gebhart/patrepeval huggingface dataset:
Driving reconfigurable photonic metamaterials with light and electrical signals: exploiting forces and fields at the nanoscale (2013)

Metamaterials, artificial electromagnetic media achieved by structuring on the sub-wavelength scale, were initially suggested as negative index media for the “superlens” and for transforming electromagnetic space to control the propagation of waves. The research agenda is now shifting to achieving tuneable, switchable, nonlinear and sensing functionalities using metamaterials. We show how engaging the changing balance of forces and plasmonic light confinement at the nanoscale opens up the burgeoning field of reconfigurable photonic metadevices - structures that can be controlled by external electric and magnetic signals and by light by engaging Coulomb, Ampere and Lorentz forces.
Video-rate volumetric neuronal imaging with multi-z confocal microscopy (Conference Presentation) (2019)

Fast, volumetric imaging over large scales has been a long-standing challenge in biological microscopy. To address this issue, we developed a variant of confocal microscopy that provides simultaneous multiplane imaging over large field of view and at video rate. Our apparatus, called multi-Z confocal microscopy, differs from a conventional confocal microscope in both its illumination and detection parts. First, axially elongated illumination is achieved by under filling the back aperture of the microscope objective. The resulting low NA provides an axial extent of the illumination of the order of 100 µm. The light from the sample is then collected by the same objective, now taking advantage of the full NA which ensures high collection efficiency, and send to the detection unit. The latter is comprised by four reflecting pinholes axially distributed in the image plane such that they are conjugated to different depths within the sample. Each detection channel spans a probe volume at a different depth and volumetric imaging is obtained by simply combining the four channels. In our current configuration, each imaging plane covers a field of view of 1.2 mm and the distance between two planes is equal to 25 µm. In other words, we image 1200x1200x100 µm3 at 30Hz. We first demonstrated the applicability of our technique by imaging entire C. elegans in vivo with a cellular resolution. Secondly we applied our technique to image multiple layers of neurons in mouse brain. We were able to record the activity of 550 neurons, with 100-150 neurons present in each imaging plane.
Computer-aided prognosis: Predicting patient and disease outcome via multi-modal image analysis (2010)

Computer-aided prognosis (CAP) is a new and exciting complement to the field of computer-aided diagnosis (CAD) and involves developing computerized image analysis and multi-modal data fusion algorithms for helping physicians predict disease outcome and patient survival. At the Laboratory for Computational Imaging and Bioinformatics (LCIB) at Rutgers University we have been developing computerized algorithms for high dimensional data and image analysis for predicting disease outcome from multiple modalities including MRI, digital pathology, and protein expression. Additionally, we have been developing novel data fusion algorithms based on nonlinear dimensionality reduction methods (such as Graph Embedding) to quantitatively integrate prognostic information from multiple data sources and modalities. In this paper, we briefly describe 5 representative and ongoing CAP projects at LCIB. These projects include (1) an Image-based Risk Score (IbRiS) algorithm for predicting outcome of ER+ breast cancer patients based on quantitative image analysis of digitized breast cancer biopsy specimens alone, (2) segmenting and determining extent of lymphocytic infiltration (identified as a possible prognostic marker for outcome in Her2+ breast cancers) from digitized histopathology, (3) segmenting and diagnosing highly agressive triple-negative breast cancers on dynamic contrast enhanced (DCE) MRI, (4) distinguishing patients with different Gleason grades of prostate cancer (grade being known to be correlated to outcome) from digitized needle biopsy specimens, and (5) integrating protein expression measurements obtained from mass spectrometry with quantitative image features derived from digitized histopathology for distinguishing between prostate cancer patients at low and high risk of disease recurrence.
Vaccination with a fowl adenovirus chimeric fiber protein (crecFib-4/11) simultaneously protects chickens against hepatitis-hydropericardium syndrome (HHS) and inclusion body hepatitis (IBH) (2022)

In the past decades, fowl adenovirus (FAdV)-related diseases became an increasing concern for the poultry industry worldwide. Various immunization strategies against FAdVs have been experimentally investigated, with a particular focus on subunit vaccines against hepatitis-hydropericardium syndrome (HHS), caused by FAdV serotype 4, and inclusion body hepatitis (IBH), caused by serotypes 2, 8a, 8b and 11. In this study, we extended our innovative concept of recombinant chimeric fiber proteins to design a novel chimera combining epitopes from two distinct serotypes, FAdV-4 and -11, and we investigated its efficacy to simultaneously protect chickens against HHS and IBH. Specific pathogen-free chickens were vaccinated with the novel recombinant chimeric fiber and subsequently challenged with either a HHS- or IBH-causing strain. Vaccinated/challenged birds exhibited a reduction of clinical signs, limited hepatomegaly and lower levels of AST compared to the respective challenge controls. Furthermore, the vaccine prevented atrophy of HHS-affected lymphoid organs, such as thymus and bursa of Fabricius, and viral load in the target organs was significantly reduced. Clinical protection was associated with high levels of pre-challenge antibodies measured on ELISA plates coated with the vaccination antigen. Interestingly, the development of neutralizing antibodies was limited against FAdV-11 and absent against FAdV-4, indicating that protection granted by such an antigen may be linked to different immunization pathways. In conclusion, we proved that the concept of chimeric fiber vaccines can be extended across viral species boundaries and represents the first single-component FAdV subunit vaccine providing comprehensive protection against different FAdV-associated diseases.
A new rate control scheme for H.264 video coding (2005)

The H.264/MPEG-4 AVC video coding standard is very promising due to its high coding efficiency. In this paper, we propose a new constant bit rate control method based on the rate-distortion model of TMN8. The novelty of our approach is to use simple preprocessing to achieve the target bit rate more accurately, better target bit allocation and buffer management for both frame-level and macroblock-level rate control, improved perceptual quality, and adoption of virtual frame skipping. Simulations show that our method can meet the target bitrate very accurately, even for content with scene changes and scene transitions, and achieves both good subjective and objective quality. In addition, our approach adds little complexity to the encoder, and can therefore be used for a real-time encoder.
Identification and preliminary validation of novel biomarkers of acute hepatic ischaemia/reperfusion injury using dual-platform proteomic/degradomic approaches (2006)

Hepatic ischaemia/reperfusion (I/R), a major cause of liver damage associated with multiple trauma, haemorrhagic and septic shock, and liver transplantation, contributes significantly to multiple organ failure. Development of novel sensitive biomarkers that detect early stages of liver damage is vital for effective management and treatment of ischaemic liver injury. By using high-throughput immunoblotting and cation-anion exchange chromatography/reversed-phase liquid chromatography-tandem mass-spectrometry, we identified several hepatic proteins, including argininosuccinate synthase (ASS) and estrogen sulfotransferase (EST-1), which were degraded in the liver and rapidly released into circulation during I/R injury. ASS accumulated in serum within 10 min, reached a steady state at 30 min, and persisted up until 3 h after reperfusion following 30 min of total hepatic ischaemia. EST-1 appeared rapidly in blood and attained maximum within 1 hour followed by a decline at 3 h of reperfusion. No ASS or EST-1 protein was detected in serum of control or sham operated rats. ASS and EST-1 exhibited greater sensitivity and specificity toward I/R liver injury as compared with alanine aminotransferase (ALT), an established marker of hepatocellular necrosis. In contrast, serum ASS and EST-1 were undetectable in rats with chronic alcoholic liver disease, while the levels of ALT protein were significantly increased. In addition, ASS, but not EST-1 or ALT accumulated in blood only 6 h after treatment with hepatotoxic combination of lipopolysaccharide and D-galactosamine. These data demonstrate the utility of ASS and EST-1 as novel sensitive and specific biomarkers of acute liver ischaemic injury for prospective clinical studies.
An Anonymity Technique for Base Stations Against Traffic Volume Analysis in Wireless Sensor Networks and Internet of Things (2019)

Wireless Sensor Network (WSN) and Internet of Things (IoT) can be deployed in many life-critical applications such as military reconnaissance, smart grid monitoring, health-monitoring systems, etc. However, a WSN is useless without being able to convey the collected data to the Base Station (BS), which is responsible for gathering information from the sensors and forwarding it to the user/administrator. Therefore, protecting the BS is of paramount importance. In this paper, we propose an approach that can hide the physical location of the BS against an attacker carrying out traffic volume attack in a cluster-based network. The proposed approach hides the BS by controlling the amount of traffic between the cluster head (CH) and its sensor nodes. The simulation results show the ability of the proposed approach to keep the BS hidden, minimize total exchanged traffic while maintaining the required network coverage.
Adaptive test program generation: planning for the unplanned (2003)

Simulation of automatically-generated test programs is the primary means for verifying complex hardware designs and random test program generators therefore play a major role in the verification process of micro-processors. The input for a test program generator is typically an abstract specification-a template-of the tests to be generated. Due to randomness, generators often encounter situations that were not anticipated when the test specification was written. We introduce the concept of adaptive test program generation, which is designed to handle these unforeseen situations. We propose a technique that defines unexpected events together with their alternative program specifications. When an event is detected, its corresponding alternative specification is injected into the test program.
A Correctness Proof for a Practical Byzantine-Fault-Tolerant Replication Algorithm (1999)

This paper presents a formal specification for the unoptimized version of our algorithm presented in Section 4 of [4] and proves its safety (but not its liveness.) The specification uses the I/O automaton formalism of Tuttle an Lynch [8] and the proof is based on invariant assertions and simulation relations
Azo polymers for reversible optical storage. 1. Poly[4'-[[2-(acryloyloxy)ethyl]ethylamino]-4-nitroazobenzene] (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAzo polymers for reversible optical storage. 1. Poly[4'-[[2-(acryloyloxy)ethyl]ethylamino]-4-nitroazobenzene]A. Natansohn, P. Rochon, J. Gosselin, and S. XieCite this: Macromolecules 1992, 25, 8, 2268–2273Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/ma00034a031https://doi.org/10.1021/ma00034a031research-articleACS PublicationsRequest reuse permissionsArticle Views1586Altmetric-Citations423LEARN 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
HIV-1 gp41: mediator of fusion and target for inhibition. (2004)

The bipartite envelope glycoprotein (Env) of the human immunodeficiency virus type 1 (HIV-1) performs two essential functions for initiating virus infection. The gp120 surface subunit of Env binds cell receptors to attach virus to target cells and regulate viral entry. The gp41 transmembrane subunit fuses host-cell and viral membranes to deliver the viral core into the cell cytoplasm. The two subunits derive from a polyprotein precursor, gp160. Cleavage of gp160 in the biosynthetic pathway creates mature Env consisting of the noncovalently-associated gp120/gp41 that is primed for viral entry. While performing distinct operations in HIV entry, the activities of the gp120 and gp41 subunits must be highly coordinated in order to lead to successful infection. This review highlights structure-function relationships in Env, with a focus on the heptad-repeat regions in the ectodomain of gp41. The mechanism of Env-mediated membrane fusion and ways to interfere with this process using inhibitors and antibodies that target gp41 are discussed.
Cell-free conversion of δ-(<scp>l</scp>-α-aminoadipyl)-<scp>l</scp>-cysteinyl-<scp>d</scp>-valine into an antibiotic with the properties of isopenicillin N in <i>Cephalosporium acremonium</i> (1979)

Cell-free extracts of antibiotic-negative mutants of Cephalosporium acremonium converted delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (LLD-tripeptide) into an antibiotic that was destroyed by penicillinase. The enzymic activity of the extracts was destroyed by boiling, but was not inhibited by cycloheximide. LLL-Tripeptide was totally inactive as substrate. The product resembled isopenicillin N, but not penicillin N, in its antibacterial spectrum. We propose that isopenicillin N is the first product of cyclization of LLD-tripeptide.
Multi-color correlative light and electron microscopy using nanoparticle cathodoluminescence (2012)

Correlative light and electron microscopy promises to combine molecular specificity with nanoscale imaging resolution. However, there are substantial technical challenges including reliable co-registration of optical and electron images, and rapid optical signal degradation under electron beam irradiation. Here, we introduce a new approach to solve these problems: multi-color imaging of stable optical cathodoluminescence emitted in a scanning electron microscope by nanoparticles with controllable surface chemistry. We demonstrate well-correlated cathodoluminescence and secondary electron images using three species of semiconductor nanoparticles that contain defects providing stable, spectrally-distinguishable cathodoluminescence. We also demonstrate reliable surface functionalization of the particles. The results pave the way for the use of such nanoparticles for targeted labeling of surfaces to provide nanoscale mapping of molecular composition, indicated by cathodoluminescence color, simultaneously acquired with structural electron images in a single instrument.
Deep-learning-powered photonic analog-to-digital conversion (2019)

Analog-to-digital converters (ADCs) must be high speed, broadband, and accurate for the development of modern information systems, such as radar, imaging, and communications systems; photonic technologies are regarded as promising technologies for realizing these advanced requirements. Here, we present a deep-learning-powered photonic ADC architecture that simultaneously exploits the advantages of electronics and photonics and overcomes the bottlenecks of the two technologies, thereby overcoming the ADC tradeoff among speed, bandwidth, and accuracy. Via supervised training, the adopted deep neural networks learn the patterns of photonic system defects and recover the distorted data, thereby maintaining the high quality of the electronic quantized data succinctly and adaptively. The numerical and experimental results demonstrate that the proposed architecture outperforms state-of-the-art ADCs with developable high throughput; hence, deep learning performs well in photonic ADC systems. We anticipate that the proposed architecture will inspire future high-performance photonic ADC design and provide opportunities for substantial performance enhancement for the next-generation information systems.
The Biomarkers of Lupus Disease Study: A Bold Approach May Mitigate Interference of Background Immunosuppressants in Clinical Trials (2017)

Trials in active, non-organ-threatening SLE can safely withdraw background treatments if patients who have disease flares are designated nonresponders and returned to standard therapy. Immunologic effects of standard therapy vary between IFN-defined subsets. These findings provide a strategy for minimizing or optimizing treatment combinations in lupus trials and clinical care.
End-to-End Multicore Multimode Fiber Optic Link Operating up to 120 Gb/s (2012)

A full multicore fiber optic link is demonstrated, transmitting greater than 100 Gb/s through a single strand of multimode fiber for the first time. The fiber, which consists of seven graded-index multimode cores, is used to transmit up to 120 Gb/s over 100 m using a custom multicore-fiber interfacing transmitter and receiver. 2-D arrays of vertical-cavity surface-emitting lasers (VCSELs) and vertically illuminated photodiodes (PDs) are fabricated with a geometry corresponding to the outer six cores of the seven-core fiber, which is arranged in a hexagonal pattern. Both flip-chip and wire-bonding technologies are used to package the VCSEL and PD chips with multichannel transmitter and receiver integrated circuits. Amplitude and timing margins of the end-to-end signals are analyzed through bit-error-rate (BER) measurements. The effects of electrical and optical crosstalk are shown to result in negligible degradation to the BER performance.
Organometallic Titanocene–Gold Compounds as Potential Chemotherapeutics in Renal Cancer. Study of their Protein Kinase Inhibitory Properties (2014)

Early-late transition metal TiAu<sub>2</sub> compounds [(η-C<sub>5</sub>H<sub>5</sub>)<sub>2</sub>Ti{OC(O)CH<sub>2</sub>PPh<sub>2</sub>AuCl}<sub>2</sub>] (<b>3</b>) and new [(η-C<sub>5</sub>H<sub>5</sub>)<sub>2</sub>Ti{OC(O)-4-C<sub>6</sub>H<sub>4</sub>PPh<sub>2</sub>AuCl}<sub>2</sub>] (<b>5</b>) were evaluated as potential anticancer agents <i>in vitro</i> against renal and prostate cancer cell lines. The compounds were significantly more effective than monometallic titanocene dichloride and gold(I) [{HOC(O)RPPh<sub>2</sub>}AuCl] (R = -CH<sub>2</sub>- <b>6</b>, -4-C<sub>6</sub>H<sub>4</sub>- <b>7</b>) derivatives in renal cancer cell lines, indicating a synergistic effect of the resulting heterometallic species. The activity on renal cancer cell lines (for <b>5</b> in the nanomolar range) was considerably higher than that of cisplatin and highly active titanocene Y. Initial mechanistic studies in Caki-1 cells <i>in vitro</i> coupled with studies of their inhibitory properties on a panel of 35 kinases of oncological interest indicate that these compounds inhibit protein kinases of the AKT and MAPKAPK families with a higher selectivity toward MAPKAPK3 (IC<sub>50</sub><b>3</b> = 91 nM, IC<sub>50</sub><b>5</b> = 117 nM). The selectivity of the compounds <i>in vitro</i> against renal cancer cell lines when compared to a nontumorigenic human embryonic kidney cell line (HEK-293T) and the favorable preliminary toxicity profile on C57black6 mice indicate that these compounds (especially <b>5</b>) are excellent candidates for further development as potential renal cancer chemotherapeutics.
A Cancellation Technique for Reciprocal-Mixing Caused by Phase Noise and Spurs (2013)

A phase noise and spur filtering technique suppresses the phase-noise contribution to the receiver noise figure in the presence of a -15 dBm blocker by 25 dB consuming only 8 mA, bridging the performance gap between ring oscillators and LC-oscillators. The technique breaks the conventional trade-off between power and phase-noise in oscillators. It makes use of the symmetry of phase noise around the carrier by using the image of the reciprocal-mixing at double the blocker beat frequency to cancel noise in the receive-band.
Computationally optimized broadly reactive vaccine based upon swine H1N1 influenza hemagglutinin sequences protects against both swine and human isolated viruses (2019)

Swine H1 influenza viruses were stable within pigs for nearly 70 years until in 1998 when a classical swine virus reassorted with avian and human influenza viruses to generate the novel triple reassortant H1N1 strain that eventually led to the 2009 influenza pandemic. Previously, our group demonstrated broad protection against a panel of human H1N1 viruses using HA antigens derived by the COBRA methodology. In this report, the effectiveness of COBRA HA antigens (SW1, SW2, SW3 and SW4), which were designed using only HA sequences from swine H1N1 and H1N2 isolates, were tested in BALB/c mice. The effectiveness of these vaccines were compared to HA sequences designed using both human and swine H1 HA sequences or human only sequences. SW2 and SW4 elicited antibodies that detected the pandemic-like virus, A/California/07/2009 (CA/09), had antibodies with HAI activity against almost all the classical swine influenza viruses isolated from 1973-2015 and all of the Eurasian viruses in our panel. However, sera collected from mice vaccinated with SW2 or SW4 had HAI activity against ~25% of the human seasonal-like influenza viruses isolated from 2009-2015. In contrast, the P1 COBRA HA vaccine (derived from both swine and human HA sequences) elicited antibodies that had HAI activity against both swine and human H1 viruses and protected against CA/09 challenge, but not a human seasonal-like swine H1N2 virus challenge. However, the SW1 vaccine protected against this challenge as well as the homologous vaccine. These results support the idea that a pan-swine-human H1 influenza virus vaccine is possible.
Molecular heterogeneity and shedding of a high-molecular-mass melanoma-associated antigen identified with monoclonal antibodies. (1982)

This review briefly discusses some recent developments in the use of monoclonal antibodies to study antigens of high molecular mass associated with melanomas, including information on their molecular profile, their heterogeneity, and the effect of interferon on their shedding by melanoma cells.