gebhart/patrepeval huggingface dataset:
<title>Iterative approach to partial-volume artifact reduction in CT</title> (1998)

One of the basic assumptions in the computed tomography (CT) is that the scanned object has constant attenuation characteristics across the thickness of the slice. In reality, however, this assumption is often violated. The projection data set of a head CT scan, for example, is often corrupted by bony structures partially intruded into the scanning plane. As a result, severe streaking and shading artifacts appear in the reconstructed images. This phenomenon is called partial volume. In this paper, we propose an iterative approach to the partial volume artifact reduction. CT images are first reconstructed with a filtered backprojection algorithm. The generated images subsequently undergo a fuzzy membership classification process to arrive at bone-only images, which in turn will be used to produce gradient images. The projection error is then calculated based on the gradient image. For better error estimation, the scan data is collected in a helical mode and highly overlapped images are reconstructed. The error term is filtered and back-projected to produce a partial volume error image, which is scaled and subtracted from the original image. Various phantom studies have demonstrated the effectiveness of our approach.
Chemically bonded diamondlike carbon films from ion-beam deposition (1987)

Carbon films on a Ni(111) surface are deposited from 1--300-eV mass-selected ${\mathrm{C}}^{+}$ beams in a UHV chamber and the energy and dose dependence of the C Auger line shape is monitored. Initial deposition forms a carbide structure which is chemically bonded to the surface. The Auger line shape evolves with increasing ${\mathrm{C}}^{+}$ dose into that of a diamondlike structure for ion energies in the range 10--300 eV. Features of the x-ray and the ultraviolet photoemission spectra support this interpretation. The diamondlike films do not chemisorb ${\mathrm{O}}_{2}$, have a low sputtering yield with ${\mathrm{O}}^{+}$ ions, and exhibit a higher thermal stability than the carbidic films; these results are discussed in terms of a qualitative model.
Inverse ion-exchange method for glass waveguide fabrication (1990)

A new method, inverse ion exchange, is proposed and demonstrated for the fabrication of single-mode channel waveguides. In this method the channel waveguide is formed by backdiffusion of the refractive-index-increasing ions from an ion-exchanged planar waveguide. Finite-difference methods are used to model the fabrication technique and to calculate the field of the fundamental mode of the waveguide. It is also proved experimentally that single-mode waveguides can be fabricated with the the reinverse ion-exchange method using a 10-microm mask stripe width.
Identification of two homologs of the Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) in retroperitoneal fibromatosis of different macaque species (1997)

Simian retroperitoneal fibromatosis (RF) is a vascular fibroproliferative neoplasm which has many morphological and histological similarities to human Kaposi's sarcoma (KS). Like epidemic KS in AIDS patients, RF is highly associated with an immunodeficiency syndrome (simian acquired immunodeficiency syndrome [SAIDS]) caused by a retrovirus infection. Recently, a new gammaherpesvirus, called Kaposi's sarcoma-associated herpesvirus (KSHV) or human herpesvirus 8 (HHV8), has been identified in KS tumors, suggesting that KS has a viral etiology. Our previous experimental transmission studies and epidemiological data suggest that RF also has an infectious etiology. In order to determine whether a similar virus is also associated with RF, we have assayed for the presence of an unknown herpesvirus using degenerate PCR primers targeting the highly conserved DNA polymerase genes of the herpesvirus family. Here we provide DNA sequence evidence for two new herpesviruses closely related to KSHV from RF tissues of two macaque species, Macaca nemestrina and Macaca mulatta. Our data suggest that KSHV and the putative macaque herpesviruses define a new group within the subfamily Gammaherpesvirinae whose members are implicated in the pathogenesis of KS and KS-like neoplasms in different primate species.
Substituted 7-Amino-5-thio-thiazolo[4,5-<i>d</i>]pyrimidines as Potent and Selective Antagonists of the Fractalkine Receptor (CX<sub>3</sub>CR1) (2013)

We have developed two parallel series, A and B, of CX3CR1 antagonists for the treatment of multiple sclerosis. By modifying the substituents on the 7-amino-5-thio-thiazolo[4,5-d]pyrimidine core structure, we were able to achieve compounds with high selectivity for CX3CR1 over the closely related CXCR2 receptor. The structure-activity relationships showed that a leucinol moiety attached to the core-structure in the 7-position together with α-methyl branched benzyl derivatives in the 5-position displayed promising affinity, and selectivity as well as physicochemical properties, as exemplified by compounds 18a and 24h. We show the preparation of the first potent and selective orally available CX3CR1 antagonists.
Isolation of Sequences that Span the Fragile X and Identification of a Fragile X-Related CpG Island (1991)

Yeast artificial chromosomes (YACs) were obtained from a 550-kilobase region that contains three probes previously mapped as very close to the locus of the fragile X syndrome. These YACs spanned the fragile site in Xq27.3 as shown by fluorescent in situ hybridization. An internal 200-kilobase segment contained four chromosomal breakpoints generated by induction of fragile X expression. A single CpG island was identified in the cloned region between markers DXS463 and DXS465 that appears methylated in mentally retarded fragile X males, but not in nonexpressing male carriers of the mutation nor in normal males. This CpG island may indicate the presence of a gene involved in the clinical phenotype of the syndrome.
Cardiac tolerability of pertuzumab plus trastuzumab plus docetaxel in patients with HER2-positive metastatic breast cancer in the CLEOPATRA study. (2012)

533^ Background: Addition of trastuzumab (T) to chemotherapy has transformed outcomes in pts with HER2-positive breast cancer. In pts who had received anthracyclines (A), T has been associated with cardiac dysfunction. Monitoring cardiac tolerability of anticancer drugs is important, including that of a new regimen combining T with a second anti-HER2 antibody that inhibits HER2 dimerization, pertuzumab (P). In CLEOPATRA, efficacy and safety of P+T+docetaxel (D) were studied in HER2-positive 1 st -line MBC (Baselga 2012). Methods: CLEOPATRA, a randomized, double-blind, placebo-controlled, ph III trial, enrolled 808 pts; 804 were included in the safety population. A baseline (BL) LVEF ≥50%, no history of congestive heart failure, and no LVEF decline to <50% during/after prior T were required. Treatment was administered q3w until disease progression or unmanageable toxicity (P/placebo [Pla]: 840 mg, followed by 420 mg; T: 8 mg/kg, followed by 6 mg/kg; D [≥6 cycles recommended]: 75 mg/m 2 , escalating to 100 mg/m 2 if tolerated). LVEF was assessed by ECHO or MUGA at BL, every 9 wks during treatment, at discontinuation, and up to 3 yrs thereafter. Adverse events (AE) were monitored continuously and graded according to NCI-CTCAE v3.0. Results: The incidence of any cardiac disorder (grade ≥1) as assessed by the investigators was similar with Pla+T+D (16.4%) and P+T+D (14.5%). LVSD (grade ≥1) was the most frequent cardiac AE and more common with Pla+T+D. At the time of data cutoff for this analysis, 8/11 symptomatic LVSD events had resolved; none fatal. All pts who developed symptomatic LVSD had ≥1 potential cardiac risk factor (prior A, prior T, radiation, smoking, diabetes, hypertension, other). Compared to the overall pt population, only prior A and radiation were higher in pts who developed symptomatic LVSD. Conclusions: CLEOPATRA provides evidence that P+T+D does not increase overall cardiac disorders, specifically symptomatic LVSD, compared to Pla+T+D. [Table: see text]
Reconstruction of Brachial Artery Pressure From Noninvasive Finger Pressure Measurements (1996)

BAP waves can be reconstructed from noninvasive finger pressure registrations when finger pressure waves are corrected for pulse wave distortion and individual pressure gradients.
Convex Optimization for Energy Management of Parallel Hybrid Electric Vehicles (2016)

This paper presents a comparison between two optimization methods for the energy management of a parallel hybrid electric powertrain: convex programming and Pontryagin’s Minimum Principle (PMP). The objective of this comparison is to validate the analytical solution by comparing the results with the ones obtained on the original model with Dynamic Programming (DP). Therefore, before its application, some necessary approximations and convexification were made on the original nonlinear and non-convex model. The validation of the simplified model was also carried out. In this paper, two cases are studied. In the first case, the supervisory control considers only the torque split between the Internal Combustion Engine (ICE) and the Electric Machine. In the second case, a binary decision ICE On/Off is included in the optimization problem. In order to solve the problem of the binary decision, which makes the problem non-convex, a analytical solution based on PMP is then proposed. The results show that the analytical solution is close to the optimal solution given by DP.
Simulations of radio-frequency lesions with varying brain electrode dimensions (2005)

Radio-frequency (RF) lesioning is a method utilising high frequency currents for thermal coagulation of pathological tissue or signal pathways. The current is delivered from an electrode with a temperature sensor, permitting control of the current at a desired target temperature. In the brain RF-lesioning can e.g. be used for severe chronic pain and movement disorders such as Parkinson’s disease. This thesis focuses on modelling and simulation with the aim of gaining better understanding and predictability of the lesioning process in deep brain structures. The finite element method (FEM) together with experimental comparisons was used to study the effects of electrode dimensions, electrode target temperature, electric and thermal conductivity of the brain tissue, blood perfusion and cerebrospinal fluid (CSF) filled cysts. Equations for steady current, thermal transport and incompressible flow were used together with statistical factorial design and regression analysis for this purpose. Increased target temperature, electrode tip length and electrode diameter increased the simulated lesion size, which is in accordance with experimental results. The influence of blood perfusion, modelled as an increase in thermal conductivity in non-coagulated tissue, gave smaller simulated lesions with increasing blood perfusion as heat was more efficiently conducted from the rim of the lesion. If no consideration was taken to the coagulation the lesion became larger with increased thermal conductivity instead, as the increase in conducted heat was compensated for through an increased power output in order to maintain the target temperature. Simulated lesions corresponded well to experimental in-vivo lesions. The electric conductivity in a homogeneous surrounding had little impact on lesion development. However this was not valid for a heterogeneous surrounding. CSF-filled cysts have a much higher electric conductivity than brain tissue focussing the current to them if the electrode tip is in contact with both. Heating of CSF can also cause considerable convective flow and as a result a very efficient heat transfer. This affected simulated as well as experimental lesion sizes and shapes resulting in both very large lesions if sufficient power compared to the cysts size was supplied and very small lesions if the power was low, mitigating the heat over a large volume. In conclusion especially blood perfusion and CSF can greatly affect the lesioning process and appear to be important to consider when planning surgical procedures. Hopefully this thesis will help improve knowledge about and predictability of clinical lesioning.
Acousto-optic gyroscope (2018)

An Acousto-Optic Gyroscope (AOG) consisting of a Mach-Zehnder interferometer (MZI) embedded into two inherently matched piezoelectric SAW resonators sharing the same cavity is presented. This constitutes the first demonstration of a MEMS strain-based optomechanical gyroscope that uses refractive index change due to the acousto-optic effect rather than conventional displacement sensing. This first prototype integrates acoustic and photonic components on the same lithium niobate on insulator (LNOI) substrate and showcases how optical detection can provide greater stability compared to acousto-electric transduction. This approach enables the development of a new class of MEMS-based gyroscopes that combines the advantages of both conventional MEMS and optical gyroscopes.
Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes (2019)

The CRISPR-Cas9 system has raised hopes for developing personalized gene therapies for complex diseases. Its application for genetic and epigenetic therapies in humans raises concerns over immunogenicity of the bacterially derived Cas9 protein. Here we detect antibodies to Streptococcus pyogenes Cas9 (SpCas9) in at least 5% of 143 healthy individuals. We also report pre-existing human CD8+T cell immunity in the majority of healthy individuals screened. We identify two immunodominant SpCas9 T cell epitopes for HLA-A*02:01 using an enhanced prediction algorithm that incorporates T cell receptor contact residue hydrophobicity and HLA binding and evaluated them by T cell assays using healthy donor PBMCs. In a proof-of-principle study, we demonstrate that Cas9 protein can be modified to eliminate immunodominant epitopes through targeted mutation while preserving its function and specificity. Our study highlights the problem of pre-existing immunity against CRISPR-associated nucleases and offers a potential solution to mitigate the T cell immune response.
Overpressure detection from compressional‐ and shear‐wave data (1999)

By analyzing experimental data we show that in many room‐dry rocks, the Poisson's ratio (PR) decreases with decreasing differential pressure (confining minus pore pressure). This means that in gas‐saturated rocks, PR decreases with increasing pore pressure. We confirm the generality of the observed effect by theoretically reproducing it via effective medium modeling. This effect can be used as a new tool for overpressure detection from surface seismic, cross‐well, sonic logs and measurements ahead of the drill bit.
Charged Polariton Luminescence from an Organic Semiconductor Microcavity (2019)

Strong coupling light to polaron optical transitions in an organic semiconductor microcavity leads to an unusual class of polariton that possesses a net charge. This species may offer a range of technologically useful optoelectronic properties but has thus far only been observed in passive reflectivity measurements. Here, we report room-temperature photoluminescence from both upper and lower branch polaron polariton states that originate from hole excitations in a p-doped 4,4′-cyclohexylidenebis[N,N-bis(4-methylphenyl)benzenamine] (TAPC) microcavity. Our observations under nonresonant excitation are in good agreement with classical dipole emission modeling, which suggests that polariton states in this system are populated radiatively via fluorescence from the polaron excited state reservoir. These results constitute one of the first observations of polaron luminescence from an organic semiconductor thin film and are an important prerequisite for realizing a charged polariton condensate.
Middle Latency Auditory Evoked Potential Anaesthesia Correlates of Consciousness: Practicality &amp; Constraints (2005)

The hypothesis of this study is that significant differentiation of consciousness (CO) and unconsciousness (UNCO) is possible, using individual ML+AEP (10-140 msec) latency measures, within the context of a practical routine clinical depth of anaesthesia monitoring device. We have assessed individual latency band measures of the middle-latency auditory evoked potential (ML+AEP) as candidates to measure depth of CO or UNCO amongst a group of anaesthetised surgical patients. We have also compared ML+AEP correlates with conventional auditory evoked potential (AEP) index and bispectral index (BIS). This study investigates amplitude measures, limits and the practicality of using a single EEG channel ML+AEP recording system. ML+AEP amplitude-related correlates were assessed against CO and UNCO events during anaesthesia. ML+AEP measures were computed for each of the following AEP component-related latency time bins (LTB): Na;15-25msec, Pa;25-35 msec, TP41;35-45 msec; Pb/P1; 45-55 msec, N1;80-100 msec, <N1;0-80 msec, >N1;80-140 msec, and ML+AEP;0-140 msec. Twenty patients (aged 28-68 yrs) undergoing day surgery had their electroencephalography (EEG) monitored during binaural auditory stimulus presentation (6.8 clicks per second). The AEP grand mean waveform (AEP<inf>gmw</inf>) was computed for each consecutive stimulus AEP event, by way of averaging the previous 256 AEPs. The mean and SD amplitude associated with each of the ML+AEP ranges were computed for the whole study period and also for the predetermined events 1 to 13 (CO:1;2;3;12;13 and UNCO:4-11). Results included BIS data, measures derived from the AEPgmw across both the ML+AEP range (0-140 msec), and also individual LTB segments.
Truncated Actin-Targeting Macrolide Derivative Blocks Cancer Cell Motility and Invasion of Extracellular Matrix (2021)

Cancer metastasis is a complex process involving highly motile tumor cells that breach tissue barriers, enter the bloodstream and lymphatic system, and disseminate throughout the body as circulating tumor cells. The primary cellular mechanism contributing to these critical events is the reorganization of the actin cytoskeleton. Mycalolide B (MycB) is an actin-targeting marine macrolide that can suppress proliferation, migration, and invasion of breast and ovarian cancer cells at low nanomolar doses. Through structure-activity relationship studies focused on the actin-binding tail region (C24-C35) of MycB, we identified a potent truncated derivative that inhibits polymerization of G-actin and severs F-actin by binding to actin's barbed end cleft. Biological analyses of this miniature MycB derivative demonstrate that it causes a rapid collapse of the actin cytoskeleton in ovarian cancer cells and impairs cancer cell motility and invasion of the extracellular matrix (ECM) by inhibiting invadopodia-mediated ECM degradation. These studies provide essential proof-of-principle for developing actin-targeting therapeutic agents to block cancer metastasis and establish a synthetically tractable barbed end-binding pharmacophore that can be further improved by adding targeting groups for precision drug design.
<title>New high-efficiency ion trap mobility detection system for narcotics and explosives</title> (1994)

A new patented ion trap mobility spectrometer design is presented. Conventional IMS designs typically operate below 0.1% efficiency. This is due primarily to electrical-field-driven, sample ion discharge on a shutter grid. Since 99.9% of the sample ions generated in the reaction region are lost in this discharge process, the sensitivity of conventional systems is limited. The new design provides greater detection efficiency than conventional designs through the use of an `ion trap' concept. The paper describes the plasma and sample ion dynamics in the reaction region of the new detector and discusses the advantages of utilizing a `field-free' space to generate sample ions with high efficiency. Fast electronic switching is described which is used to perturb the field-free space and pulse the sample ions into the drift region for separation and subsequent detection using pseudo real-time software for analysis and display of the data. Many applications for this new detector are now being considered including the detection of narcotics and explosives. Preliminary ion spectra, reduced mobility data and sensitivity data are presented for fifteen narcotics, including cocaine, THC, and LSD are reported.
Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting (2016)

This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple MR tissue parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization.
A new method for the enzymic synthesis of nucleosides using purine nucleoside phosphorylase (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new method for the enzymic synthesis of nucleosides using purine nucleoside phosphorylaseWilliam J. Hennen and Chi Huey WongCite this: J. Org. Chem. 1989, 54, 19, 4692–4695Publication Date (Print):September 1, 1989Publication History Published online1 May 2002Published inissue 1 September 1989https://pubs.acs.org/doi/10.1021/jo00280a046https://doi.org/10.1021/jo00280a046research-articleACS PublicationsRequest reuse permissionsArticle Views409Altmetric-Citations49LEARN 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
Antibody Production and Engineering in Plants (1996)

Plants have always been important in the pharmaceutical industry, and plant biotechnology now offers new applications. The use of heterologous expression systems for production of recombinant proteins including antibodies is no longer novel. Attention has now turned towards the end-user, and specifically to engineering the antibody to precise requirements. In expanding the choice of production systems, plants offer unique alternatives for antibody users not only in the bulk production of antibody molecules but also in the ability to assemble full-length and complex, multimeric antibodies. Although the initial investment of time and effort is substantial compared to that of other expression systems, antibody production on an agricultural scale can be envisioned, and the economy of this approach opens many new areas for potential antibody applications in addition to their traditional research and pharmaceutical uses.