gebhart/patrepeval huggingface dataset:
A Monte Carlo approach to patient-specific dosimetry (1996)

In internal emitter therapy, an accurate description of the absorbed dose distribution is necessary to establish an administered dose-response relationship, as well as to avoid critical organ toxicity. Given a spatial distribution of cumulated activity, an absorbed dose distribution that accounts for the effects of attenuation and scatter can be obtained using a Monte Carlo method that simulates particle transport across the various densities and atomic numbers encountered in the human body. Patient-specific information can be obtained from CT and SPECT or PET imaging. Since the data from these imaging modalities is discrete, it is necessary to develop a technique to efficiently transport particles across discrete media. The Monte Carlo-based algorithm presented in this article produces accurate absorbed dose distributions due to patient-specific density and radionuclide activity distributions. The method was verified by creating CT and SPECT arrays for the Medical Internal Radionuclide Dose (MIRD) Committee's Standard Man phantom, and reproducing the spatially averaged specific absorbed fractions reported in MIRD Pamphlet 5. The algorithm was used to investigate the implications of replacing a mean absorbed dose with a distribution, and of neglecting atomic number and density variations for various patient geometries and energies. For example, the I-131 specific absorbed fraction for spleen to liver is the same as for liver to spleen, yet the distributions were different. Furthermore, neglecting atomic number variations across the vertebral bone led to an overestimation of I-125 absorbed dose by an order of magnitude, while no error was observed for I-131.
On the mDCT-PSNR image quality index (2009)

Full reference image quality indices assign a quality index to a pair of an undistorted reference image and a distorted image to be assessed; the quality of the index itself is then defined by its ability to predict the outcome of subjective tests performed by human observers judging the quality of the same image pair. In this article, a new DCT based image quality index is introduced whose complexity is between that of algorithms like SSIM and complex, HVS-based algorithms like VDP. Detailed experiments on the LIVE database show that the proposed algorithm performs best close to or below the visual threshold, and outperforms there existing algorithms like SSIM or VDP requiring only a mediocre complexity.
Aluminum Surface Corrosion and the Mechanism of Inhibitors Using pH and Metal Ion Selective Imaging Fiber Bundles (2002)

The localized corrosion behavior of a galvanic aluminum copper couple was investigated by in situ fluorescence imaging with a fiber-optic imaging sensor. Three different, but complementary methods were used for visualizing remote corrosion sites, mapping the topography of the metal surface, and measuring local chemical concentrations of H+, OH-, and Al3+. The first method is based on a pH-sensitive imaging fiber, where the fluorescent dye SNAFL was covalently attached to the fiber's distal end. Fluorescence images were acquired as a function of time at different areas of the galvanic couple. In a second method, the fluorescent dye morin was immobilized on the fiber-optic imaging sensor, which allowed the in situ localization of corrosion processes on pure aluminum to be visualized over time by monitoring the release of Al3+. The development of fluorescence on the aluminum surface defined the areas associated with the anodic dissolution of aluminum. We also investigated the inhibition of corrosion of pure aluminum by CeCl3 and 8-hydroxyquinoline. The decrease in current, the decrease in the number of active sites on the aluminum surface, and the faster surface passivation are all consistent indications that cerium chloride and 8-hydroxyquinoline inhibit corrosion effectively. From the number and extent of corrosion sites and the release of aluminum ions monitored with the fiber, it was shown that 8-hydroxyquinoline is a more effective inhibitor than cerium chloride.
[Drug delivery systems in gene therapy]. (1998)

The use of nonviral vectors is an attractive in vivo gene delivery strategy that is simpler and lacks some risks inherent in viral systems. Liposomes and receptor-mediated polycation systems are promising carriers for delivery and expression of plasmid DNA encoding genes into the target cells. Many barriers need to be overcome for successful in vivo DNA delivery using these carrier systems. Various factors such as the extent of DNA condensation, particle size of the DNA complex, route of administration, stability against nucleases, target sites, in vivo disposition, binding to cell surface receptor and internalization, intracellular trafficking affect the in vivo gene delivery and expression. This chapter will focus on the current status and perspectives of the plasmid DNA delivery systems for in vivo gene therapy.
Computational biology for cardiovascular biomarker discovery (2009)

Computational biology is essential in the process of translating biological knowledge into clinical practice, as well as in the understanding of biological phenomena based on the resources and technologies originating from the clinical environment. One such key contribution of computational biology is the discovery of biomarkers for predicting clinical outcomes using 'omic' information. This process involves the predictive modelling and integration of different types of data and knowledge for screening, diagnostic or prognostic purposes. Moreover, this requires the design and combination of different methodologies based on statistical analysis and machine learning. This article introduces key computational approaches and applications to biomarker discovery based on different types of 'omic' data. Although we emphasize applications in cardiovascular research, the computational requirements and advances discussed here are also relevant to other domains. We will start by introducing some of the contributions of computational biology to translational research, followed by an overview of methods and technologies used for the identification of biomarkers with predictive or classification value. The main types of 'omic' approaches to biomarker discovery will be presented with specific examples from cardiovascular research. This will include a review of computational methodologies for single-source and integrative data applications. Major computational methods for model evaluation will be described together with recommendations for reporting models and results. We will present recent advances in cardiovascular biomarker discovery based on the combination of gene expression and functional network analyses. The review will conclude with a discussion of key challenges for computational biology, including perspectives from the biosciences and clinical areas.
Morphology and Phase Diagram of Comb Block Copolymer Am+1(BC)m (2009)

The morphologies and the phase diagram of comb copolymer Am+1(BC)m are investigated by the self-consistent field theory. By changing the volume fractions of the blocks, the interaction parameters between the different blocks, and the side chain number, nine phases are found, including the two-colored lamellar phase, three-colored lamellar phase, hexagonal lattice phase, core shell hexagonal lattice phase, two interpenetrating tetragonal lattice, core shell tetragonal lattice, lamellar phase with beads inside, lamellar phase with alternating beads, and disordered phase. The phase diagrams are constructed for Am+1(BC)m with different side chain numbers of m=1, 2, 3, and 5. Due to the asymmetric topology of comb copolymer Am+1(BC)m, the phases and the diagrams are very different from linear ABC triblock copolymer or star ABC triblock copolymer. When the volume fraction of one of the blocks is the domination, the (core shell) hexagonal phase or two interpenetrating tetragonal lattice can form, depending on which block dominates and the interaction between the blocks. The (core shell) hexagonal phase easily forms at the corner of the block A (fA>or=0.5). The side chain number m affects the phase diagram largely due to the fact that the architecture of a comb copolymer is not invariant under the interchange between the three different monomers. Due to the connectivity of the blocks B and the inner blocks A, Am+1(BC)m comb copolymers with the longer main chain A or longer side chain with short block C, i.e., longer block B, are difficult to phase separate. The results are helpful to design nano- or biomaterials with complex architecture or tailor the phase behavior of comb copolymers.
MuJoCo: A physics engine for model-based control (2012)

We describe a new physics engine tailored to model-based control. Multi-joint dynamics are represented in generalized coordinates and computed via recursive algorithms. Contact responses are computed via efficient new algorithms we have developed, based on the modern velocity-stepping approach which avoids the difficulties with spring-dampers. Models are specified using either a high-level C++ API or an intuitive XML file format. A built-in compiler transforms the user model into an optimized data structure used for runtime computation. The engine can compute both forward and inverse dynamics. The latter are well-defined even in the presence of contacts and equality constraints. The model can include tendon wrapping as well as actuator activation states (e.g. pneumatic cylinders or muscles). To facilitate optimal control applications and in particular sampling and finite differencing, the dynamics can be evaluated for different states and controls in parallel. Around 400,000 dynamics evaluations per second are possible on a 12-core machine, for a 3D homanoid with 18 dofs and 6 active contacts. We have already used the engine in a number of control applications. It will soon be made publicly available.
Drug Metabolism and Individualized Medicine (2003)

Drug metabolism refers to the biochemical transformation of a compound into another more polar chemical form. Absorption, distribution, metabolism and excretion comprise an integral part in understanding the safety and efficacy of a potential new drug. Detailed in-depth knowledge of the Pharmacokinetics and Drug Metabolism of a new drug entity is considered a prerequisite to know the appropriate route of administration, correct dose etc. Sometimes there is (are) different/unwanted effect(s) of certain drugs in different populations. This is particularly true for the drug having narrow therapeutic index. Often these different effects are detrimental to an individual, thus termed as adverse drug reactions. After the raw draft of human genome has evolved, it has become increasingly clear that change(s) in the drug response between individuals, is due to the occurrence of genetic polymorphisms in the Phase I and II drug metabolizing enzymes, due to which distinct subgroups in the population differ in their ability to perform certain drug biotransformation reactions. The study about the occurrence of genetic polymorphisms in drug metabolizing enzymes is termed as Pharmacogenetics/ Pharmacogenomics. Pharmacogenetic characterization of particular drug can be both phenotypically or genotypically conducted in population groups. The study is very important to check the post-marketed drug withdrawal, if a particular percentage of population suffers from adverse drug reactions, and thus a lot of revenue be saved. The study also helps to find out Right Medicine for Right Individual or Individualized Medicine.
The effect of an applied electric field on macrophage accumulation within the subacute spinal injury. (1999)

Macrophages are implicated to play a substantive role in the acute inflammatory reaction to CNS insult in the delayed progressive secondary damage to parenchyma, espacially myelin. When placed in an electrical field in vitro, macrophages show directed pseudopodial extensions and migrate towards the positive pole (anode). We have evaluated if ED1 positive macrophage accumulations in rat spinal cord injuries were affected by the applied extracellular voltage, comparing their numbers to a sham treated group. Our hypothesis was that the applied voltage may reduce the concentration of phagocytes in the central injury and thus reduce the level of secondary damage produced by them. The applied voltage gradient did not alter the number or density of macrophage accumulations in the three week lesion, nor is there any difference in the degree of cavitation between control and experimental groups.
STIFF-FLOP surgical manipulator: Mechanical design and experimental characterization of the single module (2013)

This paper presents the concept design, the fabrication and the experimental characterization of a unit of a modular manipulator for minimal access surgery. Traditional surgical manipulators are usually based on metallic steerable needles, tendon driven mechanisms or articulated motorized links. In this work the main idea is to combine flexible fluidic actuators enabling omnidirectional bending and elongation capability and the granular jamming phenomenon to implement a selective stiffness changing. The proposed manipulator is based on a series of identical modules, each one consisting of a silicone tube with pneumatic chambers for allowing 3D motion and one central channel for the implementation of the granular jamming phenomenon for stiffening. The silicone is covered by a novel bellows-shaped braided structure maximizing the bending still limiting lateral expansion. In this paper one single module is tested in terms of bending range, elongation capability, generated forces and stiffness changing.
Redistribution of Gq/11 in the Pituitary Gonadotrope in Response to a Gonadotropin-Releasing Hormone Agonist (1998)

In the present study, we took advantage of high-resolution multilaser confocal microscopy to examine the distribution of the α-subunit of the guanyl nucleotide binding protein subfamily Gq/11 (Gq/11α). Dispersed cultures of pituitary cells were prepared from female weanling rats, fixed, permeabilized, and then stained with monoclonal antiserum (mouse) to the gonadotrope-specific form of secretogranin (SIIp), which was then tagged with Texas Red. Accordingly, the subpopulation of gonadotropes (∼15% of total cells) could be identified against a background of other pituitary cell types. Gq/11α was localized with antiserum made in rabbit, then tagged with fluorescein. Hoechst 33258 nuclear stain was also used in some experiments for topological reference. The data indicate localization of the Gq/11α in a cellular region near the plasma membrane and external to the border of the layer occupied by secretory granules. In the absence of activation, there were an average of six clusters of Gq/11α in a section 1 μm thick and through the center of the cell. This corresponds to an average of 60 clusters per cell, assuming a mean gonadotrope diameter of 10 μm. Following continuous treatment with 0.1 μg/ml Buserelin, a metabolically stable GnRH agonist, the average number of clusters increased to 200/cell after 40 min and remained approximately constant for 120 min. This increase was blocked by the protein synthesis inhibitor, cycloheximide. In response to Buserelin, there was an additional increase in the number of clusters inside the cell in the area occupied by the secretory granules and in the perinuclear area. Prolonged (24 h) treatment with Buserelin, sufficient to provoke the onset of desensitization, did not significantly change total numbers of Gq/11α clusters, although more were located in the peripheral compartment, an increase that occurred at the expense of the cytoplasmic compartment. Redistribution of the Gq/11α family may be functionally significant, because this moiety may be rate limiting at the site of regulation of signal transduction.
Topiramate: A Case Series Study in Migraine Prophylaxis (2002)

We reviewed the electronic records of 74 migraine patients treated with topiramate for more than 6 weeks. Twenty-four patients had episodic migraine and 50 had chronic (transformed) migraine. Most (81%) started treatment at 25 mg per day and reached a dose of 100 mg twice a day (mean dose on the last follow-up visit was 208 mg). The mean headache frequency decreased from 20.6 days to 13.6 days per month (P<0.0001) for all headaches (9.9-5.1 (P<0.0001) and 25.7-17.7 (P<0.001) for episodic migraine and chronic migraine, respectively). The percentage of patients whose headache frequency was reduced by > or =50% was 44.6% for all patients; 58.3 for episodic migraine and 38.0 for chronic migraine. For all patients mean headache severity (10-point scale) was reduced from 6.2 to 4.8 (P<0.0001). Patients on monotherapy (20%) and polytherapy (80%) had similar reductions in headache frequency. Adverse events were usually mild to moderate and were seen in 58.1% (paresthesias in 25%, cognitive difficulties 14.9%). Mean weight loss was 3.1 +/- 4 kg (3.8% of total body weight).
The long-term average capacity region per unit cost with application to protocols for sensor networks (2003)

We consider a wireless sensor network where K sensors must deliver their messages within a frame of N time slots by spending a given finite energy. If the messages are not transmitted within the required delay they become useless and the residual energy is wasted. The channel is block-fading, with independent fades for each sensor and each slot. Sensors know the fading levels up to the current slot, but do not know the future fading levels. The receiver collects the signal on all the slots of the frame and performs joint decoding of all the messages. We characterize the region of long-term average achievable rates and we show that the optimal policy tends to waterfilling in time (optimal policy without delay constraints) as N increases. In this setting, we also characterize the long-term average capacity region per unit energy by showing that the optimal policy is 'one-shot', totally decentralized and extremely simple, i.e., every user spends all its available energy on the first slot of the frame, the fading gain of which is larger than a pre-computed time-varying threshold. Furthermore, the 'one-shot' policy not only makes the most efficient use of the energy, but also reduces to the minimum the interference to other users as it makes all the users transmit with the minimum energy per bit required for reliable communications. These characteristics make the 'one-shot' policy appealing for systems with severe energy limitation as wireless sensor networks.
O-Alkyl- and Aryl-N,N-ethyleneurethanes. I. Preparation and Reaction with Amines1 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTO-Alkyl- and Aryl-N,N-ethyleneurethanes. I. Preparation and Reaction with Amines1YOSHIO IWAKURA and AIKO NABEYACite this: J. Org. Chem. 1960, 25, 7, 1118–1123Publication Date (Print):July 1, 1960Publication History Published online1 May 2002Published inissue 1 July 1960https://pubs.acs.org/doi/10.1021/jo01077a013https://doi.org/10.1021/jo01077a013research-articleACS PublicationsRequest reuse permissionsArticle Views297Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Lignin Chromophores. III. Syntheses of Hydroxy- and Alkoxystilbenes via Aryl Migration (1991)

Abstract Stilbenes, representing stilbenoid structures present in residual lignins, have been synthesized by condensation of monochloroacetaldehyde diethylacetal with appropriate phenols and phenol ethers, followed by alkali- or acid-promoted rearrangement of the resulting 1,1-diaryl-2-chloroethanes. It is proposed that the mechanism of these rearrangement steps involves aryl migration with formation of intermediates of the spiro-cyclohexadienone type. The yields of individual stilbenes vary within wide ranges and are in certain cases moderate. However, the method is competitive due to its simplicity and the availability of the starting materials required.
Phospholipid-associated Annexin A2-S100A10 Heterotetramer and Its Subunits (2003)

Annexin A2 (p36) is a highly alpha-helical molecule that consists of two opposing sides, a convex side that contains the phospholipid-binding sites and a concave side, which faces the extracellular milieu and contains multiple ligand-binding sites. The amino-terminal region of annexin A2 extends along the concave side of the protein and contains the binding site for the S100A10 (p11) subunit. The interaction of these subunits results in the formation of the heterotetrameric form of the protein, annexin A2-S100A10 heterotetramer (AIIt). To simulate the orientation of AIIt on the plasma membrane we bound AIIt to a phospholipid bilayer that was immobilized on a BIAcore biosensor chip. Surface plasmon resonance was used to observe in real time the molecular interactions between phospholipid-associated AIIt or its annexin A2 subunit and the ligands, tissue-type plasminogen activator (t-PA), plasminogen, and plasmin. AIIt bound t-PA (Kd = 0.68 microm), plasminogen (Kd = 0.11 microm), and plasmin (Kd = 75 nm) with moderate affinity. Contrary to previous reports, the phospholipid-associated annexin A2 subunit failed to bind t-PA or plasminogen but bound plasmin (Kd = 0.78 microm). The S100A10 subunit bound t-PA (Kd = 0.45 microm), plasminogen (Kd = 1.81 microm), and plasmin (Kd = 0.36 microm). Removal of the carboxyl-terminal lysines from the S100A10 subunit attenuated t-PA and plasminogen binding to AIIt. These results show that the carboxyl-terminal lysines of S100A10 form t-PA and plasminogen-binding sites. In contrast, annexin A2 and S100A10 contain distinct binding sites for plasmin.
Novel Speckle-Tracking Radial Strain From Routine Black-and-White Echocardiographic Images to Quantify Dyssynchrony and Predict Response to Cardiac Resynchronization Therapy (2006)

Speckle-tracking radial strain can quantify dyssynchrony and predict immediate and long-term response to CRT and has potential for clinical application.