gebhart/patrepeval huggingface dataset:
Model-updated image guidance: initial clinical experiences with gravity-induced brain deformation (1999)

Image-guided neurosurgery relies on accurate registration of the patient, the preoperative image series, and the surgical instruments in the same coordinate space. Recent clinical reports have documented the magnitude of gravity-induced brain deformation in the operating room and suggest these levels of tissue motion may compromise the integrity of such systems. We are investigating a model-based strategy which exploits the wealth of readily-available preoperative information in conjunction with intraoperatively acquired data to construct and drive a three dimensional (3-D) computational model which estimates volumetric displacements in order to update the neuronavigational image set. Using model calculations, the preoperative image database can be deformed to generate a more accurate representation of the surgical focus during an operation. In this paper, we present a preliminary study of four patients that experienced substantial brain deformation from gravity and correlate cortical shift measurements with model predictions. Additionally, we illustrate our image deforming algorithm and demonstrate that preoperative image resolution is maintained. Results over the four cases show that the brain shifted, on average, 5.7 mm in the direction of gravity and that model predictions could reduce this misregistration error to an average of 1.2 mm.
Evolutionary programming as a platform for in silico metabolic engineering (2005)

We show that evolutionary programming enables solving large gene knockout problems in relatively short computational time. The proposed algorithm also allows the optimization of non-linear objective functions or incorporation of non-linear constraints and additionally provides a family of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span several different pathways and may be necessary for solving challenging metabolic engineering problems.
Pinlight displays (2014)

We present a novel design for an optical see-through augmented reality display that offers a wide field of view and supports a compact form factor approaching ordinary eyeglasses. Instead of conventional optics, our design uses only two simple hardware components: an LCD panel and an array of point light sources (implemented as an edge-lit, etched acrylic sheet) placed directly in front of the eye, out of focus. We code the point light sources through the LCD to form miniature see-through projectors. A virtual aperture encoded on the LCD allows the projectors to be tiled, creating an arbitrarily wide field of view. Software rearranges the target augmented image into tiled sub-images sent to the display, which appear as the correct image when observed out of the viewer's accommodation range. We evaluate the design space of tiled point light projectors with an emphasis on increasing spatial resolution through the use of eye tracking. We demonstrate feasibility through software simulations and a real-time prototype display that offers a 110° diagonal field of view in the form factor of large glasses and discuss remaining challenges to constructing a practical display.
Dipolar DC Collisional Activation in a “Stretched” 3-D Ion Trap: The Effect of Higher Order Fields on rf-Heating (2012)

Applying dipolar DC (DDC) to the end-cap electrodes of a 3-D ion trap operated with a bath gas at roughly 1 mTorr gives rise to ‘rf-heating’ and can result in collision-induced dissociation (CID). This approach to ion trap CID differs from the conventional single-frequency resonance excitation approach in that it does not rely on tuning a supplementary frequency to coincide with the fundamental secular frequeny of the precursor ion of interest. Simulations using the program ITSIM 5.0 indicate that application of DDC physically displaces ions solely in the axial (inter end-cap) dimension whereupon ion acceleration occurs via power absorption from the drive rf. Experimental data shows that the degree of rf-heating in a stretched 3-D ion trap is not dependent solely on the ratio of the dipolar DC voltage/radio frequency (rf) amplitude, as a model based on a pure quadrupole field suggests. Rather, ion temperatures are shown to increase as the absolute values of the dipolar DC and rf amplitude both decrease. Simulations indicate that the presence of higher order multi-pole fields underlies this unexpected behavior. These findings have important implications for the use of DDC as a broad-band activation approach in multi-pole traps.
Safety Analysis of Ex Vivo -Expanded NK and NK-Like T Cells Administered to Cancer Patients: a Phase I Clinical Study (2009)

The chimeric state after allogeneic hematopoietic stem cell transplantation provides a platform for adoptive immunotherapy using donor-derived immune cells. The major risk with donor lymphocyte infusions (DLIs) is the development of graft-versus-host disease (GvHD). Development of new DLI products with antitumor reactivity and reduced GvHD risk represents a challenging task in cancer immunotherapy. Although natural killer (NK) and NK-like T cells are promising owing to their antitumor activity, their low concentrations in peripheral blood mononuclear cells reduces their utility in DLIs. We have recently developed a system that allows expansion of clinical-grade NK and NK-like T cells in large numbers. In this study, the safety of donor-derived long-term ex vivo-expanded human NK and NK-like T cells given as DLIs was investigated as immunotherapy for cancer in five patients following allogeneic stem cell infusion. Infusion of the cells was safe whether administered alone or with IL-2 subcutaneously. No signs of acute GvHD were observed. One patient with hepatocellular carcinoma showed markedly decreased serum alpha-fetoprotein levels following cell infusions. These findings suggest that the use of ex vivo-expanded NK and NK-like T cells is safe and appears an attractive approach for further clinical evaluation in cancer patients.
Beyond Cartesian Representations for Local Descriptors (2019)

The dominant approach for learning local patch descriptors relies on small image regions whose scale must be properly estimated a priori by a keypoint detector. In other words, if two patches are not in correspondence, their descriptors will not match. A strategy often used to alleviate this problem is to “pool” the pixel-wise features over log-polar regions, rather than regularly spaced ones. By contrast, we propose to extract the “support region” directly with a log-polar sampling scheme. We show that this provides us with a better representation by simultaneously oversampling the immediate neighbourhood of the point and undersampling regions far away from it. We demonstrate that this representation is particularly amenable to learning descriptors with deep networks. Our models can match descriptors across a much wider range of scales than was possible before, and also leverage much larger support regions without suffering from occlusions. We report state-of-the-art results on three different datasets.
Hydrolytic Cleavage of N-Terminal Peptide Bonds by a Cobalt Chelate (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrolytic Cleavage of N-Terminal Peptide Bonds by a Cobalt ChelateJames P. Collman and David A. BuckinghamCite this: J. Am. Chem. Soc. 1963, 85, 19, 3039–3040Publication Date (Print):October 1, 1963Publication History Published online1 May 2002Published inissue 1 October 1963https://pubs.acs.org/doi/10.1021/ja00902a048https://doi.org/10.1021/ja00902a048research-articleACS PublicationsRequest reuse permissionsArticle Views213Altmetric-Citations42LEARN 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
The Expanding Role of Mass Spectrometry in Metabolite Profiling and Characterization (2005)

Mass spectrometry has a strong history in drug-metabolite analysis and has recently emerged as the foremost technology in endogenous metabolite research. The advantages of mass spectrometry include a wide dynamic range, the ability to observe a diverse number of molecular species, and reproducible quantitative analysis. These attributes are important in addressing the issue of metabolite profiling, as the dynamic range easily exceeds nine orders of magnitude in biofluids, and the diversity of species ranges from simple amino acids to lipids to complex carbohydrates. The goals of the application of mass spectrometry range from basic biochemistry to clinical biomarker discovery with challenges in generating a comprehensive profile, data analysis, and structurally characterizing physiologically important metabolites. The precedent for this work has already been set in neonatal screening, as blood samples from millions of neonates are tested routinely by mass spectrometry as a diagnostic tool for inborn errors of metabolism. In this review, we will discuss the background from which contemporary metabolite research emerged, the techniques involved in this exciting area, and the current and future applications of this field.
A Y639F/H784A T7 RNA polymerase double mutant displays superior properties for synthesizing RNAs with non-canonical NTPs (2002)

A T7 RNA polymerase in which Tyr639 is mutated to Phe readily utilizes 2'-deoxy, 2'-NH2 and 2'-F NTPs as substrates and has been widely used to synthesize modified RNAs for a variety of applications. This mutant does not readily utilize NTPs with bulkier 2'-substituents, nor does it facilitate incorporation of NTPs with modifications at other positions. Introduction of a second mutation (H784A) into the Y639F background markedly enhances utilization of NTPs with bulky 2'-substituents (2'-OMe and 2'-N3), and may also enhance use of NTPs with modifications at other than the 2'-position. The Y639F/H784A double mutant may therefore be exceptionally useful for incorporation of a variety of non-canonical NMPs into RNA.
Overexpression of Orphan G–Protein-Coupled Receptor, Gpr49 , in Human Hepatocellular Carcinomas With β–Catenin Mutations (2003)

To identify the genes responsible for carcinogenesis and progression of hepatocellular carcinoma (HCC), we screened differentially expressed genes in several human HCC cell lines. Among these genes, Gpr49 was up-regulated in PLC/PRF/5 and HepG2. Gpr49 is a member of the glycoprotein hormone receptor subfamily, which includes the thyroid-stimulating hormone receptor (TSHR). However, Gpr49 remains to be an orphan G-protein-coupled receptor. By real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR) analysis, overexpression (>3-fold increase compared with the corresponding noncancerous liver tissue) of Gpr49 mRNA was observed in 18 of 38 (47%) HCCs compared with corresponding noncancerous livers. Clinicopathologically, overexpression of Gpr49 was frequently observed in HCC with mutation in beta-catenin exon 3 (14 of 16 cases, 87.5%). Moreover, introduction of mutant beta-catenin into mouse hepatocytes in culture caused up-regulation of the Gpr49 mouse homologue. Therefore, Gpr49 is likely to be a target gene activated by Wnt-signaling in HCC. In conclusion, although much is still unknown, Gpr49 may be critically involved in the development of HCCs with beta-catenin mutations and has the potential to be a new therapeutic target in the treatment of HCC.
Preparation and Partial Characterization of Old Yeast Cells (1990)

Age-synchronized populations of the binding yeast Saccharomyces cerevisiae were prepared by a combination of growth-synchronization methods and cell separation by rate-zonal sedimentation in density gradients. The procedure allowed the bulk preparation of cells of any desired age up to at least 20 generations with minimum yields of 10(8) cells per preparation, starting with 6 X 10(9) 0-generation cells. The purity of the preparations was greater than 90%, with an accuracy of +/- 2 generations. The procedure itself had no detrimental effects on the cells, as indicated by a number of physiological parameters. Cell viability and resistance to sonication remained essentially unchanged during aging. In contrast, cell size and generation time increased, providing biomarkers for the aging process. The procedure described here should help establish yeast as a useful model system for studies of cellular aging at the molecular level.
Reduced Frizzled Receptor 4 Expression Prevents WNT/β-Catenin–driven Alveolar Lung Repair in Chronic Obstructive Pulmonary Disease (2017)

Reduced FZD4 expression in COPD contributes to impaired alveolar repair capacity.
Development of superparamagnetic nanoparticles for MRI: effect of particle size, charge and surface nature on biodistribution (1996)

Twelve superparamagnetic Magnetite-Dextran (MD) nanoparticles potentially useful as contrast agents for Magnetic Resonance Imaging (MRI), with different sizes, charges and surface natures, were produced and internally labelled with (59)Fe in order to investigate the effect of their physicochemical properties on their biodistribution in mice. In a first step, neutral MD particles of a size 33-90.6 nm were studied. Next, the influence of charge was investigated with negative and positive particles (MDL, MDD, MDDEAE). The former (-25, -30 mV) were small, around 30 nm in size whereas the latter (+20 mV) were larger (104 nm). The effect of surface nature was evaluated using MD particles coated with polyoxyethylene-polyoxypropylene copolymers (Synperonic: these MDP particles were neutral and larger in size (65.9-76.4 nm). Experiments showed that 20 min post-injection (2 mg Fe/kg), liver uptake was enhanced when the mean diameter increased: 22% for the smallest and 42% for the largest. It was up to 3 X lower for electrically neutral particles than for charged particles. Coated particles presented higher vascular persistence. The diagnostic potential for liver, lymph node or vascular imaging were discussed.
Thermal conductivity of composites of aligned nanoscale and microscale wires and pores (2006)

Two-dimensional composite materials made from aligned nano- and microwires hold great promise for various applications such as thermoelectric device. Similarly, two-dimensional composites made from aligned nanoscale pores are also very important for various technologies. Phonon transport along such composites primarily involves three nondimensional parameters based on the phonon mean paths in the host medium and the wire. The first of these is the ratio of interwire distance to the phonon mean free path in the host medium, the second is the ratio of the diameter of the wire to the phonon mean free path in the host medium, and the third is the ratio of the diameter of the wire to the phonon mean free path in the wire. We develop an analytical model for the thermal conductivity in the longitudinal direction of these composites by solving the phonon Boltzmann transport equation. The analytical model includes the dependences of all three parameters and is in excellent agreement with a recently reported numerical model [Yang et al., Phys. Rev. B 72, 125418 (2005)]. Our solution shows that the scattering of phonons in the host medium at the wire interface reduces the thermal conductivity of the host medium.
Micromachined needles for the transdermal delivery of drugs (2002)

Although modern biotechnology has produced extremely sophisticated and potent drugs, many of these compounds cannot be effectively delivered using current drug delivery techniques (e.g., pills and injections). Administration across skin by transdermal drug delivery is an attractive alternative, but it is limited by the remarkably poor permeability of the skin. Because the primary barrier to transport is located in the upper 10-15 /spl mu/m of skin, and because nerves are only found in deeper tissue, we made arrays of microneedles long enough to cross the permeability barrier but not so long that they stimulate nerves, thereby causing no pain. These microneedles were fabricated using the Black Silicon Method, which is a reactive ion etching process in which an SF/sub 6//O/sub 2/ plasma etches silicon anisotropically. When inserted into skin in vitro, these microneedles demonstrated excellent mechanical properties and enhanced skin permeability to calcein, a model drug, by up to four orders of magnitude. Limited tests on humans demonstrated that microneedles were painless.
A Randomized Trial of the Activity and Safety of Ro 24-7429 (Tat Antagonist) versus Nucleoside for Human Immunodeficiency Virus Infection (1995)

Journal Article A Randomized Trial of the Activity and Safety of Ro 24-7429 (Tat Antagonist) versus Nucleoside for Human Immunodeficiency Virus Infection Get access Richard H. Haubrich, Richard H. Haubrich Reprints or correspondence: Dr. Richard H. Haubrich, UCSD Treatment Center, 2760 5th Ave., Suite 300, San Diego, CA 92103. Search for other works by this author on: Oxford Academic PubMed Google Scholar Charles Flexner, Charles Flexner Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael M. Lederman, Michael M. Lederman Search for other works by this author on: Oxford Academic PubMed Google Scholar Martin Hirsch, Martin Hirsch Search for other works by this author on: Oxford Academic PubMed Google Scholar Carla P. Pettinelli, Carla P. Pettinelli Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard Ginsberg, Richard Ginsberg Search for other works by this author on: Oxford Academic PubMed Google Scholar Paul Lietman, Paul Lietman Search for other works by this author on: Oxford Academic PubMed Google Scholar Fayez M. Hamzeh, Fayez M. Hamzeh Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen A. Spector, Stephen A. Spector Search for other works by this author on: Oxford Academic PubMed Google Scholar Douglas D. Richman Douglas D. Richman Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 172, Issue 5, November 1995, Pages 1246–1252, https://doi.org/10.1093/infdis/172.5.1246 Published: 01 November 1995 Article history Received: 13 March 1995 Revision received: 20 June 1995 Published: 01 November 1995
MALDI-TOF Analysis of Polymerase Chain Reaction Products from Methanotrophic Bacteria (1998)

Polymerase chain reaction (PCR) assays were designed to amplify 56- and 99-base regions of the pmoA gene from Methylosinus trichosporium OB3b and Methylomicrobium albus BG8, two species of methanotrophic bacteria that are of interest for monitoring bioremediation activity. The PCR product sizes are in a mass range that is accessible to analysis by MALDI-TOF mass spectrometry. A rapid purification procedure using commercially available reversed-phase cartridges was applied prior to MALDI-TOF analysis. A small aliquot (1.5%, 1.5 microL) from a single 100-microL PCR reaction was sufficient for reliable detection. No cross-amplification products were observed when primers designed for one bacterial species were used with genomic DNA of the other species. The methodology described here has potential to allow less expensive and faster characterization of the ability of microbial populations to destroy pollutants in groundwater and soil at contaminated industrial sites.
Scalable parallel programming with CUDA (2008)

Is CUDA the parallel programming model that application developers have been waiting for?
[Prolonged action preparation of cefaclor]. (1985)

This study was conducted to develop a prolonged action preparation of cefaclor (CCL) which can offer, with the twice-a-day administration, as much effectiveness as its conventional preparation (Kefral capsule) with the 3 times-a-day administration. Absorption site of CCL in gastrointestinal tract, preparation form (enteric coated granules) which slowly release CCL, dissolution property of the form, and mixed ratio of the form and rapid release form (nonenteric coated granules) were studied and complex granules consisting of 40% of nonenteric coated granules and 60% of enteric coated granules which dissolve at pH 6 were chosen as a prolonged action preparation of CCL. Bactericidal activity of the prolonged action preparation (S6472) was confirmed to be the same as that of the conventional preparation by comparative viable cell count study in which concentrations of CCL simulated to plasma concentrations following the administration of S6472 at the dosage of 375 mg b.i.d. and the conventional preparation at the dosage of 250 mg t.i.d. were used. From the above, S6472 is considered to be a prolonged action preparation of CCL which serve our purpose. Since S6472 can be given with the twice-a-day administration, its daytime administration is not necessary. Therefore, S6472 is considered to be much useful preparation for the patients.
Current Directions in Computer Music Research (1990)

An expensive laboratory luxury just 25 years ago, computer music is now entering the public domain. Inexpensive digital keyboards and related hardware are more widely available than the piano. These 21 original contributions by composers, behavioral scientists, engineers, and other specialists from many of the international centers of research in computer music provide an inside report on the most sophisticated aspects of digital synthesis, control and understanding of musical sound, and related work on perception. The use of the computer to analyze and synthesize complex sounds has resulted in faster and more accurate experimental study of this key aspect of human perception. Many of the chapters in this book provide new insights into sounds and hearing. These include the investigation of loudness, masking, and binaural phenomena, and also an extensive study of the perceived pitch of sounds, many of which are remote from sounds ever heard in nature. Among the specific topics covered are speech songs, synthesis of the singing voice, spatial reverberation, Fourier-transform-based timbral manipulations, the simulation of bowed instruments, automatic counterpoint, and a conductor program utilizing a mechanical baton. A chapter authored jointly by Mathews and Pierce describes a new musical scale they have been working on over the past few years. Max V. Mathews and John R. Pierce are members of the music faculty at Stanford University. Both spent the major part of their professional lives at Bell Telephone Laboratories, where Mathews directed the Acoustical & Behavioral Research Center, and Pierce directed the Communication Sciences Division.Current Directions in Computer Music Research isincluded in the System Development Foundation Benchmark series. The System Development Foundation was one of the first major supporters of computer music research.