gebhart/patrepeval huggingface dataset:
The Interaction and Colocalization of Sam68 with the Splicing-associated Factor YT521-B in Nuclear Dots Is Regulated by the Src Family Kinase p59fyn (1999)

Alternative pre-mRNA splicing patterns can change an extracellular stimulus, but the signaling pathways leading to these changes are still poorly characterized. Here, we describe a tyrosine-phosphorylated nuclear protein, YT521-B, and show that it interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. Northern blot analysis demonstrated ubiquitous expression, but detailed RNA in situ analysis revealed cell type specificity in the brain. YT521-B protein is localized in the nucleoplasm and concentrated in 5-20 large nuclear dots. Deletion analysis demonstrated that the formation of these dots depends on the presence of the amino-terminal glutamic acid-rich domain and the carboxyl-terminal glutamic acid/arginine-rich region. We show that the latter comprises an important protein-protein interaction domain. The Src family kinase p59(fyn)-mediated tyrosine phosphorylation of Sam68 negatively regulates its association with YT521-B, and overexpression of p59(fyn) dissolves nuclear dots containing YT521-B. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. Together, our data indicate that YT521-B and Sam68 may be part of a signal transduction pathway that influences splice site selection.
Verification of a Monte Carlo dose calculation engine in proton minibeam radiotherapy in a passive scattering beamline for preclinical trials (2019)

This is the first Monte Carlo dose engine for pMBRT that is being used to guide preclinical trials in a clinical proton therapy centre.
ICN "Begin-End" Hop by Hop Fragmentation (2016)

This document describes a simple hop-by-hop fragmentation scheme for
ICN and mappings to the CCNx 1.0 and NDN packet formats, called
begin-end fragmentation. This scheme may be used at Layer 3 when ICN
packets are used natively over a Layer 2 media which does not reorder
packets.
Prospects for Theranostics in Neurosurgical Imaging: Empowering Confocal Laser Endomicroscopy Diagnostics via Deep Learning (2018)

Confocal laser endomicroscopy (CLE) is an advanced optical fluorescence imaging technology that has potential to increase intraoperative precision, extend resection, and tailor surgery for malignant invasive brain tumors because of its subcellular dimension resolution. Despite its promising diagnostic potential, interpreting the gray tone fluorescence images can be difficult for untrained users. CLE images can be distorted by motion artifacts, fluorescence signals out of detector dynamic range, or may be obscured by red blood cells, and thus interpreted as nondiagnostic (ND). However, just a single CLE image with a detectable pathognomonic histological tissue signature can suffice for intraoperative diagnosis. Dealing with the abundance of images from CLE is not unlike sifting through a myriad of genes, proteins, or other structural or metabolic markers to find something of commonality or uniqueness in cancer that might indicate a potential treatment scheme or target. In this review, we provide a detailed description of bioinformatical analysis methodology of CLE images that begins to assist the neurosurgeon and pathologist to rapidly connect on-the-fly intraoperative imaging, pathology, and surgical observation into a conclusionary system within the concept of theranostics. We present an overview and discuss deep learning models for automatic detection of the diagnostic CLE images and discuss various training regimes and ensemble modeling effect on power of deep learning predictive models. Two major approaches reviewed in this paper include the models that can automatically classify CLE images into diagnostic/ND, glioma/nonglioma, tumor/injury/normal categories, and models that can localize histological features on the CLE images using weakly supervised methods. We also briefly review advances in the deep learning approaches used for CLE image analysis in other organs. Significant advances in speed and precision of automated diagnostic frame selection would augment the diagnostic potential of CLE, improve operative workflow, and integration into brain tumor surgery. Such technology and bioinformatics analytics lend themselves to improved precision, personalization, and theranostics in brain tumor treatment.
Synthesis and Structure–Activity Relationship of Tetra-Substituted Cyclohexyl Diol Inhibitors of Proviral Insertion of Moloney Virus (PIM) Kinases (2020)

Overexpression of PIM 1, 2, and 3 kinases is frequently observed in many malignancies. Previously, we discovered a potent and selective pan-PIM kinase inhibitor, compound <b>2</b>, currently in phase I clinical trials. In this work, we were interested in replacing the amino group on the cyclohexane ring in compound <b>2</b> with a hydroxyl group. Structure-based drug design led to cellularly potent but metabolically unstable tetra-substituted cyclohexyl diols. Efforts on the reduction of Log D by introducing polar heterocycles improved metabolic stability. Incorporating fluorine to the tetra-substituted cyclohexyl diol moiety further reduced Log D, resulting in compound <b>14</b>, a cellularly potent tetra-substituted cyclohexyl diol inhibitor with moderate metabolic stability and good permeability. We also describe the development of efficient and scalable synthetic routes toward synthetically challenging tetra-substituted cyclohexyl diol compounds. In particular, intermediate <b>36</b> was identified as a versatile intermediate, enabling a large-scale synthesis of highly substituted cyclohexane derivatives.
Restoration of metabolic functional metrics from label-free, two-photon cervical tissue images using multiscale deep-learning-based denoising algorithms (2023)

Label-free, two-photon imaging captures morphological and functional metabolic tissue changes and enables enhanced understanding of numerous diseases. However, this modality suffers from low signal arising from limitations imposed by the maximum permissible dose of illumination and the need for rapid image acquisition to avoid motion artifacts. Recently, deep learning methods have been developed to facilitate the extraction of quantitative information from such images. Here, we employ deep neural architectures in the synthesis of a multiscale denoising algorithm optimized for restoring metrics of metabolic activity from low-SNR, two-photon images. Two-photon excited fluorescence (TPEF) images of reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavoproteins (FAD) from freshly excised human cervical tissues are used. We assess the impact of the specific denoising model, loss function, data transformation, and training dataset on established metrics of image restoration when comparing denoised single frame images with corresponding six frame averages, considered as the ground truth. We further assess the restoration accuracy of six metrics of metabolic function from the denoised images relative to ground truth images. Using a novel algorithm based on deep denoising in the wavelet transform domain, we demonstrate optimal recovery of metabolic function metrics. Our results highlight the promise of denoising algorithms to recover diagnostically useful information from low SNR label-free two-photon images and their potential importance in the clinical translation of such imaging.
Testing the relation of a spin gap to superconductivity in the copper oxides (1996)

In the hope of demonstrating the influence of a spin gap on the transport properties in underdoped cuprates, it has been suggested that the opening of a spin gap at ${\mathit{T}}_{\mathit{s}}$ may correlate with a change at ${\mathit{T}}_{\mathit{D}}$ in the slope of the a-axis resistivity versus temperature observed in a ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{4}$${\mathrm{O}}_{8}$ crystal. Comparison of ${\mathrm{\ensuremath{\rho}}}_{\mathit{a}}$ in ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{4}$${\mathrm{O}}_{8}$ with ${\mathrm{\ensuremath{\rho}}}_{\mathit{a}}$ in a fully oxygenated, twin-free ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$ crystal leads to the conclusion that ${\mathit{T}}_{\mathit{D}}$ has little to do with the opening of a spin gap, but it might be correlated with a change in the c-axis coupling in ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{4}$${\mathrm{O}}_{8}$ and ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$. \textcopyright{} 1996 The American Physical Society.
Real-time wireless monitoring of workpiece material and debris characteristics in micro-electro-discharge machining (2008)

Wireless signals are generated with each discharge in micro-electro-discharge machining (muEDM), providing an opportunity to directly monitor discharge quality. Unlike traditional methods of monitoring progress in machining, which rely on electrical characteristics at the discharge supply terminals, this method is less affected by parasitics. The depth location of a metal-metal interface can be distinguished in the wireless signal. This is useful for determining the stop depth in certain processes. For example, in machining through samples of stainless steel into an electroplated Cu backing layer, a 10 dBm change in wireless signal strength for the 300-350 MHz band and a 5 dBm average change across the full 1 GHz bandwidth defined the transition. As debris accumulate in the discharge gaps, shifts in the wireless spectra can also indicate spurious discharges that could damage workpiece and tool. For example, when copper micromachining became debris dominated, the 800-850 MHz band dropped 4 dBm in signal strength with a 2.2 dBm average drop across the full 1 GHz bandwidth.
Brotli (2018)

Brotli is an open source general-purpose data compressor introduced by Google in late 2013 and now adopted in most known browsers and Web servers. It is publicly available on GitHub and its data format was submitted as RFC 7932 in July 2016. Brotli is based on the Lempel-Ziv compression scheme and planned as a generic replacement of Gzip and ZLib. The main goal in its design was to compress data on the Internet, which meant optimizing the resources used at decoding time, while achieving maximal compression density. This article is intended to provide the first thorough, systematic description of the Brotli format as well as a detailed computational and experimental analysis of the main algorithmic blocks underlying the current encoder implementation, together with a comparison against compressors of different families constituting the state-of-the-art either in practice or in theory. This treatment will allow us to raise a set of new algorithmic and software engineering problems that deserve further attention from the scientific community.
Hierarchical Assembly of TiO2 Nanoparticles on WS2 Nanotubes Achieved Through Multifunctional Polymeric Ligands (2007)

Particles on the tube: Here, novel surface functionalization of WS2 nanotubes with polymeric ligands, by complexation with a combination of Ni2+ through a scorpionate-type nitrilotriacetic acid, and immobilization of TiO2 nanoparticles onto the surface of nanotubes is demonstrated (see schematic representation). The synthesis of the functional polymeric ligands was achieved through a reactive polymer precursor route.
Design of FeIII–LnIII binuclear complexes using compartmental ligands: synthesis, crystal structures, magnetic properties, and ab initio analysis (2021)

Three new binuclear FeIII–LnIII complexes, with similar structures, have been synthesized using the end-off compartmental proligand, H2valpn, resulting from the Schiff condensation between o-vanillin and 1,3-propylenediamine: [FeIIILnIII(valpn)(hfac)2(OAc)Cl] (Ln = Gd, Tb, Dy; hfac− = hexafluoroacetylacetonate; AcO− = acetate). The metal ions are triply bridged by two phenoxido oxygen atoms and by the acetato ligand (syn–syn bridging mode). Among all these compounds the FeIII–LnIII exchange interaction was found to be ferromagnetic (JFeGd = +1.004(4) cm−1; H = −JSFeSGd). The [FeIIIDyIII] derivative shows field-induced slow relaxation of the magnetization. The interpretation of the magnetic properties for the [FeIIIGdIII], [FeIIITbIII] and [FeIIIDyIII] is done through ab initio calculations. It was concluded that the temperature behavior of the relaxation time in the [FeIIIDyIII] derivative is due to dominant Orbach relaxation processes between states at the opposite sides and opposite heights of the blocking barrier. From this understanding, the relaxation mechanism for similar systems where a transition metal is in exchange coupling with a strong anisotropic lanthanide ion is elucidated, which could provide a strategy to synthesize other binuclear complexes with better magnetic properties.
Wave-vector analysis of plasmon-assisted distributed nonlinear photoluminescence along Au nanowires (2020)

We report a quantitative analysis of the wave-vector diagram emitted by nonlinear photoluminescence generated by a tightly focused pulsed laser beam and distributed along Au nanowire via the mediation of surface plasmon polaritons. The nonlinear photoluminescence is locally excited at key locations along the nanowire in order to understand the different contributions constituting the emission pattern measured in a conjugate Fourier plane of the microscope. Polarization-resolved measurements reveal that the nanowire preferentially emits nonlinear photoluminescence polarized transverse to the long axis at close to the detection limit wave vectors with a small azimuthal spread in comparison to the signal polarized along the long axis. We utilize the finite-element method to simulate the observed directional scattering by using localized incoherent sources placed on the nanowire. Simulation results faithfully mimic the directional emission of the nonlinear signal emitted by the different portions of the nanowire.
Ruthenium-Catalyzed Two-Component Addition To Form 1,3-Dienes:  Optimization, Scope, Applications, and Mechanism (2001)

A two component coupling of an allene and an activated olefin to form 1,3-dienes has been developed. The requisite allenes are synthesized either from terminal alkynes by a one carbon homologation using copper(I) iodide, paraformaldehyde, and diisopropylamine, via an ortho ester-Claisen rearrangement from a propargylic alcohol, or via a Wittig type reaction on a ketene generated in situ from an acid chloride. Mono- through tetrasubstituted allenes could be synthesized by these methods. Either cyclopentadienylruthenium(II) cyclooctadiene chloride or cyclopentadienylruthenium(II) trisacetonitrile hexafluorophosphate catalyze the addition reaction. When the former catalyst is employed, an alkyne activator is added to help generate the active catalyst. Through systematic optimization studies, a range of conditions was examined. The optimal conditions consisted of the use of cerium(III) trichloride heptahydrate as a cocatalyst in dimethylformamide as a solvent at 60 degrees C. The reaction was found to be chemoselective, and a wide range of functionality was tolerated, including esters, alcohols, nitriles, and amides. When substituted allenes are used, good selectivity can be obtained with proper substitution. A mechanism involving a ruthenacycle is proposed to account for the selectivity or lack thereof in product formation. With disubstituted allenes, selectivity is obtained when beta-hydrogen elimination is favored from a specific site. In tri- and tetrasubstituted allenes, steric issues concerning the C-C bond forming event appear to be the dominant factor in determining product formation. This process represents a highly atom-economical synthesis of 1,3-dienes in a controlled fashion. The utility of the 1,3-diene products was demonstrated by their use in Diels-Alder reactions to form a variety of cyclic systems including polycyclic structures. This sequence represents a convergent atom economic method for ring formation by a series of simple additions.
The Design of Nanoparticles Obtained by Solvent Evaporation:  A Comprehensive Study (2003)

The preparation of nanoparticles by emulsion solvent evaporation is a very popular method. The purpose of the present study was to clarify the mechanism by which nanoparticles of ethylcellulose (EC) and poly(lactic acid) (PLA) are formed during the emulsion solvent evaporation procedure. This study was mainly based on the measure of the variation of the emulsion and nanoparticle surface charge and size during the solvent evaporation process. From the data obtained and depending on the polymer used (EC or PLA), two different models are proposed to explain the nanoparticle formation. In the EC model, after shrinkage of the emulsion droplets as the direct consequence of solvent evaporation, coalescence occurred before stable and solvent-free nanoparticles were formed. On the contrary, in the PLA model, no or limited coalescence was found to occur so that the picture is that one PLA nanoparticle originated from one (or only a few) PLA emulsion droplet after its shrinkage.
Data from Inhibition of NOTCH Signaling by Gamma Secretase Inhibitor Engages the RB Pathway and Elicits Cell Cycle Exit in T-Cell Acute Lymphoblastic Leukemia Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;NOTCH signaling is deregulated in the majority of T-cell acute lymphoblastic leukemias (T-ALL) as a result of activating mutations in &lt;i&gt;NOTCH1&lt;/i&gt;. Gamma secretase inhibitors (GSI) block proteolytic activation of NOTCH receptors and may provide a targeted therapy for T-ALL. We have investigated the mechanisms of GSI sensitivity across a panel of T-ALL cell lines, yielding an approach for patient stratification based on pathway activity and also providing a rational combination strategy for enhanced response to GSI. Whereas the &lt;i&gt;NOTCH1&lt;/i&gt; mutation status does not serve as a predictor of GSI sensitivity, a gene expression signature of NOTCH pathway activity does correlate with response, and may be useful in the selection of patients more likely to respond to GSI. Furthermore, inhibition of the NOTCH pathway activity signature correlates with the induction of the cyclin-dependent kinase inhibitors CDKN2D (p19&lt;sup&gt;INK4d&lt;/sup&gt;) and CDKN1B (p27&lt;sup&gt;Kip1&lt;/sup&gt;), leading to derepression of RB and subsequent exit from the cell cycle. Consistent with this evidence of cell cycle exit, short-term exposure of GSI resulted in sustained molecular and phenotypic effects after withdrawal of the compound. Combination treatment with GSI and a small molecule inhibitor of CDK4 produced synergistic growth inhibition, providing evidence that GSI engagement of the CDK4/RB pathway is an important mechanism of GSI action and supports further investigation of this combination for improved efficacy in treating T-ALL. [Cancer Res 2009;69(7):3060–8]&lt;/p&gt;&lt;/div&gt;
Die wear during hot extrusion of ex-situ and in-situ aluminum composites (Letter to the Editor) (2017)

The study demonstrates a high-temperature wear of extrusion die during hot pressing of in-situ and ex-situ Al metal matrix composites (MMC). The in-situ Al-10.5vol.%AlN and ex-situ Al-10.5vol.%SiC with high Young's modulus are fabricated by powder metallurgy approach. The composite microstructure and the mechanical properties are characterized. Die wear during hot extrusion of MMC is quantified by the increase of radius of a worn edge as a function of the distance of extruded bars. In-situ Al-AlN exhibited a significantly lower abrasive effect in addition to higher mechanical properties compared to ex-situ Al-SiC.
Myasthenia induced by monoclonal anti‐acetylcholine receptor antibodies: Clinical and electrophysiological aspects (1981)

To investigate individual components of the humoral immune response directed against the acetylcholine receptor in experimental myasthenia, we injected monoclonal antireceptor antibody into normal rats. These antibodies were produced by cloned hybridoma lines formed by fusion of immune spleen cells with the myeloma cell line P3-X63-Ag8. Antibodies from two of seven clones induced acute experimental myasthenia, manifested by clinical weakness, decremental electromyographic response to repetitive nerve stimulation, and diminished mean amplitudes of miniature end-plate potentials (mepps): 0.55 +/- 0.02 mv (SEM) versus 0.71 mv for controls (p less than 0.001). In clinically affected animals, mepp amplitudes from the diaphragm correlated with decremental responses in the gastronemius muscle (r = -0.91, p less than 0.01). The results suggest that binding of a single antibody species to a single determinant on the acetylcholine receptor molecule is sufficient to induce acute experimental myasthenia gravis.
A supervised machine learning approach of extracting coexpression relationship among genes from literature (2010)

It is vital to develop automatic information extraction systems to help researchers cope up with the vast amount of data available on the Internet. In this paper, we describe a framework to extract precise information about coexpression relationship among genes, from published literature using a supervised machine learning approach. We use a graphical model, Dynamic Conditional Random Fields (DCRFs), for training our classifier. Our approach is based on semantic analysis of text to classify the predicates describing coexpression relationship rather than detecting the presence of keywords. We compared our results of sentence classification with the baseline technique of word matching and a Naïve Bayes classification algorithm. Our framework outperformed the baseline by almost 45%, with DCRFs showing superior performance to Naïve Bayes.
Composition control of Zn 1- x Mg x O thin films grown using mist chemical vapor deposition (2019)

Abstract In equilibrium reaction processes, the precise control of composition ratios in multi-component thin films is problematic due to the changes in the state of precursor materials, which are caused by differences in metal ion stabilities. We have identified a strategy to resolve this problem by first developing a theory and then constructing a fine-channel type mist chemical vapor deposition (mist-CVD) system with two solution chambers and a mist-mixing chamber. Zn 1- x Mg x O thin films were fabricated using the conventional and the developed mist-CVD systems to verify the theory. The properties of the Zn 1- x Mg x O thin films produced using the two systems were significantly different. The Mg composition ratio in the film was clearly influenced by the Mg ion stability and all the measurement results support the theory.
Redox Gene Therapy Protects Human IB-3 Lung Epithelial Cells Against Ionizing Radiation-Induced Apoptosis (1998)

Toxicity to nontumor-derived tissue has proven to be a significant obstacle in achieving therapeutic levels of gamma irradiation in the treatment of cancer. The formation of reactive oxygen species (ROS) such as superoxide radicals (O2-) following irradiation is thought to be a major determinant of cellular damage. To this end, we describe the generation of two recombinant adenoviral vectors expressing the radical-scavenging enzymes MnSOD and CuZnSOD to test therapeutic strategies of radioprotection. Using a human lung epithelial cell line (IB-3), we have demonstrated that infections with both Ad.CMVMnSOD or Ad.CMVCuZnSOD significantly increase both the levels of SOD protein and enzymatic activity as compared to control cells. This increase in SOD expression reduced the level of apoptosis at 72 hr post-irradiation by 50% as compared to mock- or Ad.CMVLacZ-infected cells. Such studies provide the foundation for radioprotective gene therapies in the treatment of cancer.