gebhart/patrepeval huggingface dataset:
Abstract IA021: Targeting epigenetic regulators of oncogenic transcription factors (2022)

Abstract The switch/sucrose non-fermentable (SWI/SNF) complex has a crucial role in chromatin remodeling and is altered in over 20% of cancers. We recently developed and evaluated a proteolysis-targeting chimera (PROTAC) degrader of the SWI/SNF ATPase subunits, SMARCA2 and SMARCA4, called AU-15330. Androgen receptor (AR)+ forkhead box A1 (FOXA1)+ prostate cancer cells are exquisitely sensitive to dual SMARCA2 and SMARCA4 degradation relative to normal and other cancer cell lines. SWI/SNF ATPase degradation rapidly compacts cis-regulatory elements bound by transcription factors that drive prostate cancer cell proliferation, namely AR, FOXA1, ERG and MYC, which dislodges them from chromatin, disables their core enhancer circuitry, and abolishes the downstream oncogenic gene programs. SWI/SNF ATPase degradation also disrupts super-enhancer and promoter looping interactions that wire supraphysiologic expression of the AR, FOXA1 and MYC oncogenes themselves. AU-15330 induces potent inhibition of tumor growth in xenograft models of prostate cancer and synergizes with the AR antagonist enzalutamide, even inducing disease remission in castration-resistant prostate cancer (CRPC) models without toxicity. Thus, impeding SWI/SNF-mediated enhancer accessibility represents a promising therapeutic approach for enhancer-addicted cancers. Citation Format: Arul M. Chinnaiyan. Targeting epigenetic regulators of oncogenic transcription factors. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr IA021.
MoS2 Nanoplates Consisting of Disordered Graphene-like Layers for High Rate Lithium Battery Anode Materials (2011)

MoS(2) nanoplates, consisting of disordered graphene-like layers, with a thickness of ∼30 nm were prepared by a simple, scalable, one-pot reaction using Mo(CO)(6) and S in an autoclave. The product has a interlayer distance of 0.69 nm, which is much larger than its bulk counterpart (0.62 nm). This expanded interlater distance and disordered graphene-like morphology led to an excellent rate capability even at a 50C (53.1 A/g) rate, showing a reversible capacity of 700 mAh/g. In addition, a full cell (LiCoO(2)/MoS(2)) test result also demonstrates excellent capacity retention up to 60 cycles.
In-line phase-contrast imaging of a biological specimen using a compact laser-Compton scattering-based x-ray source (2008)

Laser-Compton scattering (LCS) x-ray sources have recently attracted much attention for their potential use at local medical facilities because they can produce ultrashort pulsed, high-brilliance, and quasimonochromatic hard x rays with a small source size. The feasibility of in-line phase-contrast imaging for a “thick” biological specimens of rat lumbar vertebrae using the developed compact LCS-X in AIST was investigated for the promotion of clinical imaging. In the higher-quality images, anatomical details of the spinous processes of the vertebrae are more clearly observable than with conventional absorption radiography. The results demonstrate that phase-contrast radiography can be performed using LCS-X.
A UNIFIED ANALYSIS OF MAGNETIC SATURATION IN ORTHOGONAL AXIS MODELS OF ELECTRIC MACHINES (1987)

Abstract This paper presents an alternative method to develop the equations of orthogonal axis model of elective machines including the main path flux saturation. A physical orthogonal axis model is defined which resembles the synchronous machine with damper windings. The equations of synchronous, induction, and dc machines, with main path flux saturation included are given under the state-space form as particular cases from the physical orthogonal axis model equations.
La lecture numérique (2015)

La lecture numérique n’est pas équivalente à la lecture sur papier. Depuis plus d’une vingtaine d’années, les données montrent un déficit général de la perception et de la compréhension, lié à l’emploi des supports électroniques.Ce problème est plus que jamais d’actualité avec le développement croissant des réseaux informatiques, des bibliothèques virtuelles, des logiciels multimédia, des liseuses et des tablettes qui impliquent de nouveaux comportements et de nouvelles compétences du lecteur.L’ouvrage synthétise les découvertes et les développements théoriques apportés par la psychologie cognitive et l’ergonomie cognitive dans le domaine de la lecture numérique. Trois grands thèmes majeurs sont abordés : la visibilité, la lisibilité et la compréhension.On y trouvera également une description de méthodes expérimentales telles que l’analyse des mouvements des yeux ou des trajectoires de la souris et une partie appliquée concernant l’ergonomie des interfaces homme/ordinateur.
Plant Chitinase Mutants as the Catalysts for Chitooligosaccharide Synthesis Using the Sugar Oxazoline Derivatives (2022)

Sugar oxazolines, (GlcNAc)<i><sub>n</sub></i>-oxa (<i>n</i> = 2, 3, 4, and 5), were synthesized from a mixture of chitooligosaccharides, (GlcNAc)<i><sub>n</sub></i> (<i>n</i> = 2, 3, 4, and 5), and utilized for synthesis of (GlcNAc)<sub>7</sub> with higher elicitor activity using plant chitinase mutants as the catalysts. From isothermal titration calorimetry, the binding affinity of (GlcNAc)<sub>2</sub>-oxa toward an inactive mutant obtained from <i>Arabidopsis thaliana</i> GH18 chitinase was found to be higher than those of the other (GlcNAc)<i><sub>n</sub></i>-oxa (<i>n</i> = 3, 4, and 5). To synthesize (GlcNAc)<sub>7</sub>, the donor/acceptor substrates with different size combinations, (GlcNAc)<sub>2</sub>-oxa/(GlcNAc)<sub>5</sub> (1), (GlcNAc)<sub>3</sub>-oxa/(GlcNAc)<sub>4</sub> (2), (GlcNAc)<sub>4</sub>-oxa/(GlcNAc)<sub>3</sub> (3), and (GlcNAc)<sub>5</sub>-oxa/(GlcNAc)<sub>2</sub> (4), were incubated with hypertransglycosylating mutants of GH18 chitinases from <i>A. thaliana</i> and <i>Cycas revoluta</i>. The synthetic activities of these plant chitinase mutants were lower than that of a mutant of <i>Bacillus circulans</i> chitinase A1. Nevertheless, in the plant chitinase mutants, the synthetic efficiency of combination (1) was higher than those of the other combinations (2), (3), and (4), suggesting that the synthetic reaction is mostly dominated by the binding affinities of (GlcNAc)<i><sub>n</sub></i>-oxa. In contrast, the <i>Bacillus</i> enzyme mutant with a different subsite arrangement synthesized (GlcNAc)<sub>7</sub> from combination (1) in the lowest efficiency. Donor/acceptor-size dependency of the enzymatic synthesis appeared to be strongly related to the subsite arrangement of the enzyme used as the catalyst. The <i>A. thaliana</i> chitinase mutant was found to be useful when combination (1) is employed for the substrates.
Radionuclide Imaging of Infection in the Immunocompromised Host (1996)

Early diagnosis of infection in the immunocompromised patient is often difficult because of an impaired inflammatory response to microbial invasion. Radioscintigraphy has certain advantages in approaching this problem: because it is based upon either delivery of leukocytes to the site of infection or the leakiness of capillaries to radiolabeled proteins, earlier diagnosis is possible, even in patients with surgically altered anatomy; whole-body imaging allows the detection of focal sites of infection that are unsuspected clinically; and the semiquantitative nature of the information obtained allows for serial studies to assess the response to therapy. Three reagents are either currently available (gallium-67 citrate and radiolabeled leukocytes) or soon to be available (indium-111-labeled nonspecific polyclonal IgG) for this purpose. A major disadvantage of all three techniques is that a delay of 18-24 hours between injection and imaging is required. Experimental reagents such as technetium-99m-labeled chemotactic peptides appear to require < 3 hours between injection and imaging.
Collaborative Learning and Assessment of Science (2017)

In order to understand potential applications of collaborative problem solving (CPS) assessment tasks, it is necessary to examine empirically the multi-faceted student performance that may be distributed across collaboration methods and purposes of the assessment. Ideally, each student should be matched with various types of group members and must apply the skills in varied contexts and tasks. One solution to these assessment demands is to use computer-based (virtual) agents to serve as the collaborators in the interactions with students. This paper proposes human-to-agent (H-A) approach for formative CPS assessment and describes an international pilot study aimed to provide preliminary empirical findings on the use of H-A CPS assessment to inform collaborative learning. Overall, the findings showed promise in terms of using H-A CPS assessment task as a formative tool for structuring effective groups in the context of CPS online learning.
Microcirculation After Standardized Application of Essaven Gel on Normal Skin (2001)

Essaven gel (EG) is a naturally derived compound indicated for the treatment of impaired venous circulation and, in microcirculatory disorders, hematomas, swelling, sprains, and all minor sport injuries. The aim of this randomized, placebo-controlled, double-blind study was to evaluate the standardized application of EG on normal skin and its effects on the microcirculation. Standardization of gel application (particularly EG) has been recently described (in healthy subjects and in clinical studies) in defined steps. The results of this study indicate that topical treatment with EG is effective in improving or positively altering the microcirculation in normal skin both at the deeper capillary levels (thermoregulatory, whole-thickness capillary bed [as shown by laser Doppler flowmetry] as well as at the nutritional capillary layer (as shown by PO2). The application of EG can be standardized to obtain consistent results with topical treatment.
GENETIC MAPPING OF THE pho2, PHO82–pho4 AND pho85 LOCI OF YEAST (1980)

The PHO82-pho4 (PHOO-phoD) locus was mapped on the right arm of chromosome VI, 6.5 cM centromere-distal to met10. A pho85 (phoU) mutant was newly isolated, and its map location was determined on the left arm of chromosome XVI, 15 cM centromere-distal to rad1. A mutant gene that causes temperature-sensitive growth on nutrient medium was found very near (or at) the pho85 locus. The supertriploid method was successfully applied to locate the pho2 (phoB) locus on chromosome IV. The pho2 locus was 40 cM from rna11 on the left arm of chromosome IV.
Energy transport in DC and AC vortex stabilised arcs (1982)

By measuring the power balance for high current AC and DC vortex stabilised arcs it has been shown that the radiative efficiencies of AC and DC arcs are comparable to each other at similar power input levels. The electrode power balance has also been determined as a function of the significant arc parameters (current I, gas pressure, flow direction and rate). Further details on electrode heat transport were obtained by measuring the spatial and temporal variations of electrode surface temperature using a two-wavelength pyrometric technique. The heat transfer to the walls and exhaust gas depend linearly on the radiation losses. The former loss is larger than expected from laminar heat flow models indicating that heat losses are enhanced by turbulence in the gas flow. The power balance data confirm that the AC vortex stabilised arc lamp is comparable to the DC arc and has the added prospect of lower electrode erosion because of the smaller average electrode heat fluxes in the AC arc.
Designing for the eye (2012)

Eye gaze tracking provides a natural and fast method of interacting with computers. Many click alternatives have been proposed so far, each with their own merits and drawbacks. We focus on the most natural selection method, i.e. the dwell, with which a user can select an on-screen object by just gazing at it for a pre-defined dwell time.
Quantum Shells Boost the Optical Gain of Lasing Media (2022)

Auger decay of multiple excitons represents a significant obstacle to photonic applications of semiconductor quantum dots (QDs). This nonradiative process is particularly detrimental to the performance of QD-based electroluminescent and lasing devices. Here, we demonstrate that semiconductor quantum shells with an "inverted" QD geometry inhibit Auger recombination, allowing substantial improvements to their multiexciton characteristics. By promoting a spatial separation between multiple excitons, the quantum shell geometry leads to ultralong biexciton lifetimes (>10 ns) and a large biexciton quantum yield. Furthermore, the architecture of quantum shells induces an exciton-exciton repulsion, which splits exciton and biexciton optical transitions, giving rise to an Auger-inactive single-exciton gain mode. In this regime, quantum shells exhibit the longest optical gain lifetime reported for colloidal QDs to date (>6 ns), which makes this geometry an attractive candidate for the development of optically and electrically pumped gain media.
Odd spin-triplet superconductivity in a multilayered superconductor-ferromagnet Josephson junction (2010)

We study the dc Josephson effect in a diffusive multilayered ${\text{SF}}^{\ensuremath{'}}{\text{FF}}^{\ensuremath{'}}\text{S}$ structure, where S is a superconductor and F and ${\text{F}}^{\ensuremath{'}}$ are different ferromagnets. We assume that the exchange energies in the ${\text{F}}^{\ensuremath{'}}$ and F layers are different ($h$ and $H$, respectively) and the middle F layer consists of two layers with parallel or antiparallel magnetization vectors $M$. The $M$ vectors in the left and right ${\text{F}}^{\ensuremath{'}}$ layers are generally not collinear to those in the F layer. In the limit of a weak proximity effect we use a linearized Usadel equation. Solving this equation, we calculate the Josephson critical current for arbitrary temperatures, arbitrary thicknesses of the ${\text{F}}^{\ensuremath{'}}$ and F layers (${L}_{h}$ and ${L}_{H}$) in the case of parallel and antiparallel $M$ orientations in the F layer. The part of the critical current ${I}_{c\text{SR}}$ formed by the short-range singlet and $S=0$ triplet condensate components decays on a short length ${\ensuremath{\xi}}_{H}=\sqrt{D/H}$, whereas the part ${I}_{c\text{LR}}$ due to the long-range triplet $|S|=1$ component decreases with increasing ${L}_{H}$ on the length ${\ensuremath{\xi}}_{N}=\sqrt{D/\ensuremath{\pi}T}$. Our results are in a qualitative agreement with the experiment [T. S. Khaire, M. A. Khasawneh, W. P. Pratt, Jr., and N. O. Birge, Phys. Rev. Lett. 104, 137002 (2010)].
Stochastic rasterization using time-continuous triangles (2007)

We present a novel algorithm for stochastic rasterization which can rasterize triangles with attributes depending on a parameter, t, varying continuously from t = 0 to t = 1 inside a single frame. These primitives are called time-continuous triangles, and can be used to render motion blur. We develop efficient techniques for rasterizing time-continuous triangles, and specialized sampling and filtering algorithms for improved image quality. Our algorithm needs some new hardware mechanisms implemented on top of today's graphics hardware pipelines. However, our algorithm can leverage much of the already existing hardware units in contemporary GPUs, which makes the implementation fairly inexpensive. We introduce time-dependent textures, and show that motion blurred shadows and motion blurred reflections can be handled in our framework. In addition, we also present new techniques for efficient rendering of depth of field and glossy planar reflections using our stochastic rasterizer.
Computational Tools For Protein Modeling (2000)

Protein modeling is playing a more and more important role in protein and peptide sciences due to improvements in modeling methods, advances in computer technology, and the huge amount of biological data becoming available. Modeling tools can often predict the structure and shed some light on the function and its underlying mechanism. They can also provide insight to design experiments and suggest possible leads for drug design. This review attempts to provide a comprehensive introduction to major computer programs, especially on-line servers, for protein modeling. The review covers the following aspects: (1) protein sequence comparison, including sequence alignment/search, sequence-based protein family classification, domain parsing, and phylogenetic classification; (2) sequence annotation, including annotation/prediction of hydrophobic profiles, transmembrane regions, active sites, signaling sites, and secondary structures; (3) protein structure analysis, including visualization, geometry analysis, structure comparison/classification, dynamics, and electrostatics; (4) three-dimensional structure prediction, including homology modeling, fold recognition using threading, ab initio prediction, and docking. We will address what a user can expect from the computer tools in terms of their strengths and limitations. We will also discuss the major challenges and the future trends in the field. A collection of the links of tools can be found at http://compbio.ornl.gov/structure/resource/.
Supporting Information document from The ultrafast snap of a finger is mediated by skin friction (2021)

Supporting figures and extended mathematical model.
Analysis of propolis: some parameters and procedures for chemical quality control (1998)

SUMMARYA set of parameters and respective procedures for the establishment of chemical profiles of samples of tinctures and crude propolis is presented. It is proposed that estimations of the content of total phenolic substances, flavonoids, waxes, ash, volatile substances and dry residue be used as parameters to characterize samples of crude propolis. For tinctures, the estimations of total phenolic substances, flavonoids, waxes, specific gravity and ethanol are proposed. Total phenolic substances and flavonoids are measured by spectrophotometric methods, waxes gravimetrically and ethanol by gas chromatography. The accuracy of the spectrophotometric procedures was tested by assaying a mixture with a known composition of phenolic acids and flavonoids. The use of the procedures is exemplified by the analyses of six samples of crude propolis from different localities in Brazil and of tinctures prepared with absolute and 70% aqueous ethanol. The contents of total phenolic substances, flavonoids, waxes and volatile compounds of the samples analysed are relatively low in comparison with data from the literature. Samples of propolis from nearby localities may have quite different chemical profiles. Compared with absolute ethanol, extraction with aqueous ethanol results in wax-free tinctures, containing higher amounts of phenolic substances.
Improving accuracy of self-reported diagnoses of rheumatoid arthritis in the French prospective E3N-EPIC cohort: a validation study (2019)

Accuracy of self-reported RA is poor but adding answers to a specific questionnaire or data from a medication reimbursement database performed satisfactorily to identify RA cases in our cohort. It will subsequently allow investigating many potential risk factors of RA in women.
Developments in Miniaturization of Gas Chromatography (2021)

The tendency towards miniaturization is visible in many areas of the wider word. The downsizing of many everyday used items (e.g. wristwatches, i-phones) is possible mainly due to the avaailability of newly developed technology. The same trend is also observed in many fields of analytical chemistry. It is related with the contemporary movement in analytics to perform analysis at the place where analytes are present. The miniaturization of conventional analytical instruments can provide many attractive features, e. g. reduced space requirements, better flexibility and faster results, without sacrifice in performance, and perhaps, with improved performance. The chapter provides a general overview of the progress and current status of miniaturization of one of the most widely used analytical technique – gas chromatography (GC). First, the general characteristics of miniaturized gas chromatographs and a brief history of the miniaturized GC systems is presented. Next, the technologies used for fabrication of miniaturized gas chromatographs and the developments of a key components of micro gas chromatographs (?GC) systems, i.e. injectors/preconcentrators, columns and detectors, based on microelectromechanical technology (MEMS), are discussed. In the last section, the hybrid miniaturized systems, with emphasis on coupling of gas chromatographs with mass and ion mobility spectrometers (MS and IMS), are discussed. Finally, the examples of selected applications of gas chromatographs with MS (GC-MS) and IMS (GC-IMS) are given.
Surface wave suppression of microstrip antenna using different EBG designs (2015)

This paper describes the antenna performance enhancement by employing electromagnetic band gap (EBG) structures as the substrate of the antenna operating around 11 GHz, that suppress the surface waves and help the whole field to radiate by patch. Three different bandgap structures like mushroom EBG, partial substrate removal and grid EBG have been designed and investigated for their bandgap characteristics and their results has been compared. Among all these EBG structures, the partial substrate removal technique is most simple to implement but gain improvement is less as compare to others. On other hand the mushroom EBG gives maximum gain improvement but its design and incorporation as an antenna substrate is most complex among them. Grid type EBG shows good gain improvement and also quite simple and easy to implement.
Efficient and Reusable Sorbents Based on Nanostructured BN Coatings for Water Treatment from Antibiotics (2022)

Increasing contamination of wastewater with antibiotics used in agriculture, animal husbandry, and medicine is a serious problem for all living things. To address this important issue, we have developed an efficient platform based on a high specific surface area hexagonal boron nitride (BN) coating formed by numerous nanopetals and nanoneedles. The maximum sorption capacity of 1 × 1 cm<sup>2</sup> BN coatings is 502.78 µg/g (tetracycline, TET), 315.75 µg/g (ciprofloxacin, CIP), 400.17 µg/g (amoxicillin, AMOX), and 269.7 µg/g (amphotericin B, AMP), which exceeds the sorption capacity of many known materials. Unlike nanoparticles, BN-coated Si wafers are easy to place in and remove from antibiotic-contaminated aqueous solutions, and are easy to clean. When reusing the adsorbents, 100% efficiency was observed at the same time intervals as in the first cleaning cycle: 7 days (TET) and 14 days (CIP, AMOX, AMP) at 10 µg/mL, 14 days (TET, CIP, and AMOX) and 28 days (AMP) at 50 µg/mL, and 14 days (TET) and 28 days (CIP, AMOX and AMP) at 100 µg/mL. The results obtained showed that TET and CIP are best adsorbed on the surface of BN, so TET was chosen as an example for further theoretical modeling of the sorption process. It was found that adsorption is the main mechanism, and this process is spontaneous and endothermic. This highlights the importance of a high specific surface area for the efficient removal of antibiotics from aqueous solutions.
Congestion-Aware Routing, Rebalancing, and Charging Scheduling for Electric Autonomous Mobility-on-Demand System (2021)

In this paper, we investigate the problem of routing, rebalancing, and charging for electric autonomous mobility-on-demand systems concerning traffic congestion. We analyze the problem at the macroscopical level and use a volume-delay function to capture traffic congestion. To address this problem, we first formulate an optimization problem for routing and rebalancing. Then, we present heuristic algorithms to find the loop of the traffic flow and examine the energy constraints within the resulting loop. We impose charging constraints on the re-routing problem so that the new solution satisfies the energy constraint. Finally, we verify the effectiveness of our method through simulation.