acetyl groups reduced its activity (37%). Comparing this heparin derivative with 2,3-O-desulphated heparin, the placement of sulphate groups appears important for activity since the two structures have similar nominal linear charge density. In addition, unsubstituted uronic acids are nonessential for inhibition since their modification (periodate-oxidation/borohydride-reduction) enhanced rather than reduced heparanase-inhibitory activity. The most effective heparanase inhibitors (2,3-O-desulphated heparin, and [periodate-oxidized, borohydride-reduced] heparin) were tested in the chick chorioallantoic membrane (CAM) bioassay for anti-angiogenic activity and found to be at least as efficacious as heparin. 2,3-O-desulphated heparin also significantly decreased the tumor growth of a subcutaneous human pancreatic (Ca-Pan-2) adenocarcinoma in nude mice and prolonged the survival times of C57BL/6N mice in a B16-F10 melanoma experimental lung metastasis assay.
A panel of nine cerebrospinal fluid biomarkers may identify patients with atypical parkinsonian syndromes (2015)

A panel of nine CSF biomarkers was able to differentiate APS from patients with PD and dementia. This may have important clinical utility in improving diagnostic accuracy, allowing better prognostication and earlier access to potential disease-modifying therapies.
Comparison of Methods for Photochemical Phosphoramidite-Based DNA Synthesis (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparison of Methods for Photochemical Phosphoramidite-Based DNA SynthesisMichael C. Pirrung and Jean-Claude BradleyCite this: J. Org. Chem. 1995, 60, 20, 6270–6276Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/jo00125a010https://doi.org/10.1021/jo00125a010research-articleACS PublicationsRequest reuse permissionsArticle Views586Altmetric-Citations48LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts