gebhart/patrepeval huggingface dataset:
Supplementary Figure 6 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer (2023)

&lt;p&gt;Validation of tumor fraction confidence interval and effects of biological variability on tumor fraction inference. (A) Confidence intervals inferred from simulated data were aggregated into coverage probability for each condition and compared against theoretical coverage probability of 95% (see Methods). (B) Biological variability of clonal evolution loss was simulated by removing tumor evidence from a fraction of the fingerprint panel. Tumor fraction was calculated for simulated and original samples for comparison.&lt;/p&gt;
Influence of Quercetin and Its Methylglyoxal Adducts on the Formation of α-Dicarbonyl Compounds in a Lysine/Glucose Model System (2017)

Increasing evidence has identified α-dicarbonyl compounds, the reactive intermediates generated during Maillard reaction, as the potential factors to cause protein glycation and the development of chronic diseases. Therefore, there is an urgent need to decrease the levels of reactive dicarbonyl compounds in foods. In this study, we investigated the inhibitory effect of quercetin, a major dietary flavonoid, and its major mono- and di-MGO adducts on the formation of dicarbonyl compounds, such as methylglyoxal (MGO) and glyoxal (GO), in a lysine/glucose aqueous system, a model system to reflect the Maillard reaction in food process. Our result indicated that quercetin could efficiently inhibit the formation of MGO and GO in a time-dependent manner. Further mechanistic study was conducted by monitoring the formation of quercetin oxidation and conjugation products using LC-MS/MS. Quercetin MGO adducts, quercetin quinones, and the quinones of quercetin MGO adducts were detected in the system, indicating quercetin plays a dual role in inhibiting the formation of MGO and GO by scavenging free radicals generated in the system and trapping of MGO and GO to form MGO adducts. In addition, we prepared the mono- and di-MGO quercetin adducts and investigated their antioxidant activity and trapping capacity of MGO and GO. Our results indicated that both mono- and di-MGO quercetin adducts could scavenge the DPPH radical in a dose-dependent manner with >40% DPPH scavenged by the MGO adducts at 10 μM, and the di-MGO quercetin adduct could further trap MGO to generate tri-MGO adducts. Therefore, we demonstrate for the first time that quercetin MGO adducts retain the antioxidant activity and trapping capacity of reactive dicarbonyl species.
The Incremental Maintenance of Transition Tour (2014)

While evolutionary development methodologies have become increasingly prevalent, incremental testing methods are lagging behind. Most traditional test generation algorithms – including the Transition Tour method – rebuild test sequences from scratch even if minimal changes to the system have been made. In the current paper we propose two incremental algorithms to update a Transition Tour test sequence after changes in a deterministic finite state machine model. Our solution uses existing information – the Eulerian graph of a previous version of the system and an Euler tour in it – to update the test cases of the system in response to modification. The first algorithm keeps an Eulerian graph up to date, while the second algorithm maintains an Euler tour in the augmented graph. Analytical and practical analyses show that our algorithms are very efficient in the case of changing specifications. We also demonstrate our methods through an example.
Laser nanosurgery of single microtubules reveals location-dependent depolymerization rates (2007)

In this study, 532-nm picosecond and 800-nm femtosecond lasers are used in combination with fluorescently labeled tubulin to further elucidate microtubule depolymerization and the effect lasers may have on the resulting depolymerization. Depolymerization rates of targeted single microtubules are dependent on location with respect to the nucleus. Microtubules located near the nucleus exhibit a significantly faster depolymerization rate when compared to microtubule depolymerization rates near the periphery of the cell. Microtubules cut with the femtosecond laser depolymerize at a slower rate than unirradiated controls (p=0.002), whereas those cut with the picosecond laser depolymerize at the same rate as unirradiated controls (p=0.704). Our results demonstrate the ability of both the picosecond and femtosecond lasers to cut individual microtubules. The differences between the two ablation results are discussed.
Leukemic challenge unmasks a requirement for PI3Kδ in NK cell–mediated tumor surveillance (2008)

Specific inhibitors of PI3K isoforms are currently evaluated for their therapeutic potential in leukemia. We found that BCR/ABL(+) human leukemic cells express PI3Kdelta and therefore explored its impact on leukemia development. Using PI3Kdelta-deficient mice, we define a dual role of PI3Kdelta in leukemia. We observed a growth-promoting effect in tumor cells and an essential function in natural killer (NK) cell-mediated tumor surveillance: Abelson-transformed PI3Kdelta-deficient cells induced leukemia in RAG2-deficient mice with an increased latency, indicating that PI3Kdelta accelerated leukemia progression in vivo. However, the absence of PI3Kdelta also affected NK cell-mediated tumor surveillance. PI3Kdelta-deficient NK cells failed to lyse a large variety of target cells because of defective degranulation, as also documented by capacitance recordings. Accordingly, transplanted leukemic cells killed PI3Kdelta-deficient animals more rapidly. As a net effect, no difference in disease latency in vivo was detected if both leukemic cells and NK cells lack PI3Kdelta. Other tumor models confirmed that PI3Kdelta-deficient mice succumbed more rapidly when challenged with T- or B-lymphoid leukemic or B16 melanoma cells. Thus, the action of PI3Kdelta in the NK compartment is as relevant to survival of the mice as the delayed tumor progression. This dual function must be taken into account when using PI3Kdelta inhibitors as antileukemic agents in clinical trials.
Growth Inhibition ofPseudomonas solanacearumby Substituted 3-Indolepropionic Acids and Related Compounds (1993)

Antibacterial Activities of Indole and Its Related Compounds against Pseudomonas solanacearum, IV. For Part III, see ref. 9 A variety of substituted 3-indolepropionic acids and related compounds were synthesized and their antibacterial activities were examined against Pseudomonas solanacearum. In most cases, substitution in the indole ring greatly reduced the antibacterial activity, but some compounds substituted at the 4 position could effectively suppress bacterial growth at a concentration higher than 25μg/ml.
Deep Learning for Fast Adaptive Beamforming (2019)

The real-time nature that makes diagnostic ultrasonography so appealing to clinicians imposes strong constraints on the computational complexity of image reconstruction algorithms. As such, these typically rely on traditional delay-and-sum beamforming, a low-complexity approach that unfortunately comes at the cost of reduced image quality as compared to more advanced and content-adaptive beamformers. Here, we propose a model-aware deep learning strategy to ultrasound image reconstruction, which leverages knowledge of minimum variance beamforming while exploiting the efficiency of deep neural networks. Our approach yields high quality images with strong contrast at real-time reconstruction rates. The neural network is trained using in vivo and simulated radio frequency channel data of a single plane wave transmit, and corresponding high-quality minimum-variance beamformed reconstructions. Performance is benchmarked using simulated acquisitions from the PICMUS [1] dataset, demonstrating the convincing generalizability and image quality of the proposed beamformer.
Huygens Excitation in Debye Media in the FDTD Method (2016)

The total-field/scattered-field method, also called the Huygens surface method, is a common method to enforce an incident wave in a finite-difference time domain grid filled with a vacuum. In this communication, it is shown that it can also be used in such dispersive media as the Debye media. The incident wave to be enforced on the Huygens surface is computed either by an analytical calculation in the general case or by means of the auxiliary grid technique in special cases. As in a vacuum, the leakage of energy outside the Huygens surface is lower than -40 dB with the analytical incident wave and it can be far lower with the auxiliary grid incident wave.
Learning Global Features for Coreference Resolution (2016)

There is compelling evidence that coreference prediction would benefit from modeling global information about entity-clusters. Yet, state-of-the-art performance can be achieved with systems treating each mention prediction independently, which we attribute to the inherent difficulty of crafting informative clusterlevel features. We instead propose to use recurrent neural networks (RNNs) to learn latent, global representations of entity clusters directly from their mentions. We show that such representations are especially useful for the prediction of pronominal mentions, and can be incorporated into an end-to-end coreference system that outperforms the state of the art without requiring any additional search.
Mobil methanol-to-gasoline process (1980)

This paper explains that 2 major concerns in the development of the methanol-to-gasoline (MTG) process are heat removal from the reactor and the formation of durene (1-,2-,4-,5-tetramethylbenzene). Conversion of methanol to gasoline is highly exothermic (about 1510-1740 kJ/kg of methanol converted) and the adiabatic temperature rise would be almost 600C. Within Mobil, 2 types of reactor configurations were adopted for development: an adiabatic fixed-bed and a fluid-bed reactor. The fixed-bed reactor is ready for immediate commercialization and is more suitable for smaller scale operation. The fluid-bed reactor is under development and possesses the following potential advantages over the fixed-bed reactor: reaction heat removal is simplified by using the superior heat transfer characteristics of a fluid bed; when coupled with alkylation, the fluid bed gives a higher gasoline yield than the fixed bed; and constant catalyst activity, gasoline selectivity, and gasoline quality can be maintained with the fluid-bed operation. Fixed-bed is cyclic.
Allosteric activators of muscarinic receptors as novel approaches for treatment of CNS disorders (2010)

Abstract Muscarinic acetylcholine receptors (mAChRs) represent exciting therapeutic targets for the treatment of multiple CNS disorders. The high degree of conservation of amino acids comprising the orthosteric acetylcholine (ACh) binding site between individual mAChR subtypes has hindered the development of subtype-selective compounds that bind to this site. As a result, many academic and industry researchers are now focusing on developing allosteric activators of mAChRs including both positive allosteric modulators (PAMs) and allosteric agonists. In the past 10 years major advances have been achieved in the discovery of allosteric ligands that possess much greater selectivity for individual mAChR subtypes when compared to previously developed orthosteric agents. These novel allosteric modulators of mAChRs may provide therapeutic potential for treatment of a number of CNS disorders such as Alzheimer’s disease and schizophrenia.
Shooting The Mountain At Hindman: August, 1979, and: Ring-Necked Snake (1980)

TWO POEMS Richard Hague Shooting The Mountain At Hindman: August, 1979 Uncle Dust has got his thunder up and roars at all the windows, rattling dishes in the Hindman Lunch, spilling the homemade stew. Sparking his nitro eyes, he rises yellow with the dawn and lights his diesel pipe. All day, he gnashes split pine roots, grows belly-fat on rock. Watch out: at night old Uncle Dust will lie down where he wants to: on the Hindman Hotel roof, on the gritty Court House steps, on the beds of Hindman girls. Watch out: the sleeping under Uncle Dust is deep. Ring-Necked Snake for Gurney Norman It was long shadows and light, that place, a patched landscape of windfall, rockface, and rattler, and we threw a board down on the downhill slant to sit on. Fire joined us then for pleasure in our smokingsmall fire, flaring like the quick glint of a reptile's eyes. Then we snaked out talking from the two far places that we were: 50 tongued county speaking to tongued county, landscape to landscape, life to life. And as you scratched a snake's track in a soft rock with your knife, I watched the copperheads of fallen leaves on lie still on our downward path. Then, return and silence earned, we stood and started back. We stepped across a wet patch, and in a half-filled footprint saw the ring-necked snake, no longer than a handspan, its back coal-dark, its belly smooth and pale, a root. A root: I named it, told you how the first I'd ever caught way up in Ohio was that kind. We held it. each and each, then let it go. But we'd had a proof of all we'd talked about up there, of a world that's common, shared, and in the ring-necked snake a name to give a piece of it that lived. Quiet, we lingered in familiar light to see it moving easily away, deep into the heartrock of that home-place we both had come to grow to. 51 ...
Frenkel defect process in amorphous silica (2011)

Point defects strongly influence optical properties of synthetic amorphous silica (synthetic a-SiO<sub>2</sub>) used in excimer laser photolithography and their properties are intensively studied. Decomposition of an Si-O-Si bond into a pair of oxygen vacancy and interstitial oxygen species is an intrinsic defect process in a-SiO<sub>2</sub>. It is similar to the creation of vacancy-interstitial pairs in crystalline materials and is regarded as "Frenkel defect process" in an amorphous material. Oxygens are also known to be emitted from a-SiO<sub>2</sub> surfaces under irradiation with vacuumultraviolet (VUV) light or electron beam. However, the anion part of the Frenkel pair in a-SiO<sub>2</sub>, interstitial oxygen atom, lacks reliable spectroscopic signatures. Therefore, Frenkel process has been studied much less than another intrinsic defect process in a-SiO<sub>2</sub>, a simple cleavage of an Si-O bond, yielding a pair of silicon and oxygen dangling bonds. Interstitial oxygen molecule (O2), a common form of the interstitial oxygen species in a-SiO<sub>2</sub>, exhibits characteristic infrared photoluminescence (PL) at 1272 nm. This PL band allows interstitial O<sub>2</sub> to be detected selectively with a high sensitivity, and is useful in studying Frenkel defect processes in both a-SiO2 and crystalline SiO<sub>2</sub>. The Frenkel process is dominant over the formation of the dangling bond pairs in highpurity synthetic a-SiO<sub>2</sub>. Both these processes are influenced by the degree of the structural disorder of a-SiO<sub>2</sub>characterized by distribution of Si-O-Si angles. Fluorine doping promotes the structural relaxation and is useful in decreasing the concentration of "strained" Si-O-Si bonds, which have Si-O-Si bond angles widely different from the relaxed angle and are vulnerable to radiation. Moderate fluorine doping is effective in improving both UV-VUV transparency and radiation hardness, whereas heavy fluorine doping tends to enhance defect processes involving the Frenkel mechanism and to degrade the radiation hardness.
Proteomics in uveal melanoma research: opportunities and challenges in biomarker discovery (2007)

Uveal melanoma (UM) is the most frequent primary intraocular tumor in adult humans. Despite the significant advances in diagnosis and treatment of UM in the last decades, the prognosis of UM sufferers is still poor. Metastatic liver disease is the leading cause of death in UM and can develop after a long disease-free interval, suggesting the presence of occult micrometastasis. Proteomics technology has opened new opportunities for elucidating the molecular mechanism of complex diseases, such as cancer. This article will review the recent developments in biomarker discovery for UM research by proteomics. In the last few years, the first UM proteomics-based analyses have been launched, yielding promising results. An update on recent developments on this field is presented.
<title>Data reduction procedure for principal cast and other talking head detection</title> (2001)

We describe a technique for reducing the data set for a technique for reducing the data set for principal cast and other taking head detection in broadcast news content using the spatial attributes of MPEG-7 Motion Activity descriptor. The fact that these descriptors are easy to extract from compressed domain and also work well when used for matching talking head sequences, motivated us to utilize them for rapidly pruning the data set for subsequent sophisticated face detection techniques. We are thus able to speed up the process of finding the principal cast from broadcast news content by reducing the number of segments on which computationally more expensive face detection and recognition is employed. We present the experimental results of two from the centroid of ground truth set and is computationally less expensive. The second clustering procedure is based on multiple templates, which are the mean feature vectors of the component Gaussians of a Gaussian Mixture Model (GMM) trained best to fit the training data. We are able to save 50% on computation measured in terms of number of rejected shots to total number of shots while missing 25% of talking head shots in the news program. We also observe that the second clustering procedure while being slightly computationally intensive allows for higher pruning factors with more accuracy.
Summary (1998)

The plasma membrane H(+)-ATPase in higher plants has been implicated in nutrient uptake, phloem loading, elongation growth and establishment of turgor. Although a C-terminal regulatory domain has been identified, little is known about the physiological factors involved in controlling the activity of the enzyme. To identify components which play a role in the regulation of the plant H(+)-ATPase, a fusicoccin responsive yeast expressing Arabidopsis plasma membrane H(+)-ATPase AHA2 was employed. By testing the fusicoccin binding activity of yeast membranes, the C-terminal regulatory domain of AHA2 was found to be part of a functional fusicoccin receptor, a component of which was the 14-3-3 protein. ATP hydrolytic activity of AHA2 expressed in yeast internal membranes was activated by all tested isoforms of the 14-3-3 protein of yeast and Arabidopsis, but only in the presence of fusicoccin, and activation was prevented by a phosphoserine peptide representing a known 14-3-3 protein binding motif in Raf-1. The results demonstrate that the 14-3-3 protein is an activator molecule of the H(+)-ATPase and provides the first evidence of a protein involved in activation of plant plasma membrane H(+)-ATPase.
Model coordination-based decentralized control of composite multivariable system (2009)

Consideration was given to the model coordination-based decentralized control of a system of MIMO subsystems for each of which a reference model of response to the input action is defined. Weakened—as compared with what is known from the literature—existence conditions were determined for solution and analytical description of the control laws of local controllers assuring for all local subsystems the desired transfer matrices of forced output motion. At that, tracking of the reference models is related with realization of a collection of precompensators defined by the resulting formulas and does not constrain the choice of feedbacks of each subsystem. A numerical example was given.
Pojazdy autonomiczne jako ułatwienie mobilności kierowców z niepełnosprawnością (2018)

Mobilność osób z niepełnosprawnością jest ważnym zagadnieniem cywilizacyjnym. W celu ułatwienia prowadzenia pojazdu osobie z niepełnosprawnością konieczne jest odpowiednie przygotowanie samochodu. Rozwiązania takie koncentrują się dotychczas na ułatwieniu wsiadania i wysiadania osoby z samochodu oraz na pomocy w obsłudze urządzeń sterujących pojazdem. Pomimo imponującego rozwoju nauki i techniki w tym względzie, wciąż prowadzenie samochodu przez osobę z niepełnosprawnością bywa trudne, uciążliwe lub niemożliwe. Dlatego istnieje potrzeba ciągłego poszukiwania nowych rozwiązań. Jednym z całkowicie innowacyjnych kierunków rozwoju jest wykorzystanie samochodów o częściowej autonomizacji ruchu. Celem artykułu jest omówienie podstawowych zagadnień związanych z wykorzystaniem pojazdów autonomicznych. Zostaną tu rozważone poszczególne poziomy autonomiczności w kontekście różnych typów dysfunkcji motorycznych kierowców z niepełnosprawnościami. Wydaje się, że rozwój pojazdów z automatycznym systemem sterowania może być krokiem milowym w kwestii mobilności osób z niepełnosprawnościami, ponieważ funkcje motoryczne, które dotychczas pozwalały na pokonywanie jedynie krótkich tras i wiązały się z dużym wysiłkiem, teraz umożliwią jazdę międzymiastową. Obecny stan rozwoju samochodów autonomicznych jest doskonałym momentem na wykorzystanie potencjału pojazdów autonomicznych dla osób z niepełnosprawnościami, kreując tym samym ich szczególne zastosowanie.
Service-oriented SCADA and MES supporting Petri nets based orchestrated automation systems (2012)

The fusion of mechatronics, communication, control and information technologies has allowed the introduction of new automation paradigms into the production environment. The virtualization of the production environment facilitated by the application of the service-oriented architecture paradigm is one of major outcomes of that fusion. On one side, service-oriented automation works based on exposition, subscription and use of automation functions represented by e.g. web services. On the other side, the evolution of traditional industrial systems, particularly in the production area, as a response to architectural and behavioural (functional) viewpoints of the ISA95 enterprise architecture, where a close inter-relation between SCADA, DCS and MES systems facilitate the management and control of the production environment. Automation functions are increasingly performed by the composition and orchestration of services. Among other methods, the application of formal Petri net based orchestration approaches is being industrially established. This paper presents the major characteristics that such a Petri net based orchestration presents when it is developed, implemented and deployed in an industrial environment.