gebhart/patrepeval huggingface dataset:
A modified Lax-Wendroff correction for wave propagation in media described by Zener elements (1997)

A modified Lax-Wendroff correction for wave propagation in attenuating and dispersive media described by Zener elements is presented. As opposed to the full correction, this new technique is explicit and offers large computational savings. The technique may be applied to a wide variety of hyperbolic problems. Here, the concept is illustrated for wave propagation in visco-acoustic media.
Stochastic Cubic Regularization for Fast Nonconvex Optimization (2017)

This paper proposes a stochastic variant of a classic algorithm---the cubic-regularized Newton method [Nesterov and Polyak 2006]. The proposed algorithm efficiently escapes saddle points and finds approximate local minima for general smooth, nonconvex functions in only $\mathcal{\tilde{O}}(ε^{-3.5})$ stochastic gradient and stochastic Hessian-vector product evaluations. The latter can be computed as efficiently as stochastic gradients. This improves upon the $\mathcal{\tilde{O}}(ε^{-4})$ rate of stochastic gradient descent. Our rate matches the best-known result for finding local minima without requiring any delicate acceleration or variance-reduction techniques.
Scanning probe surface modification (1993)

Nanometer‐scale manipulation of surfaces by scanning probe devices has expanded amazingly since the first reports in the mid‐1980s. General approaches to scanning probe microscope induced surface patterning are discussed. The Figure shows a scanning electron micrograph of an STM‐defined pattern of a HS(CH 2 ) 17 CH 3 monolayer resist on a Au(111) substrate. magnified image
Experimental Study of Particle Structuring in Vertical Stratifying Films from Latex Suspensions (1997)

Two independent interference methods, based on wavelength and intensity measurements, are applied to establish the type of packing of latex particles contained within vertical stratifying films. The films are formed in a ring-shaped frame after its pulling out from a latex suspension. They exhibit a stepwise profile, which appears as a set of parallel stripes of uniform intensity varying from stripe to stripe. Both interference methods allow a study of the stratification phenomenon “in vivo”, i.e. during the process of film drainage. To fit the data from each of these two methods, we assume a given type of particle packing, in our case hexagonal or tetragonal, and then we check which type is consistent with the data. In all cases the data indicate the presence of hexagonal packing and do not agree with tetragonal packing. The developed technique can be further applied to examine the particle structuring in stratifying films containing smaller particles, such as surfactant micelles or protein globules. The results can be helpful for a deeper understanding of the stratification phenomenon and the underlying oscillatory structural forces.
Dispersion, adsorption and retardation effects of phosphonated small molecule superplasticisers in cement hydration (2018)

A series of phosphonated small molecule superplasticisers were synthesised by the Mannich reaction of functionalised amines with formaldehyde and phosphonic acid. Their chemical structures and molecular weights were determined by 1 H nuclear magnetic resonance and size exclusion chromatography, respectively. Their dispersion ability, adsorption behaviour and retardation effect in cement hydration were investigated. Results of the cement paste tests indicated that the phosphonated small molecule superplasticisers with longer polyether chain and fewer phosphonate groups exhibited better initial water-reducing ability but weaker retarding ability, and those with shorter polyether chain and more phosphonate groups turned out to be more effective in slump-retaining ability and retarding ability. These findings provide useful information for optimising the performance of phosphonated small molecule chemical admixtures in the future.
Nonthermal Intramolecular Vibrational Energy Distribution in Infrared-Multiphoton-Excited CF2Cl2 (1987)

The intramolecular vibrational energy distribution of infrared-multiphoton-excited C${\mathrm{F}}_{2}$${\mathrm{Cl}}_{2}$ molecules is studied with time-resolved spontaneous Raman scattering. The time evolution of the signals from three vibrational modes is studied up to 600 ns after excitation, and in the presence of ${\mathrm{N}}_{2}$ buffer gas. Following collisionless infrared multiphoton excitation a nonthermal distribution of vibrational energy is observed. This nonequilibrium distribution persists up to high levels of vibrational excitation, with at least 10 000 ${\mathrm{cm}}^{\ensuremath{-}1}$ in three out of the nine vibrational modes.
Crystal structure of UDP-glucose:anthocyanidin 3-O-glucosyltransferase fromClitoria ternatea (2013)

Flowers of the butterfly pea (Clitoria ternatea) accumulate a group of polyacylated anthocyanins, named ternatins, in their petals. The first step in ternatin biosynthesis is the transfer of glucose from UDP-glucose to anthocyanidins such as delphinidin, a reaction catalyzed in C. ternatea by UDP-glucose:anthocyanidin 3-O-glucosyltransferase (Ct3GT-A; AB185904). To elucidate the structure-function relationship of Ct3GT-A, recombinant Ct3GT-A was expressed in Escherichia coli and its tertiary structure was determined to 1.85 Å resolution by using X-ray crystallography. The structure of Ct3GT-A shows a common folding topology, the GT-B fold, comprised of two Rossmann-like β/α/β domains and a cleft located between the N- and C-domains containing two cavities that are used as binding sites for the donor (UDP-Glc) and acceptor substrates. By comparing the structure of Ct3GT-A with that of the flavonoid glycosyltransferase VvGT1 from red grape (Vitis vinifera) in complex with UDP-2-deoxy-2-fluoro glucose and kaempferol, locations of the catalytic His-Asp dyad and the residues involved in recognizing UDP-2-deoxy-2-fluoro glucose were essentially identical in Ct3GT-A, but certain residues of VvGT1 involved in binding kaempferol were found to be substituted in Ct3GT-A. These findings are important for understanding the differentiation of acceptor-substrate recognition in these two enzymes.
Lithium Hexamethyldisilazide-Mediated Enolization of Highly Substituted Aryl Ketones: Structural and Mechanistic Basis of the E/Z Selectivities (2017)

Enolizations of highly substituted acyclic ketones used in the syntheses of tetrasubstituted olefin-based anticancer agents are described. Lithium hexamethyldisilazide (LiHMDS)-mediated enolizations are moderately Z-selective in neat tetrahydrofuran (THF) and E-selective in 2.0 M THF/hexane. The results of NMR spectroscopy show the resulting enolates to be statistically distributed ensembles of E,E-, E,Z-, and Z,Z-enolate dimers with subunits that reflect the selectivities. The results of rate studies trace the preference for E and Z isomers to tetrasolvated- and pentasolvated-monomer-based transition structures, respectively. Enolization using LiHMDS in N,N-dimethylethylamine or triethylamine in toluene affords a 65:1 mixture of LiHMDS-lithium enolate mixed dimers containing E and Z isomers, respectively. Spectroscopic studies show that condition-dependent complexation of ketone to LiHMDS occurs in trialkylamine/toluene. Rate data attribute the high selectivity exclusively to monosolvated-dimer-based transition structures.
Fluorescence-based tracing of transplanted intestinal epithelial cells using confocal laser endomicroscopy (2019)

Abstract Background Intestinal stem cell transplantation has been shown to promote mucosal healing and to engender fully functional epithelium in experimental colitis. Hence, stem cell therapies may provide an innovative approach to accomplish mucosal healing in patients with debilitating conditions such as inflammatory bowel disease. However, an approach to label and trace transplanted cells, in order to assess engraftment efficiency and to monitor wound healing, is a key hurdle to overcome prior to initiating human studies. Genetic engineering is commonly employed in animal studies, but may be problematic in humans due to potential off-target and long-term adverse effects. Methods We investigated the applicability of a panel of fluorescent dyes and nanoparticles to label intestinal organoids for visualization using the clinically approved imaging modality, confocal laser endomicroscopy (CLE). Staining homogeneity, durability, cell viability, differentiation capacity, and organoid forming efficiency were evaluated, together with visualization of labeled organoids in vitro and ex vivo using CLE. Results 5-Chloromethylfluorescein diacetate (CMFDA) proved to be suitable as it efficiently stained all organoids without transfer to unstained organoids in co-cultures. No noticeable adverse effects on viability, organoid growth, or stem cell differentiation capacity were observed, although single-cell reseeding revealed a dose-dependent reduction in organoid forming efficiency. Labeled organoids were easily identified in vitro using CLE for a duration of at least 3Â days and could additionally be detected ex vivo following transplantation into murine experimental colitis. Conclusions It is highly feasible to use fluorescent dye-based labeling in combination with CLE to trace intestinal organoids following transplantation to confirm implantation at the intestinal target site.
Novel dry powder preparations of whole inactivated influenza virus for nasal vaccination (2020)

The purpose of these studies was to enhance mucosal and systemic antibody production in response to increased local residence time of a whole inactivated influenza virus administered as a dry powder nasal vaccine formulation. Spray-freeze-drying (SFD) particles suitable for nasal delivery were characterized for physico-chemical properties and stability. Mucoadhesive compounds (MA) were characterized for their effects on nasal residence time of vaccine powders in rats compared with published in vitro data and elicited immune responses. SFD particles (D50=26.9µm) were spherical with a specific surface area of 1.25 m2/g. Thermal analysis indicated SFD powders were amorphous and demonstrated improved stability with respect to liquid formulations under various storage conditions. In vitro physico-chemical studies and in vivo scintigraphic imaging experiments indicated sodium alginate (SA) and carboxymethylcellulose-high molecular weight (CMC-HMW) powder formulations most significantly increased residence time in Brown Norway rats. Intramuscular delivery provided equivalent serum antibody titers to intranasal (IN) powder without MA, in the presence of CMC-HMW, SA, and hydroxypropyl methylcellulose (HPMC-HMW) after initial dosing and all formulations except IN powder with chitosan after boosting. IN liquid provided equivalent serum antibody titers to all IN powders after the initial vaccination and significantly greater serum antibody titers than IN powder with chitosan after boosting. Trends were consistent between residence time studies and immune response; however, no statistically significant differences between powder and liquid formulations were observed. It was concluded that enhanced serum and mucosal antibody responses were elicited by a dry powder nasal vaccine, specifically, administered in the presence of sodium alginate.
5G New Radio for Automotive, Rail, and Air Transport (2021)

The recent and upcoming releases of the 3rd Generation Partnership Project's 5G New Radio (NR) specifications include features that are motivated by providing connectivity services to a broad set of verticals, including the automotive, rail, and air transport industries. Currently, several radio access network features are being further enhanced or newly introduced in NR to improve 5G's capability to provide fast, reliable, and non-limiting connectivity for transport applications. In this article, we review the most important characteristics and requirements of a wide range of services that are driven by the desire to help the transport sector to become more sustainable, economically viable, safe, and secure. These requirements will be supported by the evolving and entirely new features of 5G NR systems, including accurate positioning, reference signal design to enable multi-transmission and reception points, and service quality prediction.
Neurovascular Unit: Basic and Clinical Imaging with Emphasis on Advantages of Ferumoxytol (2017)

Physiological and pathological processes that increase or decrease the central nervous system's need for nutrients and oxygen via changes in local blood supply act primarily at the level of the neurovascular unit (NVU). The NVU consists of endothelial cells, associated blood-brain barrier tight junctions, basal lamina, pericytes, and parenchymal cells, including astrocytes, neurons, and interneurons. Knowledge of the NVU is essential for interpretation of central nervous system physiology and pathology as revealed by conventional and advanced imaging techniques. This article reviews current strategies for interrogating the NVU, focusing on vascular permeability, blood volume, and functional imaging, as assessed by ferumoxytol an iron oxide nanoparticle.
Single-switch zero-voltage-switching high power factor electronic ballast (2003)

This paper introduces two modified Class E circuits to achieve low crest factor of lamp current. By integrating flyback topology with Class E converter, the modified circuits can achieve improved lamp current crest factor, and still maintain high power factor and zero-voltage-switching features in conventional Class E converter. Simulation and experimental results are presented to verify the theoretical operation.
Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies (2020)

Tankyrase enzymes (TNKS), a core part of the canonical Wnt pathway, are a promising target in the search for potential anti-cancer agents. Although several hundreds of the TNKS inhibitors are currently known, identification of their novel chemotypes attracts considerable interest. In this study, the molecular docking and machine learning-based virtual screening techniques combined with the physico-chemical and ADMET (absorption, distribution, metabolism, excretion, toxicity) profile prediction and molecular dynamics simulations were applied to a subset of the ZINC database containing about 1.7 M commercially available compounds. Out of seven candidate compounds biologically evaluated in vitro for their inhibition of the TNKS2 enzyme using immunochemical assay, two compounds have shown a decent level of inhibitory activity with the IC<sub>50</sub> values of less than 10 nM and 10 μM. Relatively simple scores based on molecular docking or MM-PBSA (molecular mechanics, Poisson-Boltzmann, surface area) methods proved unsuitable for predicting the effect of structural modification or for accurate ranking of the compounds based on their binding energies. On the other hand, the molecular dynamics simulations and Free Energy Perturbation (FEP) calculations allowed us to further decipher the structure-activity relationships and retrospectively analyze the docking-based virtual screening performance. This approach can be applied at the subsequent lead optimization stages.
[Development of the thymus and immune system]. (2011)

A repertoire of T cells is primarily formed in the thymus through positive and negative selection of developing thymocytes. The medullary region of the thymus provides a microenvironment that is essential for the establishment of self-tolerance via the depletion of self-reactive T cells and the production of regulatory T cells. Within the medullary microenvironment, medullary thymic epithelial cells play a pivotal role in the establishment of self-tolerance, via the promiscuous expression of tissue-restricted self-antigens and the chemokine-mediated attraction of positively selected T cells from the cortex to the medulla. Positive selection also induces the expression of TNF-superfamily cytokines and thereby nurtures the growth and development of medullary thymic epithelial cells. We will review the mechanisms of how the thymus contributes to the development and selection of T cells, with emphasis on the establishment of self-tolerance in the thymic medulla.
Porous photonic crystal external cavity laser biosensor (2016)

We report the design, fabrication, and testing of a photonic crystal (PC) biosensor structure that incorporates a porous high refractive index TiO<sub>2</sub> dielectric film that enables immobilization of capture proteins within an enhanced surface-area volume that spatially overlaps with the regions of resonant electromagnetic fields where biomolecular binding can produce the greatest shifts in photonic crystal resonant wavelength. Despite the nanoscale porosity of the sensor structure, the PC slab exhibits narrowband and high efficiency resonant reflection, enabling the structure to serve as a wavelength-tunable element of an external cavity laser. In the context of sensing small molecule interactions with much larger immobilized proteins, we demonstrate that the porous structure provides 3.7× larger biosensor signals than an equivalent nonporous structure, while the external cavity laser (ECL) detection method provides capability for sensing picometer-scale shifts in the PC resonant wavelength caused by small molecule binding. The porous ECL achieves a record high figure of merit for label-free optical biosensors.
An Improved Relative Self-Attention Mechanism for Transformer with Application to Music Generation (2018)

Music relies heavily on self-reference to build structure and meaning. We
explore the Transformer architecture (Vaswani et al., 2017) as a generative
model for music, as self-attention has shown compelling results on tasks that
require long-term structure such as Wikipedia summary generation (Liu et al,
2018). However, timing information is critical for polyphonic music, and
Transformer does not explicitly model absolute or relative timing in its
structure. To address this challenge, Shaw et al. (2018) introduced relative
position representations to self-attention to improve machine translation.
However, the formulation was not scalable to longer sequences. We propose an
improved formulation which reduces the memory requirements of the relative
position computation from $O(l^2d)$ to $O(ld)$, making it possible to train
much longer sequences and achieve faster convergence. In experiments on
symbolic music we find that relative self-attention substantially improves
sample quality for unconditioned generation and is able to generate sequences
of lengths longer than those from the training set. When primed with an initial
sequence, the model generates continuations that develop the prime coherently
and exhibit long-term structure. Relative self-attention can be instrumental in
capturing richer relationships within a musical piece.
Data from A Phase I Trial of a Guadecitabine (SGI-110) and Irinotecan in Metastatic Colorectal Cancer Patients Previously Exposed to Irinotecan (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Chemotherapeutic resistance eventually develops in all patients with metastatic colorectal cancer (mCRC). Gene silencing through promoter demethylation is one potential reversible mechanism of resistance with administration of hypomethylating agents. We evaluated the safety and tolerability of guadecitabine and irinotecan in patients with mCRC previously treated with irinotecan.&lt;/p&gt;Patients and Methods:&lt;p&gt;In this 3+3 dose-escalation study, patients with mCRC previously exposed to irinotecan received guadecitabine days 1 to 5 of a 28-day cycle and irinotecan 125 mg/m&lt;sup&gt;2&lt;/sup&gt; days 8 and 15 [dose level (DL) 1, guadecitabine 45 mg/m&lt;sup&gt;2&lt;/sup&gt;; DL −1: guadecitabine 30 mg/m&lt;sup&gt;2&lt;/sup&gt;; DL −1G: guadecitabine 30 mg/m&lt;sup&gt;2&lt;/sup&gt; with growth factor support (GFS); DL 1G: guadecitabine 45 mg/m&lt;sup&gt;2&lt;/sup&gt; with GFS].&lt;/p&gt;Results:&lt;p&gt;Twenty-two patients were treated across four DLs. Dose-limiting toxicities were neutropenic fever (DL 1 and −1G), biliary drain infection (DL −1), colonic obstruction (DL −1), and severe dehydration (DL 1G). Most common toxicities were neutropenia (82% any grade, 77% Grade 3/4), neutropenic fever (23%), leukopenia (73% any grade, 50% Grade 3/4), and injection site reactions (64% total, 0% Grade 3/4). Patients received a median of 4.5 cycles of treatment; 12/17 evaluable patients had stable disease as best response, with one having initial disease progression but subsequently durable partial response. Circulating tumor DNA showed decrease in global demethylation by LINE-1 after treatment.&lt;/p&gt;Conclusions:&lt;p&gt;We report the first study of chemo-priming with epigenetic therapy in gastrointestinal cancers. Guadecitabine 45 mg/m&lt;sup&gt;2&lt;/sup&gt; and irinotecan 125 mg/m&lt;sup&gt;2&lt;/sup&gt; with GFS was safe and tolerable in patients with mCRC, with early indication of benefit. These data have provided the basis for an ongoing phase II randomized, multicenter trial.&lt;/p&gt;&lt;/div&gt;
Adaptive Intermediate Representations for Video Understanding (2021)

A common strategy to video understanding is to incorporate spatial and motion information by fusing features derived from RGB frames and optical flow. In this work, we introduce a new way to leverage semantic segmentation as an intermediate representation for video understanding and use it in a way that requires no additional labeling. Second, we propose a general framework which learns the intermediate representations (optical flow and semantic segmentation) jointly with the final video understanding task and allows the adaptation of the representations to the end goal. Despite the use of intermediate representations within the network, during inference, no additional data beyond RGB sequences is needed, enabling efficient recognition with a single network. Finally, we present a way to find the optimal learning configuration by searching the best loss weighting via evolution. We obtain more powerful visual representations for videos which lead to performance gains over the state-of-the-art.
Comparative analysis between endometrial proteomes of pregnant and non-pregnant ewes during the peri-implantation period (2015)

These analysis imply that dysfunction of these biological processes or pathways of DEP in the endometrium is highly associated with early pregnancy loss. In addition, many proteins that are essential for the establishment of pregnancy showed dysregulation in the endometrium of non-pregnant ewes. These proteins, as potential candidates, may contribute to early pregnancy loss.
Endurance-based Dynamic V<inf>TH</inf>Distribution Shaping of 3D-TLC NAND Flash Memories to Suppress Both Lateral Charge Migration and Vertical Charge De-trap and Increase Data-retention Time by 2.7x (2018)

Lateral charge migration and vertical charge detrap degrade the reliability of 3D-Triple-Level Cell (TLC) NAND flash. Lateral charge migration is dominant at the low write/erase (W/E) endurance and vertical charge de-trap is dominant at the high endurance. Conventional techniques address only one of these problems. This paper proposes Endurance-based Dynamic V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</sub> Distribution Shaping (DVDS) to suppress both errors at a wide range of the endurance. At low (1) and high (2k) endurance, measured errors decrease by 27% and 20% and measured acceptable data-retention time increases by 1.7x and 2.7x, respectively.