gebhart/patrepeval huggingface dataset:
Detection of Aneurysms by 64-Section Multidetector CT Angiography in Patients Acutely Suspected of Having an Intracranial Aneurysm and Comparison with Digital Subtraction and 3D Rotational Angiography (2007)

In comparison with the available literature, 64MSCTA may have improved the detection of less than 4-mm aneurysms compared with 4- or 16-section CTA. However, the combination of DSA with 3DRA is currently the most sensitive technique to detect untreated aneurysms and should be considered in suspicious cases of SAH where the aneurysm is not depicted by 64MSCTA, because 64MSCTA may occasionally miss aneurysms less than 3-4 mm size.
A functional map of HIV-host interactions in primary human T cells (2022)

Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.
Geometrical Properties of Modelled Robot Elasticity: Part I — Decomposition (1992)

Abstract A new geometric decomposition is introduced that diagonalizes the 6 × 6 stiffness and compliance matrices which model robot elasticity. Using screw theory, a congruence transformation is developed from the three orthogonal wrench-compliant axes and the three orthogonal twist-compliant axes. The diagonal elements are the stationary values of linear and rotational compliance and stiffness. This generalizes and is analogous to principal axes and principal values for stress, strain, and rotational inertia. It is proved that the decomposition always exists for both the nonsingular and singular cases.
NGC 1097 - The structure of the central 3 kiloparsecs at 10 microns (1981)

It is found that the central, optically bright region of the spiral galaxy NGC 1097 is a strong 10 micron source. A striking correlation is seen between the optical and infrared surface brightnesses. The properties of these sources imply that young stars power the infrared emission. It is inferred that the central 30 arcsec of NGC 1097 has a large bolometric luminosity of about 10 to the 11th solar luminosities, most of which originates in a ring approximately 2 kpc in diameter. These observations strongly support the hypothesis that the infrared emission from galaxies is often associated with bursts of star formation.
Implementation of serological and molecular tools to inform COVID-19 patient management: protocol for the GENCOV prospective cohort study (2021)

This study was approved by Clinical Trials Ontario Streamlined Ethics Review System (CTO Project ID: 3302) and the research ethics boards at participating hospitals. Study findings will be disseminated through peer-reviewed publications, conference presentations and end-users.
Antigens of Hepatitis Delta Virus in the Liver and Serum of Humans and Animals (1986)

Journal Article Antigens of Hepatitis Delta Virus in the Liver and Serum of Humans and Animals Get access Katherine F. Bergmann, Katherine F. Bergmann Division of Molecular Virology and Immunology, Georgetown University, Rockville, Maryland Please address requests for reprints to Dr. Katherine F. Bergmann, Division of Molecular Virology and Immunology, 5640 Fishers Lane, Rockville, Maryland 20852. Search for other works by this author on: Oxford Academic PubMed Google Scholar John L. Gerin John L. Gerin Division of Molecular Virology and Immunology, Georgetown University, Rockville, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 154, Issue 4, October 1986, Pages 702–706, https://doi.org/10.1093/infdis/154.4.702 Published: 01 October 1986 Article history Received: 10 March 1986 Revision received: 12 May 1986 Published: 01 October 1986
COMBINING BACKGROUND MEMORY MANAGEMENT AND REGULAR ARRAY CO-PARTITIONING, ILLUSTRATED ON A FULL MOTION ESTIMATION KERNEL (2000)

Abstract In this paper an approach is presented to combine the design of background memory architectures and processor arrays for data dominated real-time applications. The formalized data transfer and storage exploration (DTSE) approach of IMEC involves a methodology for the design of a low-power small-size background memory organizations, meeting real-time constraints. The systematic space-time transformation and the subsequent co-partitioning approach of the Dresden University of Technology, allow the design of realistic processor arrays adapted to a given memory architecture. However, neither methodology can derive on its own the complete solution of a fully optimized memory organization, combining background and foreground memory. Extensions to enable this important problem will be presented here. First, both complementary methodologies will be summarized. Next, the main emphasis in this paper will be on the approach to design the processor array within the context of an already optimized and hence given memory architecture. The feasibility of the proposed combination is demonstrated on a representative test-vehicle for an important class of applications, namely a full motion estimation kernel in MPEG.
Different subsets of peripheral blood dendritic cells show distinct phenotypic and functional abnormalities in HIV-1 infection. (2005)

These results support the existence of a selective interaction between HIV-1 and both mDC and pDC, associated with HCV co-infection-independent spontaneous production of inflammatory cytokines, reflecting the occurrence of in vivo activation of the immune system, which might further contribute to the impaired DC functionality.
Can all bulk-phase reactions be accelerated in microdroplets? (2017)

Recent studies have shown that microdroplet reactions are markedly accelerated compared to the corresponding bulk-phase reactions. This raises the question whether all reactions can be sped up by this means. We present a counter example, and we show that the reaction mechanism in microdroplets can differ sharply from that in bulk, especially because of the distinct microdroplet surface environment. This analysis helps to guide us how to choose and control reactions in microdroplets and provides a possible perspective on utilizing microdroplet chemistry to scale up synthesis.
ChemInform Abstract: Total Synthesis of (+)‐Lactacystin (X) from (R)‐Glutamate. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Neurotoxicity and Neurodegeneration When PrP Accumulates in the Cytosol (2002)

Changes in prion protein (PrP) folding are associated with fatal neurodegenerative disorders, but the neurotoxic species is unknown. Like other proteins that traffic through the endoplasmic reticulum, misfolded PrP is retrograde transported to the cytosol for degradation by proteasomes. Accumulation of even small amounts of cytosolic PrP was strongly neurotoxic in cultured cells and transgenic mice. Mice developed normally but acquired severe ataxia, with cerebellar degeneration and gliosis. This establishes a mechanism for converting wild-type PrP to a highly neurotoxic species that is distinct from the self-propagating PrP(Sc) isoform and suggests a potential common framework for seemingly diverse PrP neurodegenerative disorders.
Inhibiting androgen receptor splice variants with cysteine-selective irreversible covalent inhibitors to treat prostate cancer (2022)

Androgen receptor (AR) and its splice variants (AR-SVs) promote prostate cancer (PCa) growth by orchestrating transcriptional reprogramming. Mechanisms by which the low complexity and intrinsically disordered primary transactivation domain (AF-1) of AR and AR-SVs regulate transcriptional programming in PCa remains poorly defined. Using omics, live and fixed fluorescent microscopy of cells, and purified AF-1 and AR-V7 recombinant proteins we show here that AF-1 and the AR-V7 splice variant form molecular condensates by liquid-liquid phase separation (LLPS) that exhibit disorder characteristics such as rapid intracellular mobility, coactivator interaction, and euchromatin induction. The LLPS and other disorder characteristics were reversed by a class of small-molecule-selective AR-irreversible covalent antagonists (SARICA) represented herein by UT-143 that covalently and selectively bind to C406 and C327 in the AF-1 region. Interfering with LLPS formation with UT-143 or mutagenesis resulted in chromatin condensation and dissociation of AR-V7 interactome, all culminating in a transcriptionally incompetent complex. Biochemical studies suggest that C327 and C406 in the AF-1 region are critical for condensate formation, AR-V7 function, and UT-143's irreversible AR inhibition. Therapeutically, UT-143 possesses drug-like pharmacokinetics and metabolism properties and inhibits PCa cell proliferation and tumor growth. Our work provides critical information suggesting that clinically important AR-V7 forms transcriptionally competent molecular condensates and covalently engaging C327 and C406 in AF-1, dissolves the condensates, and inhibits its function. The work also identifies a library of AF-1-binding AR and AR-SV-selective covalent inhibitors for the treatment of PCa.
Atomic Layer Deposition Growth of BaB2O4 Thin Films from an Exceptionally Thermally Stable Tris(pyrazolyl)borate-Based Precursor (2009)

The atomic layer deposition growth of BaB2O4 thin films was investigated using Ba(TpEt2)2 and water as precursors between 240 and 400 °C. The process provided uniform films and exhibited a large ALD window between 250 and 375 °C, in which a constant growth rate of 0.23 Å/cycle was observed.
Redundant and Opposing Functions of Two Tyrosine Kinases, Btk and Lyn, in Mast Cell Activation (2000)

Protein-tyrosine kinases play crucial roles in mast cell activation through the high-affinity IgE receptor (FcepsilonRI). In this study, we have made the following observations on growth properties and FcepsilonRI-mediated signal transduction of primary cultured mast cells from Btk-, Lyn-, and Btk/Lyn-deficient mice. First, Lyn deficiency partially reversed the survival effect of Btk deficiency. Second, FcepsilonRI-induced degranulation and leukotriene release were almost abrogated in Btk/Lyn doubly deficient mast cells while singly deficient cells exhibited normal responses. Tyrosine phosphorylation of cellular proteins including phospholipases C-gamma1 and C-gamma2 was reduced in Btk/Lyn-deficient mast cells. Accordingly, FcepsilonRI-induced elevation of intracellular Ca2+ concentrations and activation of protein kinase Cs were blunted in the doubly deficient cells. Third, in contrast, Btk and Lyn demonstrated opposing roles in cytokine secretion and mitogen-activated protein kinase activation. Lyn-deficient cells exhibited enhanced secretion of TNF-alpha and IL-2 apparently through the prolonged activation of extracellular signal-related kinases and c-Jun N-terminal kinase. Potentially accounting for this phenomenon and robust degranulation in Lyn-deficient cells, the activities of protein kinase Calpha and protein kinase CbetaII, low at basal levels, were enhanced in these cells. Fourth, cytokine secretion was severely reduced and c-Jun N-terminal kinase activation was completely abrogated in Btk/Lyn-deficient mast cells. The data together demonstrate that Btk and Lyn are involved in mast cell signaling pathways in distinctly different ways, emphasizing that multiple signal outcomes must be evaluated to fully understand the functional interactions of individual signaling components.
Identification of fungal limonene-3-hydroxylases for biotechnological menthol production (2020)

Abstract More than 30,000 tons of menthol are produced every year as a flavor and fragrance compound or as medical component. So far, only extraction from plant material or chemical synthesis is possible. A sustainable alternative approach for menthol production could be a biotechnological-chemical two-step conversion, starting from (+)-limonene, which is a side product of the citrus processing industry. The first step requires a limonene-3-hydroxylase (L3H) activity that specifically catalyzes hydroxylation of limonene at carbon atom 3. Several protein engineering strategies already attempted to create limonene-3-hydroxylases from bacterial cytochrome P450 monooxygenases (CYPs or P450s), which can be efficiently expressed in bacterial hosts. However, their regiospecificity is rather low, if compared to the highly selective L3H enzymes from the biosynthetic pathway towards menthol in Mentha species. The only naturally occurring limonene-3-hydroxylase activity identified in microorganisms so far, was reported for a strain of the black yeast-like fungus Hormonema sp. in South Africa. We have discovered further fungi that can catalyze the intended reaction and identified potential CYP-encoding genes within the genome sequence of one of the strains. Using heterologous gene expression and biotransformation experiments in yeasts, we were able to identify limonene-3-hydroxylases from Aureobasidium pullulans and Hormonema carpetanum . Further characterization of the A. pullulans enzyme demonstrated its high stereospecificity and regioselectivity, its potential for limonene-based menthol production and its additional ability to convert α-and β-pinene to verbenol and pinocarveol, respectively. Importance (−)-Menthol is an important flavor and fragrance compound and furthermore has medicinal uses. To realize a two-step synthesis starting from renewable (+)-limonene, a regioselective limonene-3-hydroxylase enzyme is necessary. We identified enzymes from two different fungi, which catalyze this hydroxylation reaction and represent an important module for the development of a biotechnological process for (−)-menthol production from renewable (+)-limonene.
Multi-Omics Analysis to Characterize Cigarette Smoke Induced Molecular Alterations in Esophageal Cells (2020)

Though smoking remains one of the established risk factors of esophageal squamous cell carcinoma, there is limited data on molecular alterations associated with cigarette smoke exposure in esophageal cells. To investigate molecular alterations associated with chronic exposure to cigarette smoke, non-neoplastic human esophageal epithelial cells were treated with cigarette smoke condensate (CSC) for up to 8 months. Chronic treatment with CSC increased cell proliferation and invasive ability of non-neoplastic esophageal cells. Whole exome sequence analysis of CSC treated cells revealed several mutations and copy number variations. This included loss of high mobility group nucleosomal binding domain 2 (HMGN2) and a missense variant in mediator complex subunit 1 (MED1). Both these genes play an important role in DNA repair. Global proteomic and phosphoproteomic profiling of CSC treated cells lead to the identification of 38 differentially expressed and 171 differentially phosphorylated proteins. Bioinformatics analysis of differentially expressed proteins and phosphoproteins revealed that most of these proteins are associated with DNA damage response pathway. Proteomics data revealed decreased expression of HMGN2 and hypophosphorylation of MED1. Exogenous expression of HMGN2 and MED1 lead to decreased proliferative and invasive ability of smoke exposed cells. Immunohistochemical labeling of HMGN2 in primary ESCC tumor tissue sections (from smokers) showed no detectable expression while strong to moderate staining of HMGN2 was observed in normal esophageal tissues. Our data suggests that cigarette smoke perturbs expression of proteins associated with DNA damage response pathways which might play a vital role in development of ESCC.
Speech Perception after Cochlear Implantation over a 4-Year Time Period (2003)

The extent of hypometabolism as assessed by FDG-PET seemed to be one of the major factors predicting the outcome of cochlear implantation.
Microarray Embedding/Sectioning for Parallel Analysis of 3D Cell Spheroids (2019)

Three-dimensional cell spheroid models can be used to predict the effect of drugs and therapeutics and to model tissue development and regeneration. The utility of these models is enhanced by high throughput 3D spheroid culture technologies allowing researchers to efficiently culture numerous spheroids under varied experimental conditions. Detailed analysis of high throughput spheroid culture is much less efficient and generally limited to narrow outputs, such as metabolic viability. We describe a microarray approach that makes traditional histological embedding/sectioning/staining feasible for large 3D cell spheroid sample sets. Detailed methodology to apply this technology is provided. Analysis of the technique validates the potential for efficient histological analysis of up to 96 spheroids in parallel. By integrating high throughput 3D spheroid culture technologies with advanced immunohistochemical techniques, this approach will allow researchers to efficiently probe expression of multiple biomarkers with spatial localization within 3D structures. Quantitative comparison of staining will have improved inter- and intra-experimental reproducibility as multiple samples are collectively processed, stained, and imaged on a single slide.
Suppressing Ion Implantation Induced Oxide Charging by Utilizing Physically Damaged Oxide Region (1996)

We report effects of ion implantation induced on gate leakage current in Metal Oxide Semiconductor Field Effect Transistors (MOSFETs) without sidewall-oxidation. It is found that the region of damage induced by the 10 keV arsenic ions implantation process is the depth of 10 nm. A has been suppressed by utilizing the physical as a path of the conduction current from the plasma which can be removed by means of wet etching after the ion implantation process. This newly developed technique is able to prevent both oxide charging of the gate oxide and direct ion impact of gate oxide.
Molecular recollision interferometry in high harmonic generation (2008)

Using extreme-ultraviolet interferometry, we measure π phase shifts in high harmonics generated from transiently aligned molecules. This data directly reflects the quantum interferences in the electron wavepacket due to the two-center molecular structure.
Long‐Term Survival in a Patient with Pulmonary Lymphangioleiomyomatosis (2002)

A patient with pulmonary lymphangioleiomyomatosis was diagnosed more than 22 years after the onset of symptoms by a thoracoscopic lung biopsy, after a high resolution computerized tomogram of the chest was highly suggestive of the disease. After nearly 30 years since the onset of her symptoms, the patient leads a relatively normal life with only mildly abnormal lung function and has minimal reduction in her exercise tolerance. There have been few reports of patients surviving for such a long time after the onset of this disease; the literature suggests that most patients die within 15 years of symptom onset.
Introduction (2008)

Wireless local area networking has experienced tremendous growth in the last ten years with the proliferation of IEEE 802.11 devices. Its beginnings date back to Hertz's discovery of radio waves in 1888, followed by Marconi's initial experimentation with transmission and reception of radio waves over long distances in 1894. In the following century, radio communication and radar proved to be invaluable to the military, which included the development of spread spectrum technology. The first packet-based wireless network, ALOHANET, was created by researchers at the University of Hawaii in 1971. Seven computers were deployed over four islands communicating with a central computer in a bi-directional star topology.
Spectral and spatial modal control of two dimensional photonic crystal Bragg lasers (2007)

We demonstrate electrically-pumped, edge-emitting, single-mode, large-area photonic crystal lasers with angled facets. We obtain the spectral and spatial modal control of the laser by designing the photonic crystal lattice and index contrast.
<title>Privacy enhanced group communication in clinical environment</title> (2005)

Privacy protection of medical records has always been an important issue and is mandated by the recent Health Insurance Portability and Accountability Act (HIPAA) standards. In this paper, we propose security architectures for a tele-referring system that allows electronic group communication among professionals for better quality treatments, while protecting patient privacy against unauthorized access. Although DICOM defines the much-needed guidelines for confidentiality of medical data during transmission, there is no provision in the existing medical security systems to guarantee patient privacy once the data has been received. In our design, we address this issue by enabling tracing back to the recipient whose received data is disclosed to outsiders, using watermarking technique. We present security architecture design of a tele-referring system using a distributed approach and a centralized web-based approach. The resulting tele-referring system (i) provides confidentiality during the transmission and ensures integrity and authenticity of the received data, (ii) allows tracing of the recipient who has either distributed the data to outsiders or whose system has been compromised, (iii) provides proof of receipt or origin, and (iv) can be easy to use and low-cost to employ in clinical environment.
A VQ-based image restoration algorithm (2003)

In this paper, we develop a novel VQ-based image restoration algorithm. The mapping between high frequency information in the original images and low frequency information in the corresponding degraded ones is established and stored in the VQ codebooks. Prototype images are used, which belong to the same class of images. During restoration, the high frequency information of a given degraded image is estimated from its low frequency information based on the designed codebook. To make the restoration process computationally efficient, the principal component analysis (PCA) and VQ-nearest neighborhood approaches are utilized. Simulation results are presented to demonstrate the effectiveness of the proposed algorithm.
Low-complexity successive intercell interference cancellation (2012)

Due to the data traffic explosion, cellular networks tend to have larger cell density and smaller cell size, which will give rise to significant intercell interference. In this work, we focus on receiver side signal processing techniques to perform intercell interference suppression and successive interference cancellation, where adaptive antenna arrays are used to develop a receiver beamforming approach within an iterative receiver. Specifically, the matrix inversion for calculating the beamforming weights is avoided, which drastically reduce the computational complexity.