gebhart/patrepeval huggingface dataset:
Probe dependency in the determination of ligand binding kinetics at a prototypical G protein-coupled receptor (2019)

Drug-target binding kinetics are suggested to be important parameters for the prediction of in vivo drug-efficacy. For G protein-coupled receptors (GPCRs), the binding kinetics of ligands are typically determined using association binding experiments in competition with radiolabelled probes, followed by analysis with the widely used competitive binding kinetics theory developed by Motulsky and Mahan. Despite this, the influence of the radioligand binding kinetics on the kinetic parameters derived for the ligands tested is often overlooked. To address this, binding rate constants for a series of histamine H<sub>1</sub> receptor (H<sub>1</sub>R) antagonists were determined using radioligands with either slow (low k<sub>off</sub>) or fast (high k<sub>off</sub>) dissociation characteristics. A correlation was observed between the probe-specific datasets for the kinetic binding affinities, association rate constants and dissociation rate constants. However, the magnitude and accuracy of the binding rate constant-values was highly dependent on the used radioligand probe. Further analysis using recently developed fluorescent binding methods corroborates the finding that the Motulsky-Mahan methodology is limited by the employed assay conditions. The presented data suggest that kinetic parameters of GPCR ligands depend largely on the characteristics of the probe used and results should therefore be viewed within the experimental context and limitations of the applied methodology.
Deepwater Four Zones Selective Washpipeless Frac-Pack Completion Inside a Bad Cemented Liner: A Case History (2004)

Abstract Fracpack completions are not new to the oil and gas industry; however, they are operations that are very critical to the results of well longevity, productivity, and are considered operationally "high-risk" completions. Some fields in deepwater Campos basin (Figure 1) - Brazil have tightly spaced productive zones that require sand control and selectivity of production. Two systems were used on the four-zone completion to allow for the tight spacing between zones. On the lower and upper middle zone a modified washpipeless isolation system (Crippled) was utilized and on the lower middle and upper zones a high pressure retrievable washpipeless isolation system (HPRWIS) was used. Both systems utilize a concentric string for isolation, not using washpipe to the bottom of the screen, like a normal land or Gulf of Mexico completion stems from unsuccessful attempts resulting in stuck washpipe in 7" liners with 2 3/8" isolation tubing on floating platforms or drillships and rough seas. The HPRWIS system also provides "live-annulus" capabilities and a method to isolate the production screen from the tubing after fracing by placing a concentric string into a lower seal bore after the treatment is over. All installation is done at the surface in both systems, but the HPRWIS is initially spaced out to allow communication through the lower most part of the production screen. After reversing operations to remove excess proppant from the workstring, a shifting prong actuates the concentric string down by means of well hydrostatic working across an atmospheric chamber connected to the gravel pack assembly. Actuation is accomplished by mechanically removing a lock ring attached to the atmospheric chamber with the previously mentioned shifting prong. The concentric string may also be retrieved on pipe by utilizing a HPRWIS retrieving tool with straight upward pull to the inner assembly. This paper outlines the utilization of "State-of-the-art" frac pack downhole equipment technology used to successfully complete, without unscheduled events, a four zone well with bad cemented liner (Figures 2–5) in the Campos Basin, Macae, Brazil.
Ultrafast optical response originating from carrier-transport processes in undoped GaAs/n-type GaAs epitaxial structures (2012)

We have investigated ultrafast optical responses of undoped GaAs/n-type GaAs (i-GaAs/n-GaAs) epitaxial structures at room temperature using a reflection-type pump-probe technique. The built-in electric field in the i-GaAs layer is controlled by its thickness. It is found that the decay time of a photoexcitation-induced reflectivity change in a sub-picosecond range decreases with an increase in the built-in electric field strength. The observed optical response is related to the transport process of photogenerated carriers from the i-GaAs layer to the n-GaAs layer. The shortest response time about 60 fs demonstrates that the i-GaAs/n-GaAs structure is useful for ultrafast optical applications.
An Electromyographical Evaluation of the Validity of the 2-Minute Sit-Up Section of the Army Physical Fitness Test in Measuring Abdominal Strength and Endurance (2002)

Hip flexors can compensate for fatigued abdominal muscles, causing sit-ups to be performed unsafely, yet are still counted as correct according to Army Physical Fitness Test standards.
Cleaning and sanitizing in milk production and processing. (2001)

All food and dairy products are handled in plants that have modern processing
equipment, utensils, and other auxiliary parts that must be cleaned and sanitized
to produce food products that are safe for human consumption. Progressively
automated cleaning systems have been developed to replace old and less efficient
ones to increase productivity, provide safe working environments and, above
all, guarantee safe and wholesome products for consumers. Good cleaning and
sanitizing of food processing equipment is essential to assure safe food products
with extended shelf life.
Constrained optimal foraging by marine bacterioplankton on particulate organic matter (2020)

Optimal foraging theory provides a framework to understand how organisms balance the benefits of harvesting resources within a patch with the sum of the metabolic, predation, and missed opportunity costs of foraging. Here, we show that, after accounting for the limited environmental information available to microorganisms, optimal foraging theory and, in particular, patch use theory also applies to the behavior of marine bacteria in particle seascapes. Combining modeling and experiments, we find that the marine bacterium <i>Vibrio ordalii</i> optimizes nutrient uptake by rapidly switching between attached and planktonic lifestyles, departing particles when their nutrient concentration is more than hundredfold higher than background. In accordance with predictions from patch use theory, single-cell tracking reveals that bacteria spend less time on nutrient-poor particles and on particles within environments that are rich or in which the travel time between particles is smaller, indicating that bacteria tune the nutrient concentration at detachment to increase their fitness. A mathematical model shows that the observed behavioral switching between exploitation and dispersal is consistent with foraging optimality under limited information, namely, the ability to assess the harvest rate of nutrients leaking from particles by molecular diffusion. This work demonstrates how fundamental principles in behavioral ecology traditionally applied to animals can hold right down to the scale of microorganisms and highlights the exquisite adaptations of marine bacterial foraging. The present study thus provides a blueprint for a mechanistic understanding of bacterial uptake of dissolved organic matter and bacterial production in the ocean-processes that are fundamental to the global carbon cycle.
Developing DNA vaccines that call to dendritic cells (2004)

DNA vaccination is a novel immunization strategy that has great potential for the development of vaccines and immune therapeutics. This strategy has been highly effective in mice, while less immunogenic in nonhuman primates and humans. Enhancing DNA vaccine potency remains a challenge. It is likely that APCs, and especially DCs, play a paramount role in the presentation of vaccine antigen to the immune system. A new study reports the synergistic recruitment, expansion, and activation of DCs in vivo in a mouse model through covaccination with plasmids encoding macrophage inflammatory protein-1 (MIP-1), fms-like tyrosine kinase 3 ligand (Flt3L), and the DNA vaccine (see the related article beginning on page 1334). Such cooperative strategies delivering vaccine in a single, simple platform result in improved cellular immunity in vivo, including enhanced tetramer responses and IFN- secretion by antigen-specific cells.
High intensity focused ultrasound cyclocoagulation in dogs with primary glaucoma: a preliminary study (2018)

The objective was to assess the effect of high intensity focused ultrasound (HIFU) on intraocular pressure (IOP) in dogs with primary glaucoma (PG). Seven dogs (13 eyes) presenting with PG as diagnosed by a raised IOP (> 20 mm Hg) associated with consistent gonioscopy and ultrasound biomicroscopy of the ciliary cleft, with no other ocular disease. Patients were divided into 3 groups, corresponding to their pre-operative IOP (group 1 ranging from 21 to 30 mm Hg, group 2 from 31 to 40 and group 3 for 40 and above). Ciliary process sonication was achieved with a probe containing one high-frequency transducer operating at 21 MHz during 5 seconds. Six sites were treated in patients from group 1, 8 in group 2, 10 in group 3, under general anesthesia. Post-operative treatment consisted of systemic meloxicam and topical carbonic anhydrase inhibitors, beta-blockers and prostaglandins analogues. No intraoperative complications were observed. Conjunctival hyperaemia occurred in eyes from group 2 (66%) and 3 (100%). Conjunctival burns were visible in 2 patients from group 3. One patient from group 3 experienced a hypertensive spike during the first hours post-op with associated pain. The hypotensive effect of HIFU was observed in all groups. Normotensive IOP (≤20 mm Hg) was reached in all patients until the last recheck at 6 months post op. Despite the small number of patients included in the study, HIFU appears to be a promising option for the management of PG in dogs.
Molecular structure and elastic behavior of poly(ethylene oxide) networks swollen to equilibrium (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular structure and elastic behavior of poly(ethylene oxide) networks swollen to equilibriumYves Gnanou, Gerard Hild, and Paul RemppCite this: Macromolecules 1987, 20, 7, 1662–1671Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/ma00173a037https://doi.org/10.1021/ma00173a037research-articleACS PublicationsRequest reuse permissionsArticle Views366Altmetric-Citations60LEARN 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
Al-2.76 Molecular Logic Gate (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
A unique microRNA signature associated with nucleophosmin mutations in normal karyotype acute myeloid leukemia (2007)

7015 Background: Nucleophosmin (NPM) mutations are present in about 30 to 50 % of the patients with normal karyotype acute myeloid leukemia (NK-AML). The mutant NPM protein shows aberrant cytoplasmic location and is frequently associated with FLT3 mutations. Little is know, however how NPM mutants promote leukemia. To obtain insights about the biology of NPM+ AML we investigated the expression of microRNAs in NK-AML patients characterized for NPM mutations. Methods: We studied 85 adult NK-AML patients characterized for NPM, FLT3 ITD and FLT3 D835 mutations using a miRNA microarray platform containing 345 mature and precursors miRNAs. Mutation analysis for NPM, FLT3 ITD and FLT3 D835 were carried out in most of the patients as previously described (Falini, Blood 2006). The distribution of the mutations were as follows: NPMc+ (54 patients), NPMc- (31), FLT3 ITD+ (27), FLT3 ITD-(51) and FLT3 D835+ (21) and FLT3 D835-(26). Data were analyzed after background subtraction and normalization with a set of housekeeping genes using Significance Analysis of Microarrays and Predictive Analysis of microarrays. The results were validated using miRNA q-RT-PCR. Results: We identified a strong miRNA signature that distinguishes NPMc+ cases with high accuracy and includes the up-regulation of miR-10a, miR-10b and several let-7 family members. Many of the down-regulated miRNAs including miR-134, miR-194, miR-204, miR-526 and miR-28 are predicted to target many HOX genes suggesting that NPM mutants may induce HOX genes through the down-modulation of miRNA regulators of these genes. The signatures associated with FLT3 mutations were not accurate to predict this abnormality. However, when we analyzed the subgroup of NPMc+ FLT3 ITD + cases a distinctive signature was found with respect to other NPMc+ FLT3 negative cases. Conclusions: A unique miRNA signature is associated with NPMc+ mutations in AML. FLT3 ITD and FLT3 D835 are not clearly associated to any characteristic miRNA signature when analyzed individually. However the subgroup of NPMc+ FLT3 ITD has a distinctive miRNA signature. This data provide with new insights about the pathogenesis of NPMc+ AML that could be exploited to generate novel therapeutic strategies for one of the most common mutations in AML. No significant financial relationships to disclose.
First-come-first-served packet dispersion and implications for TCP (2003)

We study the packet dispersion phenomenon that a traffic flow experiences when it passes through a router. We show that when there are competing flows and the router schedules packets first-come-first-served (FCFS), the dispersion is not described well by the bottleneck spacing effect. We therefore introduce the term FCFS-spacing effect. We also show that for a router implementing weighted fair queuing, dispersion is due either to the bottleneck spacing effect or the FCFS spacing effect. The results from real measurements and simulations corroborate each other. Finally, we discuss the implications of FCFS packet dispersion on TCP's self-clocking mechanism.
Method to detect the end-point for PCR DNA amplification using an ionically labeled probe and measuring impedance change (2023)

Impedance measurements are used to detect the end-point for PCR DNA amplification. A pair of spaced electrodes are located on a surface of a microfluidic channel and an AC or DC voltage is applied across the electrodes to produce an electric field. An ionically labeled probe will attach to a complementary DNA segment, and a polymerase enzyme will release the ionic label. This causes the conductivity of the solution in the area of the electrode to change. This change in conductivity is measured as a change in the impedance been the two electrodes.
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media (2019)

Cation adjusted-Mueller Hinton Broth (CA-MHB) is the standard bacteriological medium utilized in the clinic for the determination of antibiotic susceptibility. However, a growing number of literature has demonstrated that media conditions can cause a substantial difference in the efficacy of antibiotics and antimicrobials. Recent studies have also shown that minimum inhibitory concentration (MIC) tests performed in standard cell culture media (e.g. RPMI and DMEM) are more indicative of in vivo antibiotic efficacy, presumably because they are a better proxy for the human host's physiological conditions. The basis for the bacterial media dependent susceptibility to antibiotics remains undefined. To address this question, we characterized the physiological response of methicillin-resistant Staphylococcus aureus (MRSA) during exposure to sub-inhibitory concentrations of the beta-lactam antibiotic nafcillin in either CA-MHB or RPMI + 10% LB (R10LB). Here, we present high quality transcriptomic, exo-metabolomic and morphological data paired with growth and susceptibility results for MRSA cultured in either standard bacteriologic or more physiologic relevant medium.
Search for long-lived, massive particles in events with displaced vertices and missing transverse momentum in s=13  TeV pp collisions with the ATLAS detector (2018)

A search for long-lived, massive particles predicted by many theories beyond the Standard Model is presented. The search targets final states with large missing transverse momentum and at least one high-mass displaced vertex with five or more tracks, and uses $32.8\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of $\sqrt{s}=13\text{ }\text{ }\mathrm{TeV}$ $pp$ collision data collected by the ATLAS detector at the LHC. The observed yield is consistent with the expected background. The results are used to extract 95% C.L. exclusion limits on the production of long-lived gluinos with masses up to 2.37 TeV and lifetimes of $\mathcal{O}({10}^{\ensuremath{-}2})\ensuremath{-}\mathcal{O}(10)\text{ }\text{ }\mathrm{ns}$ in a simplified model inspired by split supersymmetry.
Biobanking and cryopreservation of human lung explants for omic analysis (2019)

Biobanked, cryopreserved lung cells obtained from human lung tissue are viable and valuable resources for large-scale molecular phenotyping http://bit.ly/31gtpcP
Predictive caching and prefetching of query results in search engines (2003)

We study the caching of query result pages in Web search engines. Popular search engines receive millions of queries per day, and efficient policies for caching query results may enable them to lower their response time and reduce their hardware requirements. We present PDC (probability driven cache), a novel scheme tailored for caching search results, that is based on a probabilistic model of search engine users. We then use a trace of over seven million queries submitted to the search engine AltaVista to evaluate PDC, as well as traditional LRU and SLRU based caching schemes. The trace driven simulations show that PDC outperforms the other policies. We also examine the prefetching of search results, and demonstrate that prefetching can increase cache hit ratios by 50% for large caches, and can double the hit ratios of small caches. When integrating prefetching into PDC, we attain hit ratios of over 0.53.
Lab-on-a-Bubble Surface Enhanced Raman Indirect Immunoassay for Cholera (2012)

We describe a novel sandwich assay based on surface enhanced Raman scattering (SERS) comprised of buoyant silica microspheres coated with antibodies against the β subunit of the cholera toxin (CT), and gold nanoparticles tagged with a Raman reporter, shelled with silica and coated with antibodies against the β subunit of the CT. Together these components couple to form a sandwich which, after incubation, floats on the surface of the sample. The buoyant silica microparticle/nanoparticle reporter combination has been coined a lab on a bubble (LoB). LoB materials may provide a platform for rapid detection of antigen in solution and offers advantages over lateral flow or magnetic pull-down assays. The Raman reporter provides a unique and intense signal to indicate a positive analysis. Our limit of detection for the β subunit of the CT in a buffer based system is 1100 ng.
High-Reflectivity Thermally Stable Ultrafast Induced Fiber Bragg Gratings in H$_{2}$-Loaded SMF-28 Fiber (2009)

High-temperature stable high-reflectivity gratings are fabricated in hydrogen-loaded single-mode fiber (SMF-28) using ultrafast 800-nm radiation. An index modulation of ~ 9 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> and a loss of >15 dB at the Bragg resonance is present after isochronal annealing up to 1000degC followed by 96 h of isothermal annealing.
Pervasive Pose Estimation for Fall Detection (2022)

Falls are the second leading cause of accidental or unintentional injuries/deaths worldwide. Accurate pose estimation using commodity mobile devices will help early detection and injury assessment of falls, which are essential for the first aid of elderly falls. By following the definition of fall, we propose a P ervasive P ose Est imation scheme for fall detection ( P \( ^2 \) Est ), which measures changes in tilt angle and height of the human body. For the tilt measurement, P \( ^2 \) Est leverages the pointing of the mobile device, e.g., the smartphone, when unlocking to associate the Device coordinate system with the World coordinate system. For the height measurement, P \( ^2 \) Est exploits the fact that the person’s height remains unchanged while walking to calibrate the pressure difference between the device and the floor. We have prototyped and tested P \( ^2 \) Est in various situations and environments. Our extensive experimental results have demonstrated that P \( ^2 \) Est can track the body orientation irrespective of which pocket the phone is placed in. More importantly, it enables the phone’s barometer to detect falls in various environments with decimeter-level accuracy.
Integrating High Fidelity Eye, Head and World Tracking in a Wearable Device (2021)

A challenge in mobile eye tracking is balancing the quality of data collected with the ability for a subject to move freely and naturally through their environment. This challenge is exacerbated when an experiment necessitates multiple data streams recorded simultaneously and in high fidelity. Given these constraints, previous devices have had limited spatial and temporal resolution, as well as compression artifacts. To address this, we have designed a wearable device capable of recording a subject’s body, head, and eye positions, simultaneously with RGB and depth data from the subject’s visual environment, measured in high spatial and temporal resolution. The sensors include a binocular eye tracker, an RGB-D scene camera, a high-frame-rate scene camera, and two visual odometry sensors, which we synchronize and record from, with a total incoming data rate of over 700 MB/s. All sensors are operated by a mini-PC optimized for fast data collection, and powered by a small battery pack. The headset weighs only 1.4 kg, the remainder just 3.9kg, and can be comfortably worn by the subject in a small backpack, allowing full mobility.