gebhart/patrepeval huggingface dataset:
<title>A DICOM-RT based ePR radiation therapy information system for managing brain tumor patients</title> (2005)

The need for comprehensive clinical image data and relevant information in image-guided Radiation Therapy (RT) is becoming steadily apparent. Multiple standalone systems utilizing the most technological advancements in imaging, therapeutic radiation, and computerized treatment planning systems acquire key data during the RT treatment course of a patient. One example are patients treated for brain tumors of greater sizes and irregular shapes that utilize state-of-the-art RT technology to deliver pinpoint accurate radiation doses. One such system, the Cyberknife, is a radiation treatment system that utilizes image-guided information to control a multi-jointed, six degrees of freedom, robotic arm to deliver precise and required radiation dose to the tumor site of a cancer patient. The image-guided system is capable of tracking the lesion orientations with respect to the patient’s position throughout the treatment process. This is done by correlating live radiographic images with pre-operative, CT and MR imaging information to determine relative patient and tumor position repeatedly over the course of the treatment. The disparate and complex data generated by the Cyberknife system along with related data is scattered throughout the RT department compromising an efficient clinical workflow since the data crucial for a clinical decision may be time-consuming to retrieve, temporarily missing, or even lost. To address these shortcomings, the ACR-NEMA Standards Committee extended its DICOM (Digital Imaging & Communications in Medicine) Standard from Radiology to RT by ratifying seven DICOM RT objects starting in 1997. However, they are rarely used by the RT community in daily clinical operations. In the past, the research focus of an RT department has primarily been developing new protocols and devices to improve treatment process and outcomes of cancer patients with minimal effort dedicated to integration of imaging and information systems. Our research, tightly-coupling radiology and RT information systems, represents a new frontier for medical informatics research that has never been previously considered. By combining our past experience in medical imaging informatics, DICOM-RT expertise, and system integration, we propose to test our hypothesis using a brain tumor case model that a DICOM-RT electronic patient record (ePR) system can improve clinical workflow efficiency for treatment and management of patients. This RT ePR system integrated with clinical images and RT data can impact the RT department in a similar fashion as PACS has already successfully done for Radiology. As a first step, the specific treatment case of patients with brain tumors specifically patients treated with the Cyberknife system will be the initial proof of concept for the research design, implementation, evaluation, and clinical relevance.
QSAR Study of 1,8-Naphthyridin-4-ones As Inhibitors of Photosystem II (2001)

The effect of substituents on in vitro activity of 20 1,8-naphthyridin-4-ones, a novel class of photosystem II inhibitors, was studied. A four-parameter QSAR model based on the molecular connectivity indices was developed which accounts for about 87% of the variations in inhibitory potencies of these compounds. The model suggests that the position, size, and polarity of substituents are factors that predominantly control their activity. By using physicochemical constants, a quantitative model for both 1,8-naphthyridin-4-ones and structurally related 2-trifluoromethyl-4-hydroxyquinoline derivatives was proposed.
Transforming worst-case optimal solutions for simultaneous tasks into all-case optimal solutions (2011)

Decision tasks require that nonfaulty processes make decisions based on their input values. Simultaneous decision tasks require that nonfaulty processes decide in the same round. Most decision tasks have known worst-case lower bounds. Most also have known worst-case optimal protocols that halt in the number of rounds given by the worst-case lower bound, and some have early-stopping protocols that can halt earlier than the worst-case lower bound (sometimes in as early as two rounds). We consider what might be called earliest-possible protocols for simultaneous decision tasks. We present a new technique that converts worst-case optimal decision protocols into all-case optimal simultaneous decision protocols: For every behavior of the adversary, the all-case optimal protocol decides as soon as any protocol can decide in a run with the same adversarial behavior. Examples to which this can be applied include set consensus, condition-based consensus, renaming and order-preserving renaming. Some of these tasks can be solved significantly faster than the classical simultaneous consensus task. A byproduct of the analysis is a proof that improving on the worst-case bound for any simultaneous task by even a single round is as hard as reaching simultaneous consensus.
Current–voltage relations in magnetrons (1988)

The current–voltage relationship in a magnetron plasma appears to be strongly dependent on the dynamics of the sputtered particle–gas atom interaction. Large fluxes of energetic (several eV) sputtered atoms from the cathode heat the gas in the near cathode region, resulting in a significant reduction in the local gas density as a function of discharge current (and hence particle flux). This reduction in gas density results in a lower rate of ion formation, and hence a more resistive plasma. Thus, the rate of voltage increase with current in a magnetron is related to the magnitude of the gas density rarefaction, which is dependent on the cathode sputter yield, sputtered atom energy, the cross section for sputtered atom–gas collisions, the molecular velocity of the gas, and the gas density. A model has been developed which describes the observed rate of voltage increase in a magnetron as a function of this thermalization process.
TRPM7 Induces Mechanistic Target of Rap1b Through the Downregulation of miR-28-5p in Glioma Proliferation and Invasion (2019)

<b>Objectives:</b> Our previous findings demonstrate that channel-kinase transient receptor potential (TRP) ion channel subfamily M, member 7 (TRPM7) is critical in regulating human glioma cell migration and invasion. Since microRNAs (miRNAs) participate in complex regulatory networks that may affect almost every cellular and molecular process during glioma formation and progression, we explored the role of miRNAs in human glioma progression by comparing miRNA expression profiles due to differentially expressed TRPM7. <b>Methods:</b> First, we performed miRNA microarray analysis to determine TRPM7's miRNA targets upon TRPM7 silencing in A172 cells and validated the miRNA microarray data using A172, U87MG, U373MG, and SNB19 cell lines by stem-loop RT-qPCRs. We next determined whether TRPM7 regulates glioma cell proliferation and migration/invasion through different functional domains by overexpressing wild-type human TRPM7 (wtTRPM7), two mutants with TRPM7's α-kinase domain deleted (Δkinase-DK), or a point mutation in the ATP binding site of the α-kinase domain (K1648R-KR). In addition, we determined the roles of miR-28-5p in glioma cell proliferation and invasion by overexpressing or under expressing miR-28-5p <i>in vitro</i>. Lastly, we determined whether a Ras-related small GTP-binding protein (Rap1b) is a target of miR-28-5p in glioma tumorigenesis. <b>Results:</b> The miRNA microarray data revealed a list of 16 downregulated and 10 upregulated miRNAs whose transcripts are significantly changed by TRPM7 knock-down. Cell invasion was significantly reduced in two TRPM7 mutants with inactive kinase domain, Δkinase, and K1648R transfected glioma cells. miR-28-5p overexpression suppressed glioma cells' proliferation and invasion, and miR-28-5p under expression led to a significant increase in glioma cell proliferation and migration/invasion compared to that of the controls. miR-28-5p suppressed glioma cell proliferation and migration by targeting Rap1b. Co-transfection of siRap1b with miR28-5p inhibitor reduced the glioma cell proliferation and invasion, caused by the latter. <b>Conclusions:</b> These results indicate that TRPM7's channel activity is required for glioma cell growth while the kinase domain is required for cell migration/invasion. TRPM7 regulates miR-28-5p expression, which suppresses cell proliferation and invasion in glioma cells by targeting Rap1b signaling.
Inverse Optimization (2001)

In this paper, we study inverse optimization problems defined as follows. Let S denote the set of feasible solutions of an optimization problem P, let c be a specified cost vector, and x 0 be a given feasible solution. The solution x 0 may or may not be an optimal solution of P with respect to the cost vector c. The inverse optimization problem is to perturb the cost vector c to d so that x 0 is an optimal solution of P with respect to d and ‖d−c‖ p is minimum, where ‖d−c‖ p is some selected L p norm. In this paper, we consider the inverse linear programming problem under L 1 norm (where ‖d−c‖ p = Σ i∈J w j |d j −c j |, with J denoting the index set of variables x j and w j denoting the weight of the variable j) and under L ∞ norm (where ‖d−c‖ p = max j∈J {w j |d j −c j |}). We prove the following results: (i) If the problem P is a linear programming problem, then its inverse problem under the L 1 as well as L ∞ norm is also a linear programming problem. (ii) If the problem P is a shortest path, assignment or minimum cut problem, then its inverse problem under the L 1 norm and unit weights can be solved by solving a problem of the same kind. For the nonunit weight case, the inverse problem reduces to solving a minimum cost flow problem. (iii) If the problem P is a minimum cost flow problem, then its inverse problem under the L 1 norm and unit weights reduces to solving a unit-capacity minimum cost flow problem. For the nonunit weight case, the inverse problem reduces to solving a minimum cost flow problem. (iv) If the problem P is a minimum cost flow problem, then its inverse problem under the L ∞ norm and unit weights reduces to solving a minimum mean cycle problem. For the nonunit weight case, the inverse problem reduces to solving a minimum cost-to-time ratio cycle problem. (v) If the problem P is polynomially solvable for linear cost functions, then inverse versions of P under the L 1 and L ∞ norms are also polynomially solvable.
ChemInform Abstract: Cleavage of (Octaethyl‐2,3‐dihydroxychlorinato)nickel(II) to Give the Novel 2,3‐Dioxo‐2,3‐secochlorin System. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Mild Hypoxic-Ischemic Injury in the Neonatal Rat Brain: Longitudinal Evaluation of White Matter Using Diffusion Tensor MR Imaging (2009)

Diffusion indices can reflect dysmyelination in mild HI injury, continual myelination of both injury and control ECs with growth, and the partial recovery of myelin postinjury. We propose that diffusion indices may be used as biomarkers to monitor noninvasively the longitudinal changes of mild HI-induced WM damage.
Simplification and Hardware Parallel Design of Frobenius Mapping Algorithm Based on SM9 (2019)

With the development of network technology, the leakage of information has become a severe security risk, which has led to the increasing requirements for the security and processing speed of information encryption and decryption. This paper mainly optimizes the algorithm of R-ate bilinear pairing with the parameters of the SM9 and reduces its hardware cost by simplifying the Frobenius mapping algorithm. The validity of the optimized algorithm was verified based C++ from the view of software, and hardware parallelization design also was realized based FPGA respectively. The synthesis results on Xilinx Virtex-7 of the Twelfth Domain Mode Multiplication module showed that it consumes 28% of the Slice registers and 57% of the LUT. This research proposed an effective approach for accelerating the R-ate algorithm and reducing chip area.
Characterization of a polydimethylsiloxane-polythiourethane polymer blend with potential as fouling-release coating (2017)

Developing reliable and long-lasting antifouling coatings is a most challenging task, because the mechanisms of interactions between a solid surface and the aquatic environment including all abiotic and biotic entities are incredible various. Currently there are some working strategies, but all of them have their disadvantages like negative environmental impact or mechanical instability. The aim of this study is to combine the desirable mechanical stability of the environmentally friendly polymer matrix, PTU, and the fouling-release properties of PDSM in a polymer blend with potential for large-scale applications within the maritime sector. The material, surface and fouling-release properties of the PDMS/PTU blend with varying content of PDMS were characterized and promising properties were found.
Photocontrolling Microtubule Dynamics with Photoswitchable Chemical Reagents (2021)

Microtubule dynamics can be inhibited with sub-second temporal resolution and cellular-scale spatial resolution, by using precise illuminations to optically pattern where and when photoswitchable microtubule-inhibiting chemical reagents exert their latent bioactivity. The recently-available reagents (SBTub, PST, STEpo, AzTax, PHTub) now enable researchers to use light to reversibly modulate microtubule-dependent processes in eukaryotes, in 2D and 3D cell culture as well as in vivo, across a variety of model organisms: with applications in fields from cargo transport to cell migration, cell division, and embryonic development.However, a wide knowledge gap has remained in the literature, which has blocked further translation of these and many other classes of photopharmaceuticals. No generally-applicable procedures or workflows to establish biological assays using photopharmaceuticals have been published. Accordingly, the rate of adoption of photopharmaceutical tools in the broader chemical biology community (beyond the original chemical developers of the tools) has remained very low. Vital information about assay benchmarking for photoconversion, testing for isomer solubility, proving the retention of mechanism of action, estimating the limits of phototoxicity etc has either simply not been formalised in the literature, or has remained buried in diverse reports without being unified and codified for an audience beyond that of synthetic organic chemists.Here we have developed a robust four-step assay establishment procedure to optimise assay parameters for achieving reliable photocontrol over microtubule dynamics, that is applicable to diverse families of photoswitchable inhibitors. This procedure also controls for these common sources of irreproducibility and includes numerous troubleshooting steps. We also collect together the relevant information for non-chemist "users" such as microscopists and biologists, to introduce the theory of small molecule photoswitching; the unique features, usage requirements, and limitations that photoswitchable chemical reagents have; and the specific performance features of the major classes of photoswitchable microtubule inhibitors that are currently available; to highlight their properties that suit them to different applications. The generally-applicable workflows that we present allow establishing cellular assays optically controlling microtubule dynamics in a temporally reversible fashion with spatial specificity down to a single selected cell within a field of view. These workflows and methods also equip the reader to tackle advanced uses of photoswitchable chemical reagents for general protein targets, in 3D culture and in vivo, and can represent an important bridge to reach the high-value biological applications that photopharmacology can promise.
An Automated Setup for Large-Scale Simulation-Based Fault-Injection Experiments on Asynchronous Digital Circuits (2021)

Experimental fault injection is an essential tool in the assessment and verification of fault-tolerance properties. Often, in these experiments it is impossible to reasonably cover the huge parameter space spanned by target state and fault parameters, and compromises or restrictions must be made. This is even more pronounced for asynchronous circuits where a convenient discretization of time through a synchronous clock is not possible. In this paper we present a fault-injection toolset that allows for a very efficient injection and data processing, thus bringing studies with many billions of meaningful injections into asynchronous targets within reach. The key ingredients of our solution are an auto-setup feature capable of optimizing parameter values, seamless distribution of the simulation load to many host computers, and efficient arrangement of the important settings and readings in a database. We will use the example of a comparative study of different asynchronous pipeline styles to motivate the need for such an approach and illustrate its benefits.
Development of an Infection Model for Botrytis Bunch Rot of Grapes Based on Wetness Duration and Temperature (1995)

Grape berries were dipped in conidial suspensions of Botrytis cinerea and incubated for 4, 8, 12, 16, or 20 h of wetness at temperatures ranging from 12-30 C. Berries were infected after 4 h of wetness at all temperatures tested. Incidence of berry infection increased with increasing wetness duration at all temperatures. A multiple regression model described the logit of infection as a function of the interaction of wetness duration and temperature (R 2 = 0.75). This model was incorporated into an infield environmental monitoring station and evaluated for two seasons on Thompson Seedless table grapes in the central valley of Chile. Applications of captan (3,2 kg/ha a.i.) or vinclozolin (1 kg/ha a.i.) were made according to the Botrytis model or a standard phenological spray program that consisted of four sprays (at bloom, cluster thinning, veraison, and preharvest) plus additional sprays after major rain events. Disease incidence and severity at harvest were similar whether applications were made according to a standard program (six to nine applications in 1991-1992, four to five in 1992-1993) or according to the Botrytis model (two to four applications in 1991-1992, zero to five in 1992-1993). In some vineyards, postharvest disease was significantly less when sprays were made according to the Botrytis model recommendations compared with the standard spray program
Accumulation of GdCl3in the feed of a reverse osmosis system during desalination as determined by neutron absorption (2016)

This article deals with the application of in-situ small-angle neutron scattering to investigate wastewater desalination by reverse osmosis. In a first series of experiments we take advantage of the strong neutron absorption of gadolinium (Gd) and use 0.50 g/L GdCl3 in the feed as an indicator for concentration polarization and scaling at the membrane surface. The continuous decline of scattering during the process of desalination indicates an increase of GdCl3 salt concentration which after 15 hours has achieved nearly 100% enhancement with respect to its initial concentration.
Supplementary Figure from HER2 Mediates PSMA/mGluR1-Driven Resistance to the DS-7423 Dual PI3K/mTOR Inhibitor in PTEN Wild-type Prostate Cancer Models (2023)

Supplementary Figure from HER2 Mediates PSMA/mGluR1-Driven Resistance to the DS-7423 Dual PI3K/mTOR Inhibitor in PTEN Wild-type Prostate Cancer Models
Porous Porphyrin‐Based Organosilica Nanoparticles for NIR Two‐Photon Photodynamic Therapy and Gene Delivery in Zebrafish (2018)

Abstract Periodic mesoporous organosilica nanoparticles emerge as promising vectors for nanomedicine applications. Their properties are very different from those of well‐known mesoporous silica nanoparticles as there is no silica source for their synthesis. So far, they have only been synthesized from small bis‐silylated organic precursors. However, no studies employing large stimuli‐responsive precursors have been reported on such hybrid systems yet. Here, the synthesis of porphyrin‐based organosilica nanoparticles from a large octasilylated metalated porphyrin precursor is described for applications in near‐infrared two‐photon‐triggered spatiotemporal theranostics. The nanoparticles display unique interconnected large cavities of 10–80 nm. The framework of the nanoparticles is constituted with J‐aggregates of porphyrins, which endows them with two‐photon sensitivity. The nanoparticle efficiency for intracellular tracking is first demonstrated by the in vitro near‐infrared imaging of breast cancer cells. After functionalization of the nanoparticles with aminopropyltriethoxysilane, two‐photon‐excited photodynamic therapy in zebrafish is successfully achieved. Two‐photon photochemical internalization in cancer cells of the nanoparticles loaded with siRNA is also performed for the first time. Furthermore, siRNA targeting green fluorescent protein complexed with the nanoparticles is delivered in vivo in zebrafish embryos, which demonstrates the versatility of the nanovectors for biomedical applications.
Mechanism of laser writing for optical data storage in an overcoated tellurium alloy trilayer (1986)

Mark formation by laser writing in an overcoated thin-film tellurium alloy-based optical storage media with a trilayer design was studied by transmission electron microscopy, scanning electron microscopy, optical microscopy, differential interference contrast optical microscopy, and optical interferometry. Mark formation was observed to occur through coalescence of the relatively uniform amorphous tellurium alloy film into discrete particles. The mark microstructure and, correspondingly, the optical properties of the mark, were dependent on the write laser power. At low power, incomplete breakup of the film occurred. At high power, the film coalesced into spherical particles. Laser writing also caused changes in the organic overcoat layer.
Analysis of mechanical contrast in optical coherence elastography (2013)

Optical coherence elastography (OCE) maps the mechanical properties of tissue microstructure and has potential applications in both fundamental investigations of biomechanics and clinical medicine. We report the first analysis of contrast in OCE, including evaluation of the accuracy with which OCE images (elastograms) represent mechanical properties and the sensitivity of OCE to mechanical contrast within a sample. Using phase-sensitive compression OCE, we generate elastograms of tissue-mimicking phantoms with known mechanical properties and identify limitations on contrast imposed by sample mechanics and the imaging system, including signal-processing parameters. We also generate simulated elastograms using finite element models to perform mechanical analysis in the absence of imaging system noise. In both experiments and simulations, we illustrate artifacts that degrade elastogram accuracy, depending on sample geometry, elasticity contrast between features, and surface conditions. We experimentally demonstrate sensitivity to features with elasticity contrast as small as 1.1∶1 and calculate, based on our imaging system parameters, a theoretical maximum sensitivity to elasticity contrast of 1.002∶1. The results highlight the microstrain sensitivity of compression OCE, at a spatial resolution of tens of micrometers, suggesting its potential for the detection of minute changes in elasticity within heterogeneous tissue.
ChemInform Abstract: Catalysis‐Based Enantioselective Total Synthesis of Myxothiazole Z, (14S)‐Melithiazole G and (14S)‐Cystothiazole F. (2013)

Abstract Melithiazole G (VII) is prepared via a sequence involving cross‐metathesis of alkenes (I) and (II), asymmetric transfer hydrogenation of olefin (IV), and Stille coupling reaction of bromide (III) as the key steps.