gebhart/patrepeval huggingface dataset:
Measuring exhaled nitric oxide in infants during tidal breathing: Methodological issues (2003)

Exhaled nitric oxide (FENO) may provide a tool for identifying infants at risk of developing allergic disease in childhood. In infants there is no standardized collection technique; however, the easiest method is to measure FENO during tidal breathing. In this study we investigated various methodological issues for tidal breathing (TB) FENO in infants. These included the effect of ambient NO, oral or nasal breathing, sedation, and tidal expiratory flow. Furthermore, we compared TB FENO in 88 infants with and without wheeze. Ambient NO greater than 5 ppb significantly affected FENO. There was no significant difference between NO levels measured during either oral or nasal breathing; however, there was a significant difference between levels collected from infants before and after sedation (P < 0.001). Tidal breathing FENO decreased with increasing tidal flows (P < 0.001) and increased with age (P = 0.002). There was no significant difference in mixed expired NO between healthy and wheezy children, but children with doctor-diagnosed eczema had significantly raised levels (P = 0.014). There seem to be important methodological limitations for measuring FENO in infants during TB.
In Vivo Evaluation Of Fine Needle Type Glucose Sensors Implanted In Rabbit Blood Vessel (2013)

Abstract not Available.
Two-dimensional photonic crystal defect laser (1999)

With the maturation of crystal growth along with the nanofabrication of semiconductors there has been strong interest in creating optical microcavities for spontaneous emission control. The Vertical Cavity Surface Emitting Laser (VCSEL) was the first device to shrink the optical mode to sizes on the order of the wavelength of light[l].
PS 2-3 : DNA Vaccine Encoding HCV Nonstructural Proteins Enhances Virus-Specific Cellular Immune Responses in Patients with Chronic Hepatitis C (2018)

Aims: Although direct-acting antivirals (DAA) are successfully used for the treatment of chronic hepatitis C, there are DAA-resistant cases. Furthermore, DAA-treated patients do not develop protective immunity against HCV re-infection. To complement DAA therapy, we developed a DNA vaccine (VGX- 6150) containing three plasmids encoding HCV genotype 1 NS3, NS4 and NS5A consensus immunogens and plasmid encoding IL-28B as a molecular adjuvant. In the present study, we performed a phase I clinical trial of VGX-6150 in patients with chronic hepatitis C (n=18) who had failed interferon (IFN)-based treatment.
Methods: VGX-6150 was administered 4 times in 4-week intervals with in vivo electroporation to three groups of patients (n=6 for 1, 3, and 6 mg/dose groups, respectively) followed by a 6 mg boost 24 weeks later. Significant side effects were not reported. Cellular immune responses of peripheral blood mononuclear cells (PBMCs) were evaluated by IFN-g ELISpot assays using overlapping peptides spanning NS3~NS5A and staining with HCV-specific HLA class I pentamers.
Results: The IFN-g spot number specific to NS3~NS5A was increased in 3 and 6 mg/dose groups after the initial vaccination and in all three groups after the boosting vaccination. However, the frequency of HCV-specific HLA class I pentamer+ CD8+ T-cells was not increased by the vaccination. Moreover, the frequency of PD-1+ cells in the gate of HLA class I pentamer+ CD8+ T-cells was not changed by the vaccination. Interestingly, the frequency of CD4+CD25+Foxp3+ regulatory T-cells (Treg) was significantly decreased after the vaccination, consistent with a previous report regarding the effect of an IL-28B-encoding plasmid adjuvant.
Conclusions: In the present study, we demonstrate that VGX- 6150 enhances HCV antigen-specific T-cell responses without significant side effects. The inclusion of IL-28B as an immune adjuvant was associated with a decrease in Treg cells that may have provided greater immune activation in chronic HCV infec-tion.
Recent advances in flexible photodetectors based on 1D nanostructures (2019)

Abstract Semiconductor nanowires have demonstrated excellent electronic and optoelectronic properties. When integrated into photodetectors, excellent device performance can be easily attained. Apart from the exceptional performance, these nanowires can also enable robust and mechanically flexible photodetectors for various advanced utilizations that the rigid counterparts cannot perform. These unique applications include personal healthcare, next-generation robotics and many others. In this review, we would first discuss the nanowire fabrication techniques as well as the assembly methods of constructing large-scale nanowire arrays. Then, the recent development of flexible photodetectors based on these different nanowire material systems is evaluated in detail. At the same time, we also introduce some recent advancement that allows individual photodetectors to integrate into a more complex system for advanced deployment. Finally, a short conclusion and outlook of challenges faced in the future of the community is presented.
Mutation of the Cytoplasmic Domain of the Integrin β3 Subunit (1995)

The cytoplasmic domain of the beta subunit of the alpha IIb beta 3 integrin is required for cell spreading on fibrinogen. Here we report that deletion of six amino acids from the COOH terminus of the beta 3 (I757TYRGT) totally abolished cell spreading and formation of adhesion plaques, whereas retaining Ile757 partially preserved these functions. We further found that substitution of Tyr747 with Ala also abolished alpha IIb beta a-mediated cell spreading. The effects of these and other mutations on additional functions of alpha IIb beta 3 were also studied. Progressive truncations of beta 3, in which stop codons were inserted at amino acid positions 759-756, caused partial defects in the recruitment of alpha IIb beta 3 to preestablished adhesion plaques and a gradual decrease in the ability of alpha IIb beta 3 to mediate internalization of fibrinogen-coated particles. The Tyr747-->Ala substitution mutant was almost totally inactive in both of these assays. Point mutations at Tyr759, and at a conserved area close to the transmembrane domain of beta 3, decreased integrin recruitment to preestablished adhesion plaques but allowed alpha IIb beta 3-mediated formation of these structures and partial cell spreading. Deletion of the cytoplasmic domain of beta 3 did not affect the constitutive endocytosis of alpha IIb beta 3.
Quantitative Analysis of NK1Receptor in the Human Brain Using PET with18F-FE-SPA-RQ (2008)

The regional distribution of 18F-FE-SPA-RQ was in agreement with previous PET studies and postmortem studies of NK1 receptor in the human brain. The ratio method will be useful for clinical research of psychiatric disorders, for the estimation of NK1 receptor without arterial blood sampling and long dynamic PET.
Dispersion transformer for fiber-optic systems (1987)

A significant amount of research is being performed to increase the information-carrying capacity of fiber-optic systems. One major limitation in achieving this goal has been the upper limit set by the chromatic dispersion induced by a combination of the source spectral width and the fiber dispersion.
Letters (2006)

Freeman, Brian J. C. FRCS(Tr & Orth); Fraser, Robert D. MD, FRACS; Cain, Christopher M. J. MD, FRACS; Hall, David J. FRACS; Chapple, David C. MSc, FRCS (Tr and Orth) Author Information
Abstract B063: Polyethnic-1000: Advancing cancer genomics by studying ethnically diverse, underserved patient populations in New York (2020)

Abstract Recent advances in DNA sequencing technologies have revolutionized approaches to the prevention, risk assessment, early detection, diagnosis, and treatment of cancers. However, many ethnic groups, especially nonEuropean populations, have been significantly underrepresented in cancer research, including clinical trials, and have not received equal benefits in clinical practice. As a result, our current knowledge about tumor biology, cancer risk, and response to treatment has primarily been derived from patients of European descent. These inequities limit our understanding of the many types of cancer and may exacerbate health disparities in the United States. In this proposal, we address both the scientific and social issues by creating a dynamic research platform within the greater New York area that promises to enhance the ways in which cancer is prevented, diagnosed, and treated. This initiative, named Polyethnic-1000, will involve patients and staff at several academic health centers and partner hospitals in the New York City region. It will use the genomics and informatics capabilities of the New York Genome Center to determine how inherited and somatically acquired genetic variations affect the behavior of cancers occurring in ethnically diverse populations. In a first, retrospective phase, we will establish the workflow from sample acquisition to whole-exome and RNA sequencing, data analysis, and data sharing within the consortium. Then we will start a prospective study enabling the formation of cohorts of interest for particular cancer types and particular ethnicities, with uniform consent allowing broad data sharing of the somatic variants identified. Polyethnic-1000 will establish a framework to enhance interactions among our region's academic and health centers to advance cancer genomics. These efforts should improve and widen the use of genomics for all, especially currently underserved ethnic minority populations. Citation Format: Nicolas Robine, Fieke Froeling, Benjamin Hubert, Michael C. Zody, Dayna Oschwald, Harold Varmus, Charles Sawyers, David Tuveson. Polyethnic-1000: Advancing cancer genomics by studying ethnically diverse, underserved patient populations in New York [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B063.
Pseudomonas exotoxin-anti-TAC. Cell-specific immunotoxin active against cells expressing the human T cell growth factor receptor. (1984)

An immunotoxin was constructed with an activity that discriminated between two T cell lines based on the expression of the T cell growth factor (TCGF) receptor on their cell surface. A toxic protein conjugate, designated PE-anti-TAC, was made by chemically coupling pseudomonas exotoxin (PE) to a monoclonal antibody (anti-TAC) that recognizes the human TCGF receptor. This conjugate was toxic to HUT-102 cells, a cell line that expresses the TCGF receptor, but was nontoxic for MOLT-4 cells, a receptor-negative line. The toxicity of PE-anti-TAC was enhanced 50-fold in the presence of human adenovirus type II and was reduced to control levels by adding excess anti-TAC antibody. The toxicity of PE-anti-TAC for HUT-102 cells was compared with PE-anti-transferrin receptor. To compare the route of entry for both anti-TAC and anti-TFR using electron microscopy, protein conjugates were made by coupling horseradish peroxidase (HRP) to each antibody. Anti-TFR-HRP entered HUT-102 cells by concentrative adsorptive endocytosis via coated pits, and the majority of the antibodies bound to the cell surface at 4 degrees C were seen in receptosomes by 10 min after warming to 37 degrees C. Anti-TAC-HRP was also found to enter HUT-102 cells via coated pits and receptosomes; but, in contrast to anti-TFR, anti-TAC did not selectively concentrate in coated pits, and therefore the majority of this surface-bound antibody were not internalized in HUT-102 cells by 10 min at 37 degrees C.
Photoinscription of Surface Relief Gratings on Azo-Hybrid Gels (1998)

Very stable surface gratings can be inscribed in azo-hybrid thin films prepared by the sol-gel method, as described here. It is shown that in order to obtain high modulation depths a weakly crosslinked network in the gel with a degree of condensation that can be easily controlled by heat treatment and the functionality of the sol-gel precursor is required. In addition, the simultaneous presence of an intensity gradient and a non-zero component of the resultant optical field along this gradient is required. Explanations for the mass transport mechanism are also proposed.
Proteolysis-induced N-terminal ectodomain shedding of the integral membrane glycoprotein CUB domain-containing protein 1 (CDCP1) is accompanied by tyrosine phosphorylation of its C-terminal domain and recruitment of Src and PKC? (2010)

CUB-domain-containing protein 1 (CDCP1) is an integral membrane glycoprotein with potential as a marker and therapeutic target for a number of cancers. Here we examine mechanisms regulating cellular processing of CDCP1. By analyzing cell lines exclusively passaged non-enzymatically and through use of a panel of protease inhibitors, we demonstrate that full-length 135 kDa CDCP1 is post-translationally processed in a range of cell lines by a mechanism involving serine protease activity, generating a C-terminal 70-kDa fragment. Immunopurification and N-terminal sequencing of this cell-retained fragment and detailed mutagenesis, show that proteolytic processing of CDCP1 occurs at two sites, Arg-368 and Lys-369. We show that the serine protease matriptase is an efficient, but not essential, cellular processor of CDCP1 at Arg-368. Importantly, we also demonstrate that proteolysis induces tyrosine phosphorylation of 70-kDa CDCP1 and recruitment of Src and PKCδ to this fragment. In addition, Western blot and mass spectroscopy analyses show that an N-terminal 65-kDa CDCP1 ectodomain is shed intact from the cell surface. These data provide new insights into mechanisms regulating CDCP1 and suggest that the biological role of this protein and, potentially, its function in cancer, may be mediated by both 70-kDa cell retained and 65-kDa shed fragments, as well as the full-length 135-kDa protein.
Adjuvant solution for pandemic influenza vaccine production (2012)

Extensive preparation is underway to mitigate the next pandemic influenza outbreak. New vaccine technologies intended to supplant egg-based production methods are being developed, with recombinant hemagglutinin (rHA) as the most advanced program for preventing seasonal and avian H5N1 Influenza. Increased efforts are being focused on adjuvants that can broaden vaccine immunogenicity against emerging viruses and maximize vaccine supply on a worldwide scale. Here, we test protection against avian flu by using H5N1-derived rHA and GLA-SE, a two-part adjuvant system containing glucopyranosyl lipid adjuvant (GLA), a formulated synthetic Toll-like receptor 4 agonist, and a stable emulsion (SE) of oil in water, which is similar to the best-in-class adjuvants being developed for pandemic flu. Notably, a single submicrogram dose of rH5 adjuvanted with GLA-SE protects mice and ferrets against a high titer challenge with H5N1 virus. GLA-SE, relative to emulsion alone, accelerated induction of the primary immune response and broadened its durability against heterosubtypic H5N1 virus challenge. Mechanistically, GLA-SE augments protection via induction of a Th1-mediated antibody response. Innate signaling pathways that amplify priming of Th1 CD4 T cells will likely improve vaccine performance against future outbreaks of lethal pandemic flu.
A scalable MPEG-4 wavelet-based visual texture compression system with optimized memory organization (2003)

The realization of new MPEG-4 functionality, applicable to three-dimensional graphics texture compression and image database access over the Internet, is demonstrated on a heterogeneous platform with several unique features. First, applying our system-level design methodologies effectively removes all data transfer and storage overhead that comprises the main bottleneck in the original system description. Second, a first-of-a-kind application specific solution, called Ozone, accelerates the embedded-zero-tree based encoding and is capable of compressing 30 color CIF images per second. The entire application is running on the Ozone coupled to a PC.
Multidimensional tissue imaging by matrix assisted laser desorption/ionization-ion mobility-mass spectrometry: advantages, challenges, and prospects for proteomics (2004)

MALDI-imaging mass spectrometry correlates detailed analyte information with spatial distribution in biological tissue sections. By combining post-ionization ion mobility separation with mass analysis, difficult peak assignments arising from spectrum congestion are alleviated.
Analysis of Oxidative Stress Induced by Hemin Derevatives Using Lux-Biosensors (2013)

Ранее в нашей лаборатории было показано, что производные гемина (ПГ) обладают выраженной пероксидазной активностью, причём они способны катализировать окисление восстановленных биологических субстратов (NADH) как перекисью водорода, так и модельной липофильной трет-бутилгидроперекисью. В продолжение этих исследований была продемонстрирована способность ПГ катализировать окисление полиненасыщенных жирных кислот (ПНЖК) кислородом воздуха. В настоящей работе степень окислительного стресса
Demand-driven software race detection using hardware performance counters (2011)

Dynamic data race detectors are an important mechanism for creating robust parallel programs. Software race detectors instrument the program under test, observe each memory access, and watch for inter-thread data sharing that could lead to concurrency errors. While this method of bug hunting can find races that are normally difficult to observe, it also suffers from high runtime overheads. It is not uncommon for commercial race detectors to experience 300x slowdowns, limiting their usage.
Reducing Impact of Phase Noise on Accuracy of Measured MIMO Channel Capacity (2007)

Despite the fact that time-division multiplexed switching (TDMS)-based multiple-input-multiple-output (MIMO) wireless channel sounders are cost effective implementation techniques, they may result in significant measurement errors due to phase noise (PN) in the local oscillators. In this letter, the impact of PN on the accuracy of measured MIMO channel capacity is studied by considering its effect on both the spatial multiplexing gain and on the power gain. We show that in case of a low rank physical channel matrix the impact of PN is more pronounced on the spatial multiplexing gain than on the power gain. Based on that, we propose an eigenvalue filtering (EVF) technique to improve the accuracy of measured channel capacity.
Conditional Bit Error Rate for an Impulse Radio UWB Channel with Interfering Users (2006)

We consider a multi-user impulse radio UWB physical layer in a multipath environment. We propose a fast and efficient method to compute the conditional bit error rate (BER), given some realizations of the channels from source/interferer to destination, and of delay differences. Our motivation is packet level simulation of large scale or dense impulse radio UWB networks. The conditional BER is used in a packet level simulator with block fading channel assumption to sample packet transmission error events. However, due to the timescale difference between physical layer events and network events, a pulse-level simulation of the BER in a realistic multipath channel environment is infeasible. Our solution is based on a novel combination of large deviation and importance sampling.
Kinetische Untersuchung der Jod‐Amylose‐Reaktion durch Pulsradiolyse (1972)

Abstract Wäβrige Amyloselösungen, die 10 −2 MKI und 2,5 . 10 −2 MN 2 O enthielten, wurden mit einem kurzen Puls von 1 ‐ 30 Mikrosekunden energiereicher Elektronen bestrahlt und die Reaktion des so erzeugten Jods mit der Amylose an dem Aufbau der optischen Absorption im Mikro‐ bis Zehntelsekundenbereich verfolgt. Die anfängliche Geschwindigkeit der Reaktion, gemessen an dem anfänglichen Extinktionsaufbau bei 6000 A, ist bei kleinen Jodkonzentrationen von einigen 10 −6 M der vierten bis fünften Potenz der I 2 ‐Konzentration proportional. Bei hohen Jodkonzentrationen um 10 −4 M ist die Reaktion von erster Ordnung in bezug auf [I 2 ]. Bei kleinen und hohen Jodkonzentrationen ist die Geschwindigkeit der Amylosekonzentration proportional, bei mittleren Jodkonzentrationen um 10 −5 M steigt sie aber weniger stark mit der Amylosekonzentration an. Die Form des Absorptionsspektrums ändert sich nicht während der Reaktion, wenn die Jodkonzemration klein ist. Eine geringfügige Rotverschiebung des Absorptionsmaximums wird bei hoher Jod‐ und kleiner Amylosekonzentration beobachtet. Eine starke Verschiebung erfolgt bei hoher Amylose‐ und mittlerer Jodkonzentration.
Disturbed Activation of Endoplasmic Reticulum Stress Transducers by Familial Alzheimer's Disease-linked Presenilin-1 Mutations (2001)

Recent studies have shown independently that presenilin-1 (PS1) null mutants and familial Alzheimer's disease (FAD)-linked mutants should both down-regulate signaling of the unfolded protein response (UPR). However, it is difficult to accept that both mutants possess the same effects on the UPR. Furthermore, contrary to these observations, neither loss of PS1 and PS2 function nor expression of FAD-linked PS1 mutants were reported to have a discernable impact on the UPR. Therefore, re-examination and detailed analyses are needed to clarify the relationship between PS1 function and UPR signaling. Here, we report that PS1/PS2 null and dominant negative PS1 mutants, which are mutated at aspartate residue 257 or 385, did not affect signaling of the UPR. In contrast, FAD-linked PS1 mutants were confirmed to disturb UPR signaling by inhibiting activation of both Ire1alpha and ATF6, both of which are endoplasmic reticulum (ER) stress transducers in the UPR. Furthermore, PS1 mutants also disturbed activation of PERK (PKR-like ER kinase), which plays a crucial role in inhibiting translation during ER stress. Taken together, these observations suggested that PS1 mutations could affect signaling pathways controlled by each of the respective ER-stress transducers, possibly through a gain-of-function.
Longitudinal MRI and MRSI characterization of the quinolinic acid rat model for excitotoxicity: peculiar apparent diffusion coefficients and recovery of N‐acetyl aspartate levels (2009)

Quinolinic acid (QA) induced striatal lesion is an important model for excitotoxicity that is also used for efficacy studies. To date, the morphological and spectroscopic indices of this model have not been studied longitudinally by MRI; therefore the objectives of this study were aimed at following the lesion progression and changes in N-acetyl aspartate (NAA) as viewed by MRI and MRSI, respectively, in-vivo over a period of 49 days. We found that the affected areas exhibited both high and low apparent diffusion coefficients (ADC) even 49 days post QA injection in three of the six tested animals. MRI-guided histological analysis correlated areas characterized by high ADCs on day 49 with cellular loss, while areas characterized by lower ADCs were correlated with macrophage infiltration (CD68 positive stain). Our MRSI study revealed an initial reduction of NAA levels in the lesioned striatum, which significantly recovered with time, although not to control levels. Total-striatum normalized NAA levels recovered from 0.67 +/- 0.15 (of the contralateral row) on day 1 to 0.90 +/- 0.12 on day 49. Our findings suggest that NAA should be considered as a marker for neuronal dysfunction, in addition to neuronal viability. Some behavioral indices could be correlated to permanent neuronal damage while others demonstrated a spontaneous recovery parallel to the NAA recovery. Our findings may have implications in efficacy-oriented studies performed on the QA model.