gebhart/patrepeval huggingface dataset:
Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response (2020)

Numerous monoclonal antibodies have been developed successfully for the treatment of various diseases. Nevertheless, the development of biotherapeutic antibodies is complex, expensive, and time-consuming, and to facilitate this process, careful structural analysis beyond the antibody binding site is required to develop a more efficacious antibody. In this work, we focused on protein antigens, since they induce the largest antibody changes, and provide interesting cases to compare and contrast. The structures of 15 anti-protein antibodies were analysed to compare the antigen-bound/unbound forms. Surprisingly, three different classes of binding-induced changes were identified. In class (B1), the antigen binding fragment distorted significantly, and we found changes in the loop region of the heavy chain's constant domain; this corresponds well with expected allosteric movements. In class (B2), we found changes in the same loop region without the overall distortion. In class (B3), these changes did not present, and only local changes at the complementarity determining regions were found. Consequently, structural analysis of antibodies is crucial for therapeutic development. Careful evaluation of allosteric movements must be undertaken to develop better effector responses, especially during the transformation of these antibodies from small fragments at the discovery stage to full antibodies at the subsequent development stages.
Drug Development and FDA Approval, 1938–2013 (2014)

This interactive graphic shows major legislative and regulatory events related to approval of new drugs by the Food and Drug Administration (FDA), drug approvals by year and by therapeutic category, and trends in the use of the FDA's various programs for expedited approval.
Detection of mercury in air by time-resolved laser-induced breakdown spectroscopy technique (1994)

For several years the laser-induced breakdown spectroscopy (LIBS) technique has been applied successfully to the problem of detecting small traces of pollutants in gases. The possible application of this method for the individuation of mercury in air is discussed. The laboratory prototype of the detection system is described in detail, and the sensitivity of the system for the diagnostics of small traces of mercury is determined. The reduced dimensions of the experimental apparatus and its relatively low cost make the LIBS method competitive with other laser-based methods for in situ analysis.
In Vitro Assembly of Human H/ACA Small Nucleolar RNPs Reveals Unique Features of U17 and Telomerase RNAs (2000)

The H/ACA small nucleolar RNAs (snoRNAs) are involved in pseudouridylation of pre-rRNAs. They usually fold into a two-domain hairpin-hinge-hairpin-tail structure, with the conserved motifs H and ACA located in the hinge and tail, respectively. Synthetic RNA transcripts and extracts from HeLa cells were used to reconstitute human U17 and other H/ACA ribonucleoproteins (RNPs) in vitro. Competition and UV cross-linking experiments showed that proteins of about 60, 29, 23, and 14 kDa interact specifically with U17 RNA. Except for U17, RNPs could be reconstituted only with full-length H/ACA snoRNAs. For U17, the 3'-terminal stem-loop followed by box ACA (U17/3'st) was sufficient to form an RNP, and U17/3'st could compete other full-length H/ACA snoRNAs for assembly. The H/ACA-like domain that constitutes the 3' moiety of human telomerase RNA (hTR), and its 3'-terminal stem-loop (hTR/3'st), also could form an RNP by binding H/ACA proteins. Hence, the 3'-terminal stem-loops of U17 and hTR have some specific features that distinguish them from other H/ACA RNAs. Antibodies that specifically recognize the human GAR1 (hGAR1) protein could immunoprecipitate H/ACA snoRNAs and hTR from HeLa cell extracts, which demonstrates that hGAR1 is a component of H/ACA snoRNPs and telomerase in vivo. Moreover, we show that in vitro-reconstituted RNPs contain hGAR1 and that binding of hGAR1 does not appear to be a prerequisite for the assembly of the other H/ACA proteins.
Verification of a closed-loop shaped-input controller for a five-bar-linkage manipulator (2002)

A closed-loop control strategy is verified experimentally for a five-bar-linkage manipulator with one flexible link. The prototype, a highly nonlinear system, is a prominent candidate of a class of manipulators with one flexible link. The controller combines a closed-loop shaped-input filter with conventional control techniques. Experimental results show that this technique is effective and robust enough to reduce vibrations, even for the nonlinear system. The implementation methodology and the experimental results are discussed with future research issues.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Achieving Both High Selectivity and Current Density for CO <sub>2</sub> Reduction to Formate on Nanoporous Tin Foam Electrocatalysts (2016)

Abstract Currently, low catalytic activity, selectivity and stability are the biggest challenges which restrict the large scale applications of CO 2 electrochemical reduction. Formic acid, one of the highest value‐added products from electrochemical reduction of CO 2 , has gathered much interest. Here, we develop nanoporous tin foam catalysts which exhibit significantly high selectivity and faster production rate to formate. In a 0.1 M NaHCO 3 solution, the maximum Faradaic efficiency for formate production can reach above 90 % with a current density over 23 mA cm −2 , which are among the highest reported to date under ambient conditions. The improved production rate can be attributed to the high surface area and porous structure. Moreover, the electrocatalysts are quite stable, namely, the Faradaic efficiency remains unchanged during 16 hour electrolysis.
Points-to analysis using BDDs (2003)

This paper reports on a new approach to solving a subset-based points-to analysis for Java using Binary Decision Diagrams (BDDs). In the model checking community, BDDs have been shown very effective for representing large sets and solving very large verification problems. Our work shows that BDDs can also be very effective for developing a points-to analysis that is simple to implement and that scales well, in both space and time, to large programs.The paper first introduces BDDs and operations on BDDs using some simple points-to examples. Then, a complete subset-based points-to algorithm is presented, expressed completely using BDDs and BDD operations. This algorithm is then refined by finding appropriate variable orderings and by making the algorithm propagate sets incrementally, in order to arrive at a very efficient algorithm. Experimental results are given to justify the choice of variable ordering, to demonstrate the improvement due to incrementalization, and to compare the performance of the BDD-based solver to an efficient hand-coded graph-based solver. Finally, based on the results of the BDD-based solver, a variety of BDD-based queries are presented, including the points-to query.
Immunoperoxidase Staining for Estrogen and Progesterone Receptors in Archival Formalin Fixed, Paraffin Embedded Breast Carcinomas after Microwave Antigen Retrieval (1997)

Immunoperoxidase staining was performed for estrogen and progesterone receptors in 93 cases of primary breast carcinoma. Breast tumor samples were fixed in formalin and embedded in paraffin. Antigen retrieval was performed by microwave heating in citrate buffer, pH 6.0, using precisely defined and reproducible conditions. The cases studied included material from the current year and from paraffin blocks retrieved from archival storage dating back to 1981. In all cases, estrogen and progesterone receptor values determined by biochemical assay were available for comparison with the immunohistochemical results. We found 94% agreement of results between the two methods.
How Much SSD Is Useful for Resilience in Supercomputers (2015)

We consider the use of non-volatile memories in the form of burst buffers for resilience in supercomputers. Their cost and limited lifetime demand effective use and appropriate provisioning. We develop an analytic model for the behavior of workloads on systems with burst buffers, and use it to explore questions of cost-effective provisioning, and mission-directed allocation of burst-buffer (SSD) lifetime.
Essays on product returns: The impact of customer product return behavior on profitability (2008)

The firm-customer exchange process consists of three parts: (1) firm-initiated marketing communications, (2) customer buying behavior and (3) customer product return behavior. Much of the research in marketing has focused on the relationship between firm-initiated marketing communications and customer buying behavior. The relationship between customer product return behavior and the other two parts of the firm-customer exchange process have been vastly ignored. As a result, it is unclear how customer product return behavior impacts the firm-customer exchange process. This is due to a lack of data availability and a lack of understanding of the role customer product return behavior plays in the firm-customer exchange process. ^ Thus, in this thesis we help to explain this relationship with two different studies. In the first study of this thesis, we present a descriptive study that empirically demonstrates the role of customer product return behavior in the firm-customer exchange process. Then in the second study of this thesis, we present an empirical application that leverages the knowledge about the role of customer product return behavior in the first study. We do this by integrating customer product return behavior into a customer value framework to help measure and maximize customer lifetime value. ^
SOME PHYSICAL CONSTANTS OF MONACETIN, MONOPROPIN AND MONO-NORMAL-BUTYRIN<sup>1</sup> (1930)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSOME PHYSICAL CONSTANTS OF MONACETIN, MONOPROPIN AND MONO-NORMAL-BUTYRIN1H. A. Schuette and John T. HaleCite this: J. Am. Chem. Soc. 1930, 52, 5, 1978–1981Publication Date (Print):May 1, 1930Publication History Published online1 May 2002Published inissue 1 May 1930https://pubs.acs.org/doi/10.1021/ja01368a033https://doi.org/10.1021/ja01368a033research-articleACS PublicationsRequest reuse permissionsArticle Views67Altmetric-Citations14LEARN 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
Cooperative molecular and cellular networks regulate Toll‐like receptor‐dependent inflammatory responses (2006)

Viral and bacterial pathogens cause inflammation via Toll-like receptor (TLR) signaling. We have shown that effective responses to LPS may depend on cooperative interactions between TLR-expressing leukocytes and TLR-negative tissue cells. The aim of this work was to determine the roles of such networks in response to agonists of TLRs associated with antiviral and autoimmune responses. The TLR3 agonist poly(I:C) activated epithelial cells, primary endothelial cells, and two types of primary human smooth muscle cells (airway [ASMC] and vascular) directly, while the TLR7/8 agonist R848 required the presence of leukocytes to activate ASMC. In keeping with these data, ASMC expressed TLR3 but not TLR7 or TLR8. Activation of ASMC by poly(I:C) induced a specific cytokine repertoire characterized by induction of CXCL10 generation and the potential to recruit mast cells. We subsequently explored the ability of TLR agonists to cooperate in the induction of inflammation. Dual stimulation with LPS and poly(I:C) caused enhanced cytokine generation from epithelial and smooth muscle cells when in the presence of leukocytes. Thus, inflammatory responses to pathogens are regulated by networks in which patterns of TLR expression and colocalization of tissue cells and leukocytes are critical.
End-to-end learning of semantic role labeling using recurrent neural networks (2015)

Jie Zhou, Wei Xu. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
Hypoperfusion and Ischemia in Cerebral Amyloid Angiopathy Documented by <sup>99m</sup>Tc-ECD Brain Perfusion SPECT (2009)

Patients with probable CAA had significantly decreased cerebral perfusion and may be at risk for leukoencephalopathy, atrophy, and ischemia.
Effect of Aqueous Ozone on the NF-κB System (2007)

Ozone has been proposed as an alternative oral antiseptic in dentistry, due to its antimicrobial power reported for gaseous and aqueous forms, the latter showing a high biocompatibility with mammalian cells. New therapeutic strategies for the treatment of periodontal disease and apical periodontitis should consider not only antibacterial effects, but also their influence on the host immune response. Therefore, our aim was to investigate the effect of aqueous ozone on the NF-kappaB system, a paradigm for inflammation-associated signaling/transcription. We showed that NF-kappaB activity in oral cells stimulated with TNF, and in periodontal ligament tissue from root surfaces of periodontally damaged teeth, was inhibited following incubation with ozonized medium. Under this treatment, IkappaBalpha proteolysis, cytokine expression, and kappaB-dependent transcription were prevented. Specific ozonized amino acids were shown to represent major inhibitory components of ozonized medium. In summary, our study establishes a condition under which aqueous ozone exerts inhibitory effects on the NF-kappaB system, suggesting that it has an anti-inflammatory capacity.
Non‐prevocalic /r/ in New Zealand Hip Hop (2005)

This paper investigates pronunciation in New Zealand hip hop, specifically the occurrence and distribution of non-prevocalic /r/. It shows that three popular hip hop artists realise /r/ after, and only after, the NURSE vowel. The study aims to stimulate interest in the variety of English that is used by rap artists in New Zealand, and suggests that New Zealand hip hop may exhibit a unique distribution of features combining local speech variants with features of pronunciation borrowed from international rap artists.
Blade-loading effects on the propagation of unsteady flow and on forcing functions in axial-turbine cascades (1992)

This article investigates the effect of tangential blade loading on the propagation of time-dependent pressure disturbance due to potential-flow interaction ans viscous-wake interaction from upstream blade rows in axial-turbine-blade rotor cascades. Results are obtained by modeling the effects of the stator viscous wake and tha stator-rotor potential-flow field on the rotor flow field. A computer program is used to calculate the unsteady flows in the rotor passages. The amplitudes for the two types of interaction are based on a review of available experimental and computational data. We study the propagation of the isolated potential-flow interaction (no viscous-wake interaction), of the isolated viscous wake interaction (no potential-flow interaction), and of the combination of interactions. We examine the propagation of both interactions in three frotor cascades of high, medium and low tangential-loading coefficient (1.2, 1.0 and 0.8 respectively) for typical values of reduced frequency. The discussion uses as example a stator-to-rotor-pitch ration R = 2. We investigate the differences when the stator-to-rotor pitch ratio is decreased (to R = 1) and increased (to R = 4). We offer new explanations of the mechanisms of generation of unsteady forces on the blades and study the effects of tangential blade and of axial gap between blade rows on th time-dependent forces acting on the blades. The potential-flow field of the rotor-leading-edge region cuts the potential-flow field of the upstream stator, and distorts and cuts the wake centerlines. The potential-flow field cut into the rotor passage propagates downstream as a potential-flow disturbance superimposed on the rotor flow field. The direction and decay rate of this interaction are determined respectively by the stator-outlet flow angle and by the stator-cascade pitch. The cut wake is sheared into the rotor passage and it results in a region of increased unsteady pressure upstream of the wake centerline and a region of decreased unsteady pressure downstream of the wake centerline. The wake shearing is more pronounced in highly-loaded cascades, and for lower stator outlet-flow angles. The potential flow interaction dominates the unsteadiness for high values of R and the wake interaction dominates the unsteadiness for low values of R. The above explanations can be used to determine locations unsteady-pressure regions, and the shape of the unsteady forcing functions.
DDoS Detection Algorithm Based on Preprocessing Network Traffic Predicted Method and Chaos Theory (2013)

Distributed denial-of-service (DDoS) flooding attacks still pose great threats to the Internet even though various approaches and systems have been proposed. In this paper, we firstly pre-process network traffic by cumulatively averaging it with a time range, and using the simple linear AR model, and then generate the prediction of network traffic. Secondly, assuming the prediction error behaves eechaoticallyee, we use chaos theory to analyze it and then propose a novel network anomaly detection algorithm (NADA) to detect the abnormal traffic. With this abnormal traffic, we lastly train a neural network to detect DDoS attacks. Our preliminary experiments and analyses indicate that our proposed DDoS detection algorithm can accurately and effectively detect DDoS attacks.
Asynchronous integrated optical multiply accumulate with sideways summer (1986)

An asynchronous method of implementing the digital multiplication by analog convolution algorithm is presented. The mixed binary output is formed in one switching time regardless of the number of bits in the word. Novel circuitry that logarithmically reduces the number of shift and add levels is shown.
A fourth-order algorithm for blind characterization of OFDM signals (2008)

In the framework of cognitive radio, electro-magnetic environment sensing is a crucial task. In order to distinguish various systems relying on OFDM modulations from each others (such as WiMAX, WiFi, DVB-T), we need to be able to estimate precisely the inter-carrier spacing used in the transmitted signal. When the ratio between cyclic prefix and OFDM symbol duration is small or when the multipath propagation channel is almost as large as the cyclic prefix, standard approaches based on detection of cyclic prefix via an autocorrelation fall down. Therefore we propose a new algorithm to estimate the parameters of an OFDM modulated signal (especially the inter-carrier spacing) relying on the fourth order statistics of the received signal. We theoretically prove its robustness to multipath channels, time offset and frequency offset. Then its performance is analysed through numerical simulations and compared to standard approach which confirms the accuracy of the new algorithm.
The Psychopharmacology of European Herbs with Cognition-Enhancing Properties (2006)

Extensive research suggests that a number of plant-derived chemicals and traditional Oriental herbal remedies possess cognition-enhancing properties. Widely used current treatments for dementia include extracts of Ginkgo biloba and several alkaloidal, and therefore toxic, plant-derived cholinergic agents. Several non-toxic, European herbal species have pan-cultural traditions as treatments for cognitive deficits, including those associated with ageing. To date they have not received research interest commensurate with their potential utility. Particularly promising candidate species include sage (Salvia lavandulaefolia/officinalis), Lemon balm (Melissa officinalis) and rosemary (Rosmarinus officinalis). In the case of sage, extracts possess anti-oxidant, estrogenic, and anti-inflammatory properties, and specifically inhibit butyryl- and acetyl-cholinesterase. Acute administration has also been found to reliably improve mnemonic performance in healthy young and elderly cohorts, whilst a chronic regime has been shown to attenuate cognitive declines in sufferers from Alzheimer's disease. In the case of Melissa officinalis, extracts have, most notably, been shown to bind directly to both nicotinic and muscarinic receptors in human brain tissue. This property has been shown to vary with extraction method and strain. Robust anxiolytic effects have also been demonstrated following acute administration to healthy humans, with mnemonic enhancement restricted to an extract with high cholinergic binding properties. Chronic regimes of aromatherapy and essential oil respectively have also been shown to reduce agitation and attenuate cognitive declines in sufferers from dementia. Given the side effect profile of prescribed cholinesterase inhibitors, and a current lack of a well tolerated nicotinic receptor agonist, these herbal treatments may well provide effective and well-tolerated treatments for dementia, either alone, in combination, or as an adjunct to conventional treatments.
Stress-tunable microwave composites and sensing media (2004)

A remarkably strong dependence of magnetoimpedance (MI) on tensile stress has been observed in the microwave frequency range for thin CoMnSiB glass-coated microwires exposed to a special thermal treatment. The MI ratio runs into more than 100% at 0.5-1.5 GHz when the tensile stress of 600 MPa is applied to the wire. It was demonstrated that a large MI change at such high frequencies is related predominantly with the dc magnetization orientation. A host of such microwires incorporated into a dielectric matrix may constitute a new sensing medium that is characterized by the stress-dependent effective permittivity. Such medium can be used for the microwave visualization of the stress distribution inside of a composite structure or on its surface.