gebhart/patrepeval huggingface dataset:
The Role of ATP Binding and Hydrolysis by UvrB during Nucleotide Excision Repair (2000)

We have isolated UvrB-DNA complexes by capture of biotinylated damaged DNA substrates on streptavidin-coated magnetic beads. With this method the UvrB-DNA preincision complex remains stable even in the absence of ATP. For the binding of UvrC to the UvrB-DNA complex no cofactor is needed. The subsequent induction of 3' incision does require ATP binding by UvrB but not hydrolysis. This ATP binding induces a conformational change in the DNA, resulting in the appearance of the DNase I-hypersensitive site at the 5' side of the damage. In contrast, the 5' incision is not dependent on ATP binding because it occurs with the same efficiency with ADP. We show with competition experiments that both incision reactions are induced by the binding of the same UvrC molecule. A DNA substrate containing damage close to the 5' end of the damaged strand is specifically bound by UvrB in the absence of UvrA and ATP (Moolenaar, G. F., Monaco, V., van der Marel, G. A., van Boom, J. H., Visse, R., and Goosen, N. (2000) J. Biol. Chem. 275, 8038-8043). To initiate the formation of an active UvrBC-DNA incision complex, however, UvrB first needs to hydrolyze ATP, and subsequently a new ATP molecule must be bound. Implications of these findings for the mechanism of the UvrA-mediated formation of the UvrB-DNA preincision complex will be discussed.
SSR-What to do when the Interest is Gone (1983)

Recently, teachers have expressed concern because, despite the adherence to the established rules of SSR, the interest in silent reading has begun to diminish after several months.
Potential Prophylactic and Therapeutic Vaccines for HSV Infections (2007)

The human herpesviruses herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) can cause severe recurrent disease in humans and establish lifelong infection in their hosts. Several antiviral therapies are available to control disease and spread, but these are not completely effective and do not affect latent virus. The need for vaccines for HSV is urgent, both for controlling initial infection and spread of disease as well as to limit recurrences. Several approaches including subunit vaccines, peptide vaccines, live virus vectors and DNA vaccine technology have been used in developing both prophylactic and therapeutic vaccines for HSV and these are reviewed here.
Fresco: a Web services based framework for configuring extensible SLA management systems (2005)

A service level agreement (SLA) is a service contract that includes the evaluation criteria for agreed service quality standards. Since agreeable specifications on the evaluation criteria cannot be limited in practice, competitive SLA management products must be extensible in terms of their support for contract-specific SLA compliance evaluations. While the need of running and managing those software products as services increases, we have found that developing a good solution for configuring them as per contractual terms is a challenging task. This paper presents the Fresco framework, which facilitates configuring extensible SLA management systems using Web services. An XML-based specification of SLA management related data called SCOL will also be presented to show how the framework supports contract-specific SLA terms and contract-specific extensions of the deployed SLA management software. The paper furthermore shows how the Fresco system uses a template-based approach to communicate with other Web services applications with support for various input and output formats. Our experience with implementing the Fresco framework for a leading commercial SLA management software product demonstrates that the framework facilitates the creation of effective and efficient solutions for configuring extensible SLA management systems.
On the Convergence of Pattern Search Algorithms (1997)

We introduce an abstract definition of pattern search methods for solving nonlinear unconstrained optimization problems. Our definition unifies an important collection of optimization methods that neither compute nor explicitly approximate derivatives. We exploit our characterization of pattern search methods to establish a global convergence theory that does not enforce a notion of sufficient decrease. Our analysis is possible because the iterates of a pattern search method lie on a scaled, translated integer lattice. This allows us to relax the classical requirements on the acceptance of the step, at the expense of stronger conditions on the form of the step, and still guarantee global convergence.
Load Balancing in a Cluster Computer (2006)

This paper proposes a load balancing algorithm for distributed use of a cluster computer. It uses load information including CPU queue length, CPU utilisation, memory utilisation and network traffic to decide the load of each node. This algorithm is compared to an algorithm using only the CPU queue length. The performance evaluation results show that the proposed algorithm performs well
Teratogenicity of sodium valproate (2005)

The teratogenicity of the widely popular antiepileptic drug (AED) and mood stabiliser sodium valproate (also known as valproate, VPA) has been evidenced by previous research; however, these findings have often been limited by a small population sample of exposed women and a retrospective study design. Many factors contribute to the teratogenicity of VPA. These include the number of drugs that are co-administered, drug dosage, differences in maternal and/or infant metabolism, the gestational age of the fetus at exposure, and hereditary susceptibility. VPA has been associated with a variety of major and minor malformations, including a 20-fold increase in neural tube defects, cleft lip and palate, cardiovascular abnormalities, genitourinary defects, developmental delay, endocrinological disorders, limb defects, and autism. It has been suggested that polytherapy treatment in epileptic pregnant women increases the risk of teratogenicity in offspring. Furthermore, there is an established relationship between VPA dose and adverse outcome. Large single doses of VPA potentially cause high peak levels in the fetal serum resulting in deleterious effects. Currently there is an increase in the number of national and international pregnancy registries being formed in an effort to better identify the teratogenic effects of AEDs. These efforts hope to enhance our understanding of AEDs and their associated risks by addressing past study limitations.
Minimizing Energy Consumption with Variable Forward Body Bias for Ultra-Low Energy LSIs (2007)

Ultra-low energy LSI becomes primary concern in today's battery driven ubiquitous computing portable applications. To reduce energy per transition and to enhance performance in the ultra-low voltage region, we review the variable forward body bias scheme to make either faster pull-up or pull-down transition in the sub-threshold, near-threshold and above-threshold regimes. We begin our study for minimizing energy per transition by applying variable forward body bias asymmetrically and propose novel approaches to energy efficient design with performance advantages. To analyze and discuss, the fan-out of 3 (FO3) inverter based 51-stage delay chain is simulated in an industrial 130 nm triple well process technology.
9th Russian Summer School in Information Retrieval (RuSSIR 2015) (2016)

column Share on 9th Russian Summer School in Information Retrieval (RuSSIR 2015) Authors: Pavel Braslavski Kontur Labs & Ural Federal University, Russia Kontur Labs & Ural Federal University, RussiaView Profile , Ilya Markov University of Amsterdam, The Netherlands University of Amsterdam, The NetherlandsView Profile , Panos M. Pardalos Universiry of Florida, USA & National Research University Higher School of Economics, Russia Universiry of Florida, USA & National Research University Higher School of Economics, RussiaView Profile , Yana Volkovich Eurecat, Spain Eurecat, SpainView Profile , Sergei Koltsov National Research University Higher School of Economics, Russia National Research University Higher School of Economics, RussiaView Profile , Olessia Koltsova National Research University Higher School of Economics, Russia National Research University Higher School of Economics, RussiaView Profile , Dmitry I. Ignatov National Research University Higher School of Economics, Russia National Research University Higher School of Economics, RussiaView Profile Authors Info & Claims ACM SIGIR ForumVolume 49Issue 2December 2015 pp 72–79https://doi.org/10.1145/2888422.2888432Published:29 January 2016Publication History 3citation55DownloadsMetricsTotal Citations3Total Downloads55Last 12 Months2Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Sense: the final frontier (1998)

Despite its central role within language disability, ‘sense’ remains one of the most neglected areas of clinical linguistic study. The paper reviews the chief theoretical issues involved in investigating vocabulary, the core domain of sense, and illustrates the vagueness and randomness which traditionally characterize its study. The implications of making the conceptual jump from WORDS to LEXICAL ITEMS (LEXEMES) are discussed, and the main features of a lexical syllabus outlined, with particular reference to the role of sense relations and the unsatisfactory state of dictionary definitions in books aimed at children.
Optical detection and spectroscopy of single molecules in a solid (1989)

Using two different double-modulation techniques, we have observed the optical-absorption spectrum of single dopant molecules of pentacene in a p-terphenyl host crystal at liquid-helium temperatures. To achieve this, frequency-modulation spectroscopy was combined either with Stark or ultrasonic modulation to remove interfering background signals from residual amplitude modulation, and the number of molecules in resonance was reduced to one by operating in the wings of the inhomogeneous line. Triplet bottleneck saturation appears to be suppressed in the single-molecule regime.
Evaluation of a fast method of EPID‐based dosimetry for intensity‐modulated radiation therapy (2010)

Electronic portal imaging devices (EPIDs) could potentially be useful for intensity-modulated radiation therapy (IMRT) QA. The data density, high resolution, large active area, and efficiency of the MV EPID make it an attractive option. However, EPIDs were designed as imaging devices, not dosimeters, and as a result they do not inherently measure dose in tissue equivalent media. EPIDose (Sun Nuclear, Melbourne, FL) is a tool designed for the use of EPIDs in IMRT QA that uses raw MV EPID images (no additional build-up and independent of gantry angle, but with dark and flood field corrections applied) to estimate absolute dose planes normal to the beam axis in a homogeneous media (i.e. similar to conventional IMRT QA methods). However, because of the inherent challenges of the EPID-based dosimetry, validating and commissioning such a system must be done very carefully, by exploring the range of use cases and using well-proven "standards" for comparison. In this work, a multi-institutional study was performed to verify accurate EPID image to dose plane conversion over a variety of conditions. Converted EPID images were compared to 2D diode array absolute dose measurements for 188 fields from 28 clinical IMRT treatment plans. These plans were generated using a number of commercially available treatment planning systems (TPS) covering various treatment sites including prostate, head and neck, brain, and lung. The data included three beam energies (6, 10, and 15 MV) and both step-and-shoot and dynamic MLC fields. Out of 26,207 points of comparison over 188 fields analyzed, the average overall field pass rate was 99.7% when 3 mm/3% DTA criteria were used (range 94.0-100 per field). The pass rates for more stringent criteria were 97.8% for 2mm/2% DTA (range 82.0-100 per field), and 84.6% for 1 mm/1% DTA (range 54.7-100 per field). Individual patient-specific sites as well, as different beam energies, followed similar trends to the overall pass rates.
Innate Immunity Stimulation via Toll-Like Receptor 9 Ameliorates Vascular Amyloid Pathology in Tg-SwDI Mice with Associated Cognitive Benefits (2016)

Recent genetic studies have underscored the emerging role of microglia in Alzheimer's disease (AD) pathogenesis. Microglia lose their amyloid-β-clearing capabilities with age and as AD progresses. Therefore, the ability to modulate microglia profiles offers a promising therapeutic avenue for reducing AD pathology. Current immunotherapeutic approaches have been limited by poor clearance of a core AD lesion, cerebral amyloid angiopathy (CAA). The present study used Tg-SwDI mice, which have extensive CAA. We found that stimulation of the innate immune system and microglia/macrophage activation via Toll-like receptor 9 using CpG (cytosine-phosphate-guanine) oligodeoxynucleotides (ODNs) leads to cognitive improvements and CAA reduction, without associated toxicity. Our data indicate that this novel concept of immunomodulation represents a safer method to reduce all aspects of AD pathology and provide essential information for potential clinical use of CpG ODN.
Randomised, double blind, placebo-controlled, multi-centre, group-sequential trial of G17DT for patients with advanced pancreatic cancer unsuitable or unwilling to take chemotherapy (2004)

2511 Background: Pancreatic adenocarcinomas express CCK-2 receptors and respond to amidated gastrins resulting in transcriptional activation of EGF receptor ligands, matrix metalloproteinases and anti-apoptotic factors which collectively increase tumorigenic potential. The gastrin gene may also be activated resulting in gly-gastrin secretion. G17DT, a gastrin immunogen, induces neutralising antibodies against amidated and glycine-extended gastrin-17. Methods: Randomised, double blind, placebo-controlled, multi-centre trial of patients with advanced pancreatic cancer unsuitable or unwilling to take chemotherapy, performed outside the US. Inclusion criteria were Karnofsky performance score (KPS) ≥60, life expectancy >2 months. Patients received G17DT or the vehicle only at weeks 0, 1, 3, 24 and 52. Primary endpoint was survival; secondary endpoints included tolerability, KPS, weight change, quality of life and tumour response. Results: 154 patients: 79 randomised to G17DT, 75 to placebo. Intention to Treat (ITT) analysis gave median survival of 151 vs 82 days, G17DT:placebo, (p=0.03, Log rank). Time to deterioration of Karnofsky index was longer in the G17DT group than placebo: median 138 (95% CI: 84–165) vs 78 days (95% CI: 56–97) (p=0.038, Wilcoxon). G17DT was well tolerated; 2/79 (2.5%) G17DT patients vs 0/74 (0%) placebo patients developed sterile abscess at the injection site. Conclusion: G17DT prolongs survival, maintains performance and provides a well tolerated new therapeutic option for advanced pancreatic cancer patients. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Aphton Corp. Aphton Corp. Aphton Corporation
Thermosensitive PEG–PCL–PEG (PECE) hydrogel as an <i>in situ</i> gelling system for ocular drug delivery of diclofenac sodium (2014)

Development of efficient ocular drug delivery systems was still a challenging task. The objective of this article was to develop a thermosensitive PEG-PCL-PEG (PECE) hydrogel and investigate its potential application for ocular drug delivery of diclofenac sodium (DIC). PECE block polymers were synthesized by coupling MPEG-PCL co-polymer using IPDI reagent, and then its sol-gel transition as a function with temperature was investigated by a rheometer. The results showed that 30% (w/v) PECE aqueous solution exhibited sol-gel transition at approximately 35 °C. In vitro release profiles showed the entrapped DIC was sustained release from PECE hydrogels up to 7 days and the initial drug loading greatly effect on release behavior of DIC from PECE hydrogels. MTT assay results indicated that no matter PECE or 0.1% (w/v) DIC-loaded PECE hydrogels were nontoxic to HCEC and L929 cells after 24 h culturing. In vivo eye irritation test showed that the instillation of either 30% (w/v) PECE hydrogels or 0.1% (w/v) DIC-loaded PECE hydrogels to rabbit eye did not result in eye irritation within 72 h. In vivo results showed that the AUC0-48 h of 0.1% (w/v) DIC-loaded PECE hydrogels exhibited 1.6-fold increment as compared with that of commercial 0.1% (w/v) DIC eye drops, suggesting the better ophthalmic bioavailability could be obtained by the instillation of 0.1% (w/v) DIC-loaded PECE hydrogels.
Nanoenergetic Composites of CuO Nanorods, Nanowires, and Al‐Nanoparticles (2008)

Abstract This paper reports on the synthesis of the nanoenergetic composites containing CuO nanorods and nanowires, and Al‐nanoparticles. Nanorods and nanowires were synthesized using poly(ethylene glycol) templating method and combined with Al‐nanoparticles using ultrasonic mixing and self‐assembly methods. Poly(4‐vinylpyridine) was used for the self‐assembly of Al‐nanoparticles around the nanorods. At the optimized values of equivalence ratio, sonication time, and Al‐particle size, the combustion wave speed of 1650 m s −1 was obtained for the nanorods‐based energetics. For the composite of nanowires and Al‐nanoparticles the speed was increased to 1900 m s −1 . The maximum combustion wave speed of 2400 m s −1 was achieved for the self‐assembled composite, which is the highest known so far among the nanoenergetic materials. It is possible that in the self‐assembled composites, the interfacial contact between the oxidizer and fuel is higher and resistance to overall diffusional process is lower, thus enhancing the performance.
Discovering word associations in news media via feature selection and sparse classification (2010)

We analyze the "image" of a given query word in a given corpus of text news by producing a short list of other words with which this query is strongly associated. We use a number of feature selection schemes for text classification to help in this task. We apply these classification techniques using indicators of the query word's appearance in each document used as the document "labels" and the indicators for all other words as document predictors/features. The features selected by any scheme is then considered the list of words comprising the query word's "image".
Acid- and calcium-induced structural changes in phosphatidylethanolamine membranes stabilized by cholesteryl hemisuccinate (1985)

The membrane stabilization effect of cholesteryl hemisuccinate (CHEMS) and the sensitivity of the CHEMS-phosphatidylethanolamine membranes to protons and calcium ions were studied by differential scanning calorimetry, freeze-fracture electron microscopy, and 31P NMR. (1) At neutral pH, the addition of 8 mol % CHEMS to transesterified egg phosphatidylethanolamine (TPE) raised the lamellar-hexagonal transition temperature of TPE by 11 degrees C. Stable bilayer vesicles were formed when the incorporated CHEMS exceeded 20 mol %. (2) At a pH below 5.5, the protonation of CHEMS enhanced the formation of the hexagonal phase (HII) of TPE. At 25 mol % CHEMS the bilayer-hexagonal transition temperature was lowered by 30 degrees C at pH 4.5. (3) The endothermic acid-induced hexagonal hexagonal transition of TPE-CHEMS was suppressed at 35 mol % CHEMS. However, 31P NMR and electron microscopy indicated that a lamellar-hexagonal transition still occurred at this composition. (4) The main transition of TPE was not affected by the protonation of the incorporated CHEMS, indicating that no macroscopic phase separation occurred in TPE-CHEMS mixtures at low pH. (5) In contrast to the HII-promoting effect of H+, the neutralization of the negative charge on TPE-CHEMS by Ca2+ resulted in aggregates that remained in the lamellar structure even at the hexagonal transition temperature of TPE. It is suggested that calcium might form a complex between CHEMS in apposed bilayers. These results are related to the possible biological function of acidic cholesterol esters in biomembranes.
Predicting Final Eye Position Halfway Through a Saccade (1983)

When the visual environment is to be changed during a saccadic eye movement, it is useful to predict the final eye position before the eye comes to rest. We have built a microcomputer-based instrument to make such predictions. Two techniques were used: one based on the saccadic peak-velocity versus magnitude relationship, and the second based on peak-velocity occurring in the middle of the saccade. The second technique has been tailored to take advantage of the differences between temporal and nasal saccades. Depending on saccade duration, final eye position was predicted 4 to 60 ms before the end of the saccade.
Experimental verification of T-matrix-based inverse light scattering analysis for assessing structure of spheroids as models of cell nuclei (2009)

Inverse light scattering analysis (ILSA) seeks to associate measured scattering properties with the most probable theoretical scattering distribution, making it a useful tool for assessing structure in biological materials. The accuracy of ILSA depends on the compatibility of the light scattering geometry with the light scattering model. In this study, we compare the accuracy obtained when analyzing light scattering data from spheroids using a numerical implementation of Mie theory, and the T matrix, a numerical method of solving light scattering from spheroids. Our experimental data are acquired using novel optical phantoms containing spheroidal scatterers and angle-resolved low-coherence interferometry, a depth- and angle-resolved light scattering measurement modality. The results show that Mie theory can accurately assess spheroidal structure despite the geometric incompatibility provided measurements are taken in multiple orientations of the sample relative to the incident polarization and the measured scattering angle. In comparison, analysis using the T-matrix method is highly accurate and more reliable yet requires measurements from only a single orientation.
Effects of functionalized metal and semiconductor nanoparticles in nematic liquid crystal phases (2008)

To capitalize on the unique size and shape-dependent optical and electronic properties of nanoscale particles for liquid crystal (LC) applications, detailed structure and size-property relationship studies are critical. To enhance our understanding of the thermal, optical and electro-optic effects of nanoparticles in nematic LCs we produced numerous different nematic LC mixtures containing small quantities of dispersed metal nanoparticles (i.e. gold and silver nanoclusters) or semiconductor quantum dots (i.e. CdTe nanocrystals) and studied their optical (texture, alignment, defect formation, luminescence) and electro-optic properties. Depending on several experimental parameters such as nanoparticle functionalization and concentration, as well as thermal history in combination with an applied electric field, these nanoparticle/LC mixtures with the nanoparticles differing in surface functionality, size, and core material gave rise to unique alignment effects and electro-optic responses in the two investigated nematic LC (N-LC) hosts.