gebhart/patrepeval huggingface dataset:
Remotely-Controlled Approach for Stereotactic Neurobiopsy (2002)

The objective of this study was to develop, demonstrate, and validate a remotely controlled operation scheme coupled with prospective magnetic resonance imaging (MRI)-based stereotaxy for in vivo neurosurgical applications. The novel concept of the prospective guidance scheme is to employ tomographical imaging feedback, such as MRI or CT, to facilitate prospectively the targeting process of a biopsy needle at near-real-time speed (1 image/s). Because the orientation of a biopsy needle pivoted at an entry point on die patient's skull has 2 degrees of freedom, the alignment of its trajectory to a target point can be guided by two-dimensional (2D) images whose plane is placed perpendicular to the desired trajectory. Using near-real-time 2D visual feedback during the adjustment of the alignment guide, the required trajectory alignment can be translated into a simple targeting task on a computer monitor employing a suitable graphic presentation. Also, both adjustments for the alignment and introduction of the biopsy needle were accomplished remotely with image-based feedback. The use of the method in actual MR-guided brain lesion biopsy procedures at 1.5 T showed an improved tissue yield due to the improved targeting accuracy even in the presence of brain shift. Furthermore, the postalignment trajectory can be validated immediately using near-real-time MRI scans in two orthogonal views before needle insertion. Because the final needle position is always visualized and confirmed, the consequent tissue sampling is performed with greater certainty, even in the case of a negative diagnosis. The actual targeting error was 1.53 ± 0.17 mm from an intended target location, with the maximum distance error of 1.72 mm at a depth of 85 mm. This remotely controlled surgical approach with intraoperative MRI guidance is feasible at 1.5 T, and has allowed neurosurgeons to perform neurobiopsies comfortably and efficiently in a routine clinical MR scanner. This scheme provides a unique alternative stereotactic procedure that can take full advantage of the prospective guidance potential offered by various modern tomographic imaging systems.
A 65nm CMOS 60 GHz class F-E power amplifier for WPAN applications (2012)

This work presents a two-stage 65nm CMOS 60 GHz power amplifier composed by a Class E power stage and a Class F driver stage, dedicated to low cost Wireless Personal Area Network (WPAN) applications. To provide a switching operation at 60 GHz, an output network with distributed elements is used instead of lumped elements. The simulation results show a saturated output power of 15 dBm with a peak PAE of 26% at 60 GHz. It achieves a gain of 15dB at 60 GHz.
Demystifying Via Impedance Optimization for High Speed Channels (2018)

Signal speeds of high speed channels double almost every generation and with increasing speeds, even a slight impedance discontinuity in the channel can adversely affect signal quality. Channel discontinuities come from several sources and each source must be carefully considered. One common source of channel discontinuity is the signal via. Via impedance needs to be designed with utmost care because high speed channels inevitably encounter a lot of via transitions in the form of BGA breakout vias, AC coupling capacitor vias, connector vias and transition vias. Upfront modeling and analysis for vias can mitigate reflections in a layout to achieve the required performance. In this paper, a method to optimize vias in both time and frequency domains is explained. A lot of common mistakes made in terms of rise-time assumptions, reference impedances and impedance targets are demystified and explained in detail with examples. This paper highlights the impact on via impedance on high frequency designs and showcases how in correct modeling assumptions can lead to suboptimal designs or in unnecessary overdesigning of the channels.
Disk scrubbing versus intra-disk redundancy for high-reliability raid storage systems (2008)

Two schemes proposed to cope with unrecoverable or latent media errors and enhance the reliability of RAID systems are examined. The first scheme is the established, widely used disk scrubbing scheme, which operates by periodically accessing disk drives to detect media-related unrecoverable errors. These errors are subsequently corrected by rebuilding the sectors affected. The second scheme is the recently proposed intradisk redundancy scheme which uses a further level of redundancy inside each disk, in addition to the RAID redundancy across multiple disks. Analytic results are obtained assuming Poisson arrivals of random I/O requests. Our results demonstrate that the reliability improvement due to disk scrubbing depends on the scrubbing frequency and the workload of the system, and may not reach the reliability level achieved by a simple IPC-based intra-disk redundancy scheme, which is insensitive to the workload. In fact, the IPC-based intra-disk redundancy scheme achieves essentially the same reliability as that of a system operating without unrecoverable sector errors. For heavy workloads, the reliability achieved by the scrubbing scheme can be orders of magnitude less than that of the intra-disk redundancy scheme.
Mass spectrometry of sulphur‐containing compounds. 3. The behaviour of some diastereomeric β‐hydroxy‐γ‐fluoro alkyl aryl sulphoxides (1989)

Abstract The electron ionization and chemical ionization mass spectrometry of some diastereomeric β‐hydroxy‐γ‐fluoro alkyl aryl sulphoxides is described and the mechanisms of the common fragmentation patterns are discussed with the aid of linked scans at constant B/E and at constant B 2 /E, mass‐analysed ion kinetic energy spectra and labelling experiments.
Coordinated optimization and modeling for location discovery in sensor networks (2008)

We address several well-known and new canonical location discovery (localization) problems in wireless networks, including engineering change-based node addition, and design and operation of location discovery infrastructure for mobile users. All problems are solved using coordinated development of data-driven statistical models, and combinatorial and continuous optimization techniques. The models are built in such a way that they are amenable for consequent optimization (e.g. linear, or convex, or isotonic). The optimization procedures are conducted such that they are robust against outliers and statistical uncertainties. 
From modeling point of view, our goal is to identify factors that predominantly influence the accuracy of location discovery and to establish relationships between different properties of the network and the corresponding location error. For this task, we use a combination of nonparametric statistical methods and combinatorial optimization techniques to construct and validate three types of models: measurement error models, terrain models and localization error models. 
From optimization point of view, we formulate the location discovery problem as an instance of (integer) linear or nonlinear program due to its computational complexity. However, if a related subproblem can be solved optimally, then we linearize or approximate the system of equations and use linear or convex programming techniques to solve them. Our techniques are realized both as centralized and localized algorithms; and our models and algorithms are built and evaluated using actual data collected from deployed networks.
Structure and Biosynthesis of Cuticular Lipids (1974)

The structure and composition of the cutin monomers from the flower petals of Vicia faba were determined by hydrogenolysis (LiAlH(4)) or deuterolysis (LiAlD(4)) followed by thin layer chromatography and combined gas-liquid chromatography and mass spectrometry. The major components were 10, 16-dihydroxyhexadecanoic acid (79.8%), 9, 16-dihydroxyhexadecanoic acid (4.2%), 16-hydroxyhexadecanoic acid (4.2%), 18-hydroxyoctadecanoic acid (1.6%), and hexadecanoic acid (2.4%). These results show that flower petal cutin is very similar to leaf cutin of V. faba. Developing petals readily incorporated exogenous [1-(14)C]palmitic acid into cutin. Direct conversion of the exogeneous acid into 16-hydroxyhexadecanoic acid, 10, 16-dihydroxy-, and 9, 16-dihydroxyhexadecanoic acid was demonstrated by radio gas-liquid chromatography of their chemical degradation products. About 1% of the exogenous [1-(14)C]palmitic acid was incorporated into C(27), C(29), and C(31)n-alkanes, which were identified by combined gas-liquid chromatography and mass spectrometry as the major components of the hydrocarbons of V. faba flowers. The radioactivity distribution among these three alkanes (C(27), 15%; C(29), 48%; C(31), 38%) was similar to the per cent composition of the alkanes (C(27), 12%; C(29), 43%; C(31), 44%). [1-(14)C]Stearic acid was also incorporated into C(27), C(29), and C(31)n-alkanes in good yield (3%). Trichloroacetate, which has been postulated to be an inhibitor of fatty acid elongation, inhibited the conversion of [1-(14)C]stearic acid to alkanes, and the inhibition was greatest for the longer alkanes. Developing flower petals also incorporated exogenous C(28), C(30), and C(32) acids into alkanes in 0.5% to 5% yields. [G-(3)H]n-octacosanoic acid (C(28)) was incorporated into C(27), C(29), and C(31)n-alkanes. [G-(3)H]n-triacontanoic acid (C(30)) was incorporated mainly into C(29) and C(31) alkanes, whereas [9, 10, 11-(3)H]n-dotriacontanoic acid (C(32)) was converted mainly to C(31) alkane. Trichloroacetate inhibited the conversion of the exogenous acids into alkanes with carbon chains longer than the exogenous acid, and at the same time increased the amount of the direct decarboxylation product formed. These results clearly demonstrate direct decarboxylation as well as elongation and decarboxylation of exogenous fatty acids, and thus constitute the most direct evidence thus far obtained for an elongation-decarboxylation mechanism for the biosynthesis of alkanes.
Ski is involved in transcriptional regulation by the repressor and full-length forms of Gli3 (2002)

Transcription factor Glioblastoma-3 (Gli3) is cleaved in the anterior region of the limb bud to generate its repressor form. In contrast, Sonic hedgehog (Shh) signaling from the posterior zone of polarizing activity blocks Gli3 processing and then induces the expression of Gli3 target genes, including Gli1. Here we report that the Ski corepressor binds to Gli3 and recruits the histone deacetylase complex. The Gli3-mediated repression was impaired by anti-Ski antibody and in Ski-deficient fibroblasts, and Shh-induced Gli1 gene transcription mediated by full-length Gli3 was inhibited by Ski. Furthermore, a Ski mutation enhanced the digit abnormalities caused by the Gli3 gene mutation. Thus, Ski plays an important role in pattern formation.
The HLA Ligand Atlas: A novel immuno-oncology resource for T-cell antigen discovery. (2020)

3128 Background: The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system, which is the basis for T cell-dependent tumor rejection. Therefore, a comprehensive map of the entirety of both HLA class I- and class II-presented peptides from various benign tissues is a highly sought after resource, as it enables the definition of tumor-association on the immunologically pivotal level of the HLA ligandome. Methods: Human tissue samples were snap frozen post mortem during autopsy. The study was approved by the local IRB. HLA ligands were immunopurified and characterized using an Orbitrap Fusion Lumos mass spectrometer coupled to an Ultimate 3000 RSLC Nano UHPLC System. Data acquisition was performed as technical triplicates in data-dependent mode, and data were analyzed using the containerized, computational pipeline MHCquant. Results: In this work, we describe the HLA Ligand Atlas, a comprehensive collection of matched HLA class I and class II ligandomes from 29 non-malignant tissues and 13 human subjects (208 samples in total), covering 38 HLA class I, and 17 HLA*DRB alleles and comprising 48,381 HLA class I and 16,146 HLA class II peptides. Nearly 50% of HLA ligands have not been previously described. The HLA Ligand Atlas is publicly available as a raw data resource, but also in the form of a user-friendly web interface that allows users to quickly formulate complex queries against the data set. Both downloadable data and the query interface are available at www.hla-ligand-atlas.org. Conclusions: This data set provides a valuable tool for research in diverse fields such as systems biology, general immunology, autoimmune disease and organ transplantation. Most importantly, the HLA Ligand Atlas provides essential information for translational applications in immuno-oncology. The knowledge of HLA ligands from benign tissues strongly supports the informed design of proteogenomic HLA-dependent target discovery approaches.
Structure from Motion for Panorama-Style Videos (2019)

We present a novel Structure from Motion pipeline that is capable of reconstructing accurate camera poses for panorama-style video capture without prior camera intrinsic calibration. While panorama-style capture is common and convenient, previous reconstruction methods fail to obtain accurate reconstructions due to the rotation-dominant motion and small baseline between views. Our method is built on the assumption that the camera motion approximately corresponds to motion on a sphere, and we introduce three novel relative pose methods to estimate the fundamental matrix and camera distortion for spherical motion. These solvers are efficient and robust, and provide an excellent initialization for bundle adjustment. A soft prior on the camera poses is used to discourage large deviations from the spherical motion assumption when performing bundle adjustment, which allows cameras to remain properly constrained for optimization in the absence of well-triangulated 3D points. To validate the effectiveness of the proposed method we evaluate our approach on both synthetic and real-world data, and demonstrate that camera poses are accurate enough for multiview stereo.
P039: HLA expression status and prognostic impact of B-cell content in patients with early-stage unfavorable Hodgkin lymphoma (2022)

Figure 1: Kaplan-Meier Analysis of PFS according to B-cell content Introduction: Classical Hodgkin lymphoma (HL) is characterized by a complex, increasingly understood microenvironment which is considered crucial for survival and proliferation of the malignant Hodgkin and Reed-Sternberg cells (HRSC). HLA expression is a key component for immune cell interaction and thereby microenvironment composition. Additionally, we and others have shown that a low B-cell content is a negative prognostic factor in advanced-stage HL which can be assessed quantitatively by digital pathology using slides generated for diagnostic purposes (Jachimowicz 2021). Herein we aimed to assess HLA expression status and the prognostic relevance of B-cell content in early-stage unfavorable HL. Patients and Methods: We analyzed primary tumor biopsies of patients with newly diagnosed early-stage unfavorable HL either treated with 4xABVD or 2xBEACOPPesc followed by 2xABVD within the GHSG HD14 trial, each consolidated by 30Gy involved-field radiotherapy (von Tresckow 2012). Our project cohort was enriched for patients suffering from disease progression or relapse (20.2% vs 6.2% in the total HD14 population). Whole-slide image analysis of CD20 staining was performed using TissueStudio 64 (Definiens) to quantify the B-cell content. Immunohistochemistry for ß-2-Microglobulin (HLA-I) and HLA-DP (HLA-II) was scored by visual inspection on HRSC. Results: Major clinical variables such as sex, age, B-symptoms, GHSG risk factors and histological subtypes did not differ significantly between the project cohort (N=198) and HD14 trial population (N=1889). HLA-I and -II were expressed on HRSC in 13.3% and 49.1% of cases, respectively. Only 8.3% of cases showed positivity for both HLA-I and -II, while 45.8% were double-negative. Median B-cell content was lower in HLA-I negative (12.8% vs 18.5%, p=0.0168) and double-negative cases (11.5% vs 18.1% in double-positive cases, p=0.0392). A low B-cell content was associated with unfavorable outcome: 5-year PFS estimates are 70.6% and 83% for subjects with low (<=8%) or high (>8%) B-cell content (Figure 1, log-rank p=0.08). A stepwise multivariate analysis including type of treatment confirmed B-cell content as the only significant risk factor for PFS (p=0.0196). Conclusions: HLA expression is variable in early-stage unfavorable HL and associated with B-cell content. Similarly to advanced-stage HL, a low B-cell content measured by digital pathology of routinely available diagnostic slides is associated with unfavorable outcome.
Low profile, cavity backed spiral on thin ferrite ground plane for high power operation above 200MHz (2009)

This paper presents a small, low profile, 2" thick and 14" in aperture, spiral antenna backed by a thin ferrite ground plane. The antenna is intended to cover satellite (UHF TacSat (earth to LEO, 243-318 MHz)) and radio (PRC-148, PRC- 117F, PSC-5D (243-512 MHz)) communications. Miniaturization, ground plane treatment, and resistive loading techniques are considered, and a design optimization is carried out to determine the several material, shape and geometry parameters for best performance. In this paper, we carry out step-by-step design to achieve the challenging goals. Material treatments, inductive loading, resistive termination and impedance matching issues are addressed throughout the design. Measured and simulated data are then presented in the last section leading to impressive conclusions about the capability of materials to overcome the perennial issue associated with the ground plane's negative effects for conformal installations.
The P-Answer-State Header Extension to the Session Initiation Protocol for the Open Mobile Alliance Push to Talk over Cellular (2007)

This document describes a private Session Initiation Protocol (SIP)
header (P-header) used by the Open Mobile Alliance (OMA) for Push to
talk over Cellular (PoC) along with its applicability, which is
limited to the OMA PoC application. The P-Answer-State header is used
for indicating the answering mode of the handset, which is particular
to the PoC application. This memo provides information for the
Internet community.
Enantioselective addition of diethylzinc to aldehydes catalyzed by polymer-supported chiral amino alcohols. Evidence for a two zinc species mechanism (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective addition of diethylzinc to aldehydes catalyzed by polymer-supported chiral amino alcohols. Evidence for a two zinc species mechanismShinichi Itsuno and Jean M. J. FrechetCite this: J. Org. Chem. 1987, 52, 18, 4140–4142Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/jo00227a043https://doi.org/10.1021/jo00227a043research-articleACS PublicationsRequest reuse permissionsArticle Views656Altmetric-Citations131LEARN 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
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network (2022)

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.
Blind comparison of Abbott and Dupont HIV antigen ELISA tests for detecting antigenaemia in asymptomatic human immunodeficiency virus antibody positive homosexual men. (1990)

Three hundred and ninety eight serum samples from 270 human immunodeficiency virus (HIV) antibody positive asymptomatic homosexual men were tested in the Abbott and Dupont HIV antigen ELISA tests. In the Abbott test 62 (16%) of the sera were positive, according to the manufacturer's instructions, compared with 55 (14%) in the Dupont test. Twenty six sera were positive with the Abbott test but negative with the Dupont test and 19 sera were positive only by the Dupont test. Only 36 (9%) of the sera were positive in both tests. The Abbott confirmatory neutralisation test gave excellent agreement with the initial Abbott HIV antigen ELISA test; the Dupont confirmatory test was only in agreement with the initial positive Dupont antigen ELISA test in one third of the sera tested. Although the overall sensitivity of each of the two commercial assays tested was similar, the Abbott method may be preferable for clinical purposes if confirmation of an initial ELISA positive test result by neutralisation assay is required.
Third-Order Hyper-Rayleigh Scattering in an Azobenzene Dye Solution (2000)

We report the first observation of third-order hyper-Rayleigh scattering superimposed on three-photon-induced fluorescence in a chloroform solution of the azobenzene dye Disperse Red 1. Cubic dependence of the intensity of the scattered third-harmonic light on the intensity of the fundamental light was observed. The intensity of the scattered third-harmonic light was linearly proportional to the number density of the dye. The estimated value of third-order polarizability γ 3333 of the dye under resonance conditions was 8.7×10 -33 esu.